psidev-ms-dev — Mass spectroscopy standard development

[Psidev-ms-dev] New version 3.67.0 of psi-ms.obo

[Gerhard M. <may...@ru...>]

Dear proteomics community,

attached there is the new version 3.67.0 of the psi-ms.obo file.

It contains terms for new Thermo Scientific instruments / software
and a new term for a ProteomeDiscoverer input parameter.

The phosphoRS terms aren't anymore restricted to ProteomeDiscoverer.

In addition the whole purgatory branch is now obsoleted.


Changed CV terms in version 3.67.0 of psi-ms.obo:
=================================================
************ All terms formerly under purgatory are now obsolete.

************ Changed is_a: from 'search engine specific score for PSMs'
************ --> 'spectrum identification result details'
[Term]
id: MS:1001968
name: PTM localization score
def: "A score that assign confidence to the localization of an amino 
acid modification on a peptide sequence." [PSI:MS]
is_a: MS:1001405 ! spectrum identification result details

************ Made the following three terms more general
************ (removed the ProteomeDiscoverer: prefix)
[Term]
id: MS:1001969
name: phosphoRS score
def: "Peptide score based on the cumulative binomial probability that 
the observed match is a random event." [DOI:10.1021/pr200611n, 
PMID:22073976]
is_a: MS:1001968 ! PTM localization score

[Term]
id: MS:1001970
name: phosphoRS sequence probability
def: "Probability that the respective isoform is correct." 
[DOI:10.1021/pr200611n, PMID:22073976]
is_a: MS:1001968 ! PTM localization score

[Term]
id: MS:1001971
name: phosphoRS site probability
def: "Estimate of the probability that the respective site is truly 
phosphorylated." [DOI:10.1021/pr200611n, PMID:22073976]
is_a: MS:1001968 ! PTM localization score


New CV terms in version 3.67.0 of psi-ms.obo:
=============================================
[Term]
id: MS:1002522
name: ProteomeDiscoverer:1. Static Terminal Modification
def: "Determine 1st static terminal post-translational modifications 
(PTMs)." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter

[Term]
id: MS:1002523
name: Q Exactive HF
def: "Thermo Scientific Q Exactive." [PSI:PI]
is_a: MS:1000494 ! Thermo Scientific instrument model

[Term]
id: MS:1002524
name: PepFinder
def: "Thermo Scientific PepFinder BioPharma analysis software." [PSI:PI]
is_a: MS:1001457 ! data processing software

[Term]
id: MS:1002525
name: TSQ 8000 Evo
def: "Thermo Scientific TSQ 8000 Evo MS." [PSI:PI]
is_a: MS:1000494 ! Thermo Scientific instrument model

[Term]
id: MS:1002526
name: Exactive Plus
def: "Thermo Scientific Exactive Plus MS." [PSI:PI]
is_a: MS:1000494 ! Thermo Scientific instrument model

[Term]
id: MS:1002527
name: instrument specific scan attribute
def: "Instrument specific scan properties that are associated with a 
value." [PSI:PI]
is_a: MS:1000503 ! scan attribute

[Term]
id: MS:1002528
name: synchronous prefilter selection
def: "Synchronous prefilter selection." [PSI:PI]
synonym: "SPS" EXACT []
is_a: MS:1002527 ! instrument specific scan attribute

Best Regards,
Gerhard

-- 
---
Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
Bioinformatics / Biostatistics
Medizinisches-Proteom-Center (MPC)
Ruhr-Universität Bochum
Zentrum für klinische Forschung I (ZKF I), E.049a
Universitätsstraße 150
D-44801 Bochum
  
Phone:	+49(0)234/32-21006
Fax:	+49(0)234/32-14554
Email:	ger...@ru...
Web:	http://www.medizinisches-proteom-center.de

[Psidev-ms-dev] Release candidate 3.67.0_rc1 of psi-ms.obo

[Gerhard M. <may...@ru...>]

Dear proteomics community,

attached you find the release candidate 3.67.0_rc1 of the psi-ms.obo file.

It contains terms for new Thermo Scientific instruments / software
and a new term for a ProteomeDiscoverer input parameter.

The phosphoRS terms aren't anymore restricted to ProteomeDiscoverer.

In addition the whole purgatory branch is now obsoleted.



Changed CV terms in version 3.67.0_rc1 of psi-ms.obo:
=====================================================
************ All terms formerly under purgatory are now obsolete.

************ Changed is_a: from 'search engine specific score for PSMs'
************ --> 'spectrum identification result details'
[Term]
id: MS:1001968
name: PTM localization score
def: "A score that assign confidence to the localization of an amino 
acid modification on a peptide sequence." [PSI:MS]
is_a: MS:1001405 ! spectrum identification result details

************ Made the following three terms more general
************ (removed the ProteomeDiscoverer: prefix)
[Term]
id: MS:1001969
name: phosphoRS score
def: "Peptide score based on the cumulative binomial probability that 
the observed match is a random event." [DOI:10.1021/pr200611n, 
PMID:22073976]
is_a: MS:1001968 ! PTM localization score

[Term]
id: MS:1001970
name: phosphoRS sequence probability
def: "Probability that the respective isoform is correct." 
[DOI:10.1021/pr200611n, PMID:22073976]
is_a: MS:1001968 ! PTM localization score

[Term]
id: MS:1001971
name: phosphoRS site probability
def: "Estimate of the probability that the respective site is truly 
phosphorylated." [DOI:10.1021/pr200611n, PMID:22073976]
is_a: MS:1001968 ! PTM localization score



New CV terms in version 3.67.0_rc1 of psi-ms.obo:
=================================================
[Term]
id: MS:1002522
name: ProteomeDiscoverer:1. Static Terminal Modification
def: "Determine 1st static terminal post-translational modifications 
(PTMs)." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002101 ! ProteomeDiscoverer input parameter

[Term]
id: MS:1002523
name: Q Exactive HF
def: "Thermo Scientific Q Exactive." [PSI:PI]
is_a: MS:1000494 ! Thermo Scientific instrument model

[Term]
id: MS:1002524
name: PepFinder
def: "Thermo Scientific PepFinder BioPharma analysis software." [PSI:PI]
is_a: MS:1001457 ! data processing software

[Term]
id: MS:1002525
name: TSQ 8000 Evo
def: "Thermo Scientific TSQ 8000 Evo MS." [PSI:PI]
is_a: MS:1000494 ! Thermo Scientific instrument model

[Term]
id: MS:1002526
name: Exactive Plus
def: "Thermo Scientific Exactive Plus MS." [PSI:PI]
is_a: MS:1000494 ! Thermo Scientific instrument model

[Term]
id: MS:1002527
name: SPS
def: "Synchronous prefilter selection." [PSI:PI]
is_a: MS:1000503 ! scan attribute

Best Regards,
Gerhard

-- 
---
Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
Bioinformatics / Biostatistics
Medizinisches-Proteom-Center (MPC)
Ruhr-Universität Bochum
Zentrum für klinische Forschung I (ZKF I), E.049a
Universitätsstraße 150
D-44801 Bochum
  
Phone:	+49(0)234/32-21006
Fax:	+49(0)234/32-14554
Email:	ger...@ru...
Web:	http://www.medizinisches-proteom-center.de

[Psidev-ms-dev] CompMS

[Oliver K. <oli...@un...>]

Dear all,

as some of you know, we have recently started an effort in 
'community building' for computational mass spectrometry.

Starting with an effort at last year's Dagstuhl meeting
on Computational Mass Spectrometry, we have established 
a Computational Mass Spectrometry interest group, CompMS. 
The idea is to integrate the separate communities 
(experimentalists and bioinformaticians, metabolomics 
and proteomics, etc.), to provide information about 
upcoming events, as well as provide training and
education for computational mass spectrometry.

We have set up an initial website which will be the home
of the CompMS group at 
 http://CompMS.org 
and a mailing list at Google groups
 http://groups.google.com/group/CompMS
If you want to be kept up to date on the group's activities,
please subscribe to the mailing list.

I would be grateful, if you could spread the word and
forward this email to persons who might be interested
in the topic as well as to related mailing lists we might
not be aware of.

Thanks and best regards,
 Oliver Kohlbacher

[Psidev-ms-dev] New version 3.66.0 of psi-ms.obo

[Gerhard M. <may...@ru...>]

Dear proteomics community,

attached you find the new version 3.66.0 of the psi-ms.obo file.

It contains new terms for peptide grouping and mass spectrometry imaging.


Changed CV terms in version 3.66.0 of psi-ms.obo:
=================================================
************ Added is_a: tag
[Term]
id: MS:1002489
name: special processing
def: "Details describing a special processing." [PSI:PI]
is_a: MS:1001080 ! search type
relationship: part_of MS:1001000 ! spectrum interpretation

************ Corrected the regular expression
[Term]
id: MS:1002505
name: regular expression for modification localization scoring
def: 
"([:digit:]+:[0|1]\{1\}.[:digit:]+:[:digit:]+[|]\{1\}[:digit:]+:(true|false)\{1\})" 
[PSI:PI]
is_a: MS:1002479 ! regular expression


New CV terms in version 3.66.0 of psi-ms.obo:
=============================================
[Term]
id: MS:1002520
name: peptide group ID
def: "Peptide group identifier for peptide-level stats." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001105 ! peptide result details

[Term]
id: MS: 1002521
name: mass spectrometry imaging
def: "A technique in which mass spectra are acquired in a spatially 
resolved manner. This is typically achieved by scanning a laser or 
primary ion beam over a sample and acquiring a mass spectrum at each 
position." [PSI:MS]
is_a: MS:1000857 ! run attribute

Best Regards,
Gerhard

-- 
---
Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
Bioinformatics / Biostatistics
Medizinisches-Proteom-Center (MPC)
Ruhr-Universität Bochum
Zentrum für klinische Forschung I (ZKF I), E.049a
Universitätsstraße 150
D-44801 Bochum
  
Phone:	+49(0)234/32-21006
Fax:	+49(0)234/32-14554
Email:	ger...@ru...
Web:	http://www.medizinisches-proteom-center.de

[Psidev-ms-dev] Call for Abstracts - The 1st Unified Workshop on Proteome and Metabolome Informatics @ ECCB 2014

[Oliver K. <oli...@un...>]

Abstract submission deadline: Monday July 14th

Dear colleagues,

We invite you to submit an abstract for oral or poster presentation at The
1st Unified Workshop on Proteome and Metabolome Informatics, to be held at
ECCB 2014, Strasbourg, France on Saturday 6th September.

This workshop will be of interest to all researchers in proteomics or
metabolomics, whether at the wet-lab or informatics level. It will also be
of relevance to systems modellers and network biologists who integrate
proteomics and metabolomics data and who wish to gain a greater
understanding of how upstream processing of this data is performed. The
core aim for this workshop is for there to be an equal proportion of talks
on proteome and metabolome informatics. In particular, we will prefer
talks that already describe some synergy between the two fields. Speakers
are advised to ensure metabolomics concepts are accessible to a proteomics
audience, and vice versa.

The agenda with invited speakers and further details is available from
http://www.cadetbioinformatics.org/workshops/eccb14/ Here you can also
find the abstract submission form and details for registering. The
abstract submission deadline is Monday July 14th.

Hoping to see you in Strasbourg!

The Organsing Committee,
Andrew Dowsey
Simon Rogers
Rainer Breitling
Richard Unwin

[Psidev-ms-dev] New version 3.65.0 of psi-ms.obo

[Gerhard M. <may...@ru...>]

Dear proteomics community,

attached you find new version 3.65.0 of the psi-ms.obo file.

It contains a new "statistical threshold" term as parent of the
different thresholding mechanisms, two new terms for MassIVE and a bunch
of new terms for use in the coming mzIdentML version 1.2 (for peptide-level
scoring, modification localization re-scoring and cross-linking) and for
absolute quantitation.

According to the CID terms we now have the following hierarchy:
collision-induced association (synonyms: CID, CAD, collision –activated 
association)
beam-type collision-induced dissociation (synonym: HCD)
higher-energy beam-type collision-induced dissociation
trap-type collision-induced dissociation



Changed CV terms in version 3.65.0 of psi-ms.obo:
=================================================
************ Changed synonym to "collisionally activated dissociation"
************ instead of "collision activated dissociation"
************ in order to match the IUPAC recommendations
[Term]
id: MS:1000133
name: collision-induced dissociation
def: "The dissociation of an ion after collisional excitation. The term 
collisional-activated dissociation is not recommended." [PSI:MS]
synonym: "CID" EXACT []
synonym: "CAD" EXACT []
synonym: "collisionally activated dissociation" EXACT []
is_a: MS:1000044 ! dissociation method

************ Changed definition to
************ "... The term parent ion is deprecated."
************ in order to match the IUPAC recommendations
[Term]
id: MS:1000340
name: precursor ion
def: "An ion that reacts to form particular product ions. The reaction 
can be unimolecular dissociation, ion/molecule reaction, isomerization, 
or change in charge state. The term parent ion is not deprecated." [PSI:MS]
synonym: "parent ion" RELATED []
is_a: MS:1000506 ! ion role

************ Renamed to beam-type collision-induced dissociation
[Term]
id: MS:1000422
name: beam-type collision-induced dissociation
def: "A collision-induced dissociation process that occurs in a 
beam-type collision cell." [PSI:MS]
synonym: "HCD" EXACT []
is_a: MS:1000133 ! collision-induced dissociation

************ Added is_a relationship for search engine specific score
[Term]
id: MS:1001147
name: protein ambiguity group result details
is_a: MS:1001085 ! protein result details
is_a: MS:1001153 ! search engine specific score

************ Added the def: tag
[Term]
id: MS:1002231
name: regular expressions for a GUID
def: "([A-Fa-f0-9]\{8\}-([A-Fa-f0-9]\{4\}-)\{3\}[A-Fa-f0-9]\{12\})." 
[PSI:PI]
is_a: MS:1002479 ! regular expression

************ The following two terms are flagged as "UNDER DISCUSSION"
[Term]
id: MS:1002439
name: final PSM list UNDER DISCUSSION
def: "A flag on a list of PSMs (SpectrumIdentificationList) to indicate 
that this is the final set of identifications to be interpreted by 
consuming software. Amongst the set of SpectrumIdentificationList(s) 
that are flagged with the term, each spectrum must not be referenced 
from more than one SpectrumIdentificationResult." [PSI:PI]
is_a: MS:1002438 ! spectrum identification list result details

[Term]
id: MS:1002440
name: intermediate PSM list UNDER DISCUSSION
def: "A flag on a list of PSMs (SpectrumIdentificationList) to indicate 
that this is not the final set of identifications to be interpreted by 
consuming software. This term should be used when results are provided 
from multiple search engines for the results from each search engine 
before they are combined to give consensus identifications. Amongst the 
set of SpectrumIdentificationList(s) that are flagged with the term, 
each spectrum may be referenced from more than one 
SpectrumIdentificationResult." [PSI:PI]
is_a: MS:1002438 ! spectrum identification list result details

************ Added is_a relations for the
************ ... target-decoy thresholds to the following terms:
[Term]
id: MS:1001364
name: distinct peptide-level global FDR
def: "Estimation of the global false discovery rate for distinct 
peptides once redundant identifications of the same peptide have been 
removed (id est multiple PSMs have been collapsed to one entry)." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001105 ! peptide result details
is_a: MS:1002484 ! peptide-level target-decoy threshold
relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive

[Term]
id: MS:1001447
name: prot:FDR threshold
def: "False-discovery rate threshold for proteins." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002485 ! protein-level target-decoy threshold

[Term]
id: MS:1001448
name: pep:FDR threshold
def: "False-discovery rate threshold for peptides." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002484 ! peptide-level target-decoy threshold

[Term]
id: MS:1002369
name: protein group-level global FDR
def: "Estimation of the global false discovery rate of protein groups." 
[PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002346 ! protein group-level result details
is_a: MS:1002486 ! protein group-level target-decoy threshold

[Term]
id: MS:1002370
name: protein group-level local FDR
def: "Estimation of the local false discovery rate of protein groups." 
[PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002346 ! protein group-level result details
is_a: MS:1002486 ! protein group-level target-decoy threshold

[Term]
id: MS:1002460
name: protein group-level global FNR
def: "Estimation of the global false negative rate of protein groups." 
[PSI:PI]
is_a: MS:1002346 ! protein group-level result details
relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive
is_a: MS:1002486 ! protein group-level target-decoy threshold



New CV terms in version 3.65.0 of psi-ms.obo:
=============================================
[Term]
id: MS:1002481
name: higher energy beam-type collision-induced dissociation
def: "A collision-induced dissociation process wherein the projectile 
ion has the translational energy higher than approximately 1000 eV." 
[PSI:MS]
is_a: MS:1000422 ! beam-type collision-induced dissociation

[Term]
id: MS:1002482
name: statistical threshold
def: "Estimated statistical threshold." [PSI:MS]
is_a: MS:1001060 ! quality estimation method details

[Term]
id: MS:1002483
name: PSM-level statistical threshold
def: "Estimated statistical threshold at PSM-level." [PSI:MS]
is_a: MS:1002482 ! statistical threshold

[Term]
id: MS:1002484
name: peptide-level statistical threshold
def: "Estimated statistical threshold at peptide-level." [PSI:MS]
is_a: MS:1002482 ! statistical threshold

[Term]
id: MS:1002485
name: protein-level statistical threshold
def: "Estimated statistical threshold at protein-level." [PSI:MS]
is_a: MS:1002482 ! statistical threshold

[Term]
id: MS:1002486
name: protein group-level statistical threshold
def: "Estimated statistical threshold at protein group-level." [PSI:PI]
is_a: MS:1002482 ! statistical threshold

[Term]
id: MS:1002487
name: MassIVE dataset identifier
def: "Dataset identifier issued by the MassIVE repository. A dataset can 
refer to either a single sample as part of a study, or all samples that 
are part of the study corresponding to a publication." [PSI:PI]
is_a: MS:1000878 ! external reference identifier

[Term]
id: MS:1002488
name: MassIVE dataset URI
def: "URI that allows the access to one dataset in the MassIVE 
repository. A dataset can refer to either a single sample as part of a 
study, or all samples that are part of the study corresponding to a 
publication." [PSI:PI]
xref: value-type:xsd\:anyURI "The allowed value-type for this CV term."
is_a: MS:1000878 ! external reference identifier

[Term]
id: MS:1002489
name: special processing
def: "Details describing a special processing." [PSI:PI]
relationship: part_of MS:1001000 ! spectrum interpretation

[Term]
id: MS:1002490
name: peptide-level scoring
def: "Peptide-level scoring performed." [PSI:PI]
is_a: MS:1002489 ! special processing

[Term]
id: MS:1002491
name: modification localization scoring
def: "Modification localization scoring performed." [PSI:PI]
is_a: MS:1002489 ! special processing

[Term]
id: MS:1002492
name: consensus scoring
def: "Consensus multiple search engine approach performed." [PSI:PI]
is_a: MS:1002489 ! special processing

[Term]
id: MS:1002493
name: sample pre-fractionation
def: "Sample pre-fractionation performed." [PSI:PI]
is_a: MS:1002489 ! special processing

[Term]
id: MS:1002494
name: cross-linking search
def: "Cross-linking search performed." [PSI:PI]
is_a: MS:1002489 ! special processing

[Term]
id: MS:1002495
name: no special processing
def: "No special processing performed." [PSI:PI]
is_a: MS:1002489 ! special processing

[Term]
id: MS:1002496
name: group PSMs by sequence
def: "Group PSMs by distinct peptide sequence ignoring modifications." 
[PSI:PI]
is_a: MS:1002345 ! PSM-level result details

[Term]
id: MS:1002497
name: group PSMs by sequence with modifications
def: "Group PSMs by distinct peptide sequence with taking modifications 
into account." [PSI:PI]
is_a: MS:1002345 ! PSM-level result details

[Term]
id: MS:1002498
name: group PSMs by sequence with modifications and charge
def: "Group PSMs by distinct peptide sequence with taking modifications 
and charge into account." [PSI:PI]
is_a: MS:1002345 ! PSM-level result details

[Term]
id: MS:1002499
name: peptide level score
def: "Peptide level score." [PSI:PI]
is_a: MS:1002358 ! search engine specific score for distinct peptides

[Term]
id: MS:1002500
name: peptide passes threshold
def: "A Boolean attribute to determine whether the peptide has passed 
the threshold indicated in the file." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001105 ! peptide result details

[Term]
id: MS:1002501
name: no PSM threshold
def: "Indicating that no PSM threshold was used." [PSI:PI]
is_a: MS:1002345 ! PSM-level result details

[Term]
id: MS:1002502
name: no peptide-level threshold
def: "Indicating that no peptide-level threshold was used." [PSI:PI]
is_a: MS:1001105 ! peptide result details

[Term]
id: MS:1002503
name: PSM is used for peptide-level scoring
def: "Flags a PSM that it is used for peptide-level scoring." [PSI:PI]
is_a: MS:1001105 ! peptide result details

[Term]
id: MS:1002504
name: order
def: "The order of modifications to be referenced elsewhere in the 
document." [PSI:PI]
xref: value-type:xsd\:integer "The allowed value-type for this CV term."
is_a: MS:1001055 ! modification parameters

[Term]
id: MS:1002505
name: regular expression for modification localization scoring
def: 
"([:digit:]+:[0|1]{1}.[:digit:]+:[:digit:]+[|:digit:]*:(true|false){1})." [PSI:PI]
is_a: MS:1002479 ! regular expression

[Term]
id: MS:1002506
name: modification position score
def: "Modification position score." [PSI:PI]
is_a: MS:1001055 ! modification parameters

[Term]
id: MS:1002507
name: modification rescoring:false localization rate
def: "Mod position score: false localization rate." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002506 ! modification position score
relationship: has_regexp MS:1002505 ! regular expression for 
modification localization scoring

[Term]
id: MS:1002508
name: cross-linking attribute
def: "Cross-linking attribute." [PSI:PI]
is_a: MS:1001105 ! peptide result details

[Term]
id: MS:1002509
name: cross-link donor
def: "The Cross-linking donor, assigned according to the following 
rules: the export software SHOULD use the following rules to choose the 
cross-link donor as the: longer peptide, then higher peptide neutral 
mass, then alphabetical order." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002508 ! cross-linking attribute

[Term]
id: MS:1002510
name: cross-link receiver
def: "Cross-linking receiver, assigned according to the following rules: 
the export software SHOULD use the following rules to choose the 
cross-link donor as the: longer peptide, then higher peptide neutral 
mass, then alphabetical order." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002508 ! cross-linking attribute

[Term]
id: MS:1002511
name: cross-link spectrum identification item
def: "Cross-linked spectrum identification item." [PSI:PI]
xref: value-type:xsd\:integer "The allowed value-type for this CV term."
is_a: MS:1002508 ! cross-linking attribute

[Term]
id: MS:1002512
name: cross-linking score
def: "Cross-linking scoring value." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001153 ! search engine specific score

[Term]
id: MS:1002513
name: molecules per cell
def: "The absolute abundance of protein in a cell." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001805 ! quantification datatype

[Term]
id: MS:1002514
name: absolute quantitation analysis
def: "Absolute quantitation analysis." [PSI:PI]
is_a: MS:1001833 ! quantitation analysis summary

[Term]
id: MS:1002515
name: internal peptide reference used
def: "States whether an internal peptide reference is used or not in 
absolute quantitation analysis." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001832 ! quantitation software comment or customizations

[Term]
id: MS:1002516
name: internal protein reference used
def: "States whether an internal protein reference is used or not in 
absolute quantitation analysis." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001832 ! quantitation software comment or customizations

[Term]
id: MS:1002517
name: internal reference abundance
def: "The absolute abundance of the spiked in reference peptide or 
protein used for absolute quantitation analysis." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001805 ! quantification datatype

[Term]
id: MS:1002518
name: Progenesis:protein group normalised abundance
def: "The data type normalised abundance for protein groups produced by 
Progenesis LC-MS." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001805 ! quantification datatype

[Term]
id: MS:1002519
name: Progenesis:protein group raw abundance
def: "The data type raw abundance for protein groups produced by 
Progenesis LC-MS." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001805 ! quantification datatype

Best Regards,
Gerhard

-- 
---
Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
Bioinformatics / Biostatistics
Medizinisches-Proteom-Center (MPC)
Ruhr-Universität Bochum
Zentrum für klinische Forschung I (ZKF I), E.049a
Universitätsstraße 150
D-44801 Bochum
  
Phone:	+49(0)234/32-21006
Fax:	+49(0)234/32-14554
Email:	ger...@ru...
Web:	http://www.medizinisches-proteom-center.de

Re: [Psidev-ms-dev] Release candidate 3.65.0_rc2 of psi-ms.obo

[Stein, S. E. Dr. <ste...@ni...>]

Is as good as any and simplest.
Same scaling as a spectrum.
Relative values between peaks in a run are what really matters anyway.

Sent from my iPhone

> On Jun 13, 2014, at 4:37 AM, "Gerhard Mayer" <may...@ru...> wrote:
> 
> Dear proteomics community,
> 
> attached you find the release candidate 3.65.0_rc2 of the psi-ms.obo file.
> 
> It contains a new "statistical threshold" term as parent of the
> different thresholding mechanisms, two new terms for MassIVE and a bunch
> of new terms for use in the coming mzIdentML version 1.2 (for peptide-level
> scoring, modification localization re-scoring and cross-linking).
> 
> According to the CID terms we now have the following hierarchy:
> collision-induced association (synonyms: CID, CAD, collision –activated association)
> beam-type collision-induced dissociation (synonym: HCD)
> higher-energy beam-type collision-induced dissociation
> trap-type collision-induced dissociation
> 
> 
> 
> Changed CV terms in version 3.65.0_rc2 of psi-ms.obo:
> =====================================================
> ************ Changed synonym to "collisionally activated dissociation"
> ************ instead of "collision activated dissociation"
> ************ in order to match the IUPAC recommendations
> [Term]
> id: MS:1000133
> name: collision-induced dissociation
> def: "The dissociation of an ion after collisional excitation. The term collisional-activated dissociation is not recommended." [PSI:MS]
> synonym: "CID" EXACT []
> synonym: "CAD" EXACT []
> synonym: "collisionally activated dissociation" EXACT []
> is_a: MS:1000044 ! dissociation method
> 
> ************ Changed definition to
> ************ "... The term parent ion is deprecated."
> ************ in order to match the IUPAC recommendations
> [Term]
> id: MS:1000340
> name: precursor ion
> def: "An ion that reacts to form particular product ions. The reaction can be unimolecular dissociation, ion/molecule reaction, isomerization, or change in charge state. The term parent ion is not deprecated." [PSI:MS]
> synonym: "parent ion" RELATED []
> is_a: MS:1000506 ! ion role
> 
> ************ Renamed to beam-type collision-induced dissociation
> [Term]
> id: MS:1000422
> name: beam-type collision-induced dissociation
> def: "A collision-induced dissociation process that occurs in a beam-type collision cell." [PSI:MS]
> synonym: "HCD" EXACT []
> is_a: MS:1000133 ! collision-induced dissociation
> 
> ************ Added the def: tag
> [Term]
> id: MS:1002231
> name: ([A-Fa-f0-9]{8}-([A-Fa-f0-9]{4}-){3}[A-Fa-f0-9]{12})
> def: "Regular expressions for a GUID." [PSI:PI]
> is_a: MS:1002479 ! regular expression
> 
> ************ The following two terms are flagged as "UNDER DISCUSSION"
> [Term]
> id: MS:1002439
> name: final PSM list UNDER DISCUSSION
> def: "A flag on a list of PSMs (SpectrumIdentificationList) to indicate that this is the final set of identifications to be interpreted by consuming software. Amongst the set of SpectrumIdentificationList(s) that are flagged with the term, each spectrum must not be referenced from more than one SpectrumIdentificationResult." [PSI:PI]
> is_a: MS:1002438 ! spectrum identification list result details
> 
> [Term]
> id: MS:1002440
> name: intermediate PSM list UNDER DISCUSSION
> def: "A flag on a list of PSMs (SpectrumIdentificationList) to indicate that this is not the final set of identifications to be interpreted by consuming software. This term should be used when results are provided from multiple search engines for the results from each search engine before they are combined to give consensus identifications. Amongst the set of SpectrumIdentificationList(s) that are flagged with the term, each spectrum may be referenced from more than one SpectrumIdentificationResult." [PSI:PI]
> is_a: MS:1002438 ! spectrum identification list result details
> 
> ************ Added is_a relations for the
> ************ ... target-decoy thresholds to the following terms:
> [Term]
> id: MS:1001364
> name: distinct peptide-level global FDR
> def: "Estimation of the global false discovery rate for distinct peptides once redundant identifications of the same peptide have been removed (id est multiple PSMs have been collapsed to one entry)." [PSI:PI]
> xref: value-type:xsd\:double "The allowed value-type for this CV term."
> is_a: MS:1001105 ! peptide result details
> is_a: MS:1002484 ! peptide-level target-decoy threshold
> relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive
> 
> [Term]
> id: MS:1001447
> name: prot:FDR threshold
> def: "False-discovery rate threshold for proteins." [PSI:PI]
> xref: value-type:xsd\:double "The allowed value-type for this CV term."
> is_a: MS:1002485 ! protein-level target-decoy threshold
> 
> [Term]
> id: MS:1001448
> name: pep:FDR threshold
> def: "False-discovery rate threshold for peptides." [PSI:PI]
> xref: value-type:xsd\:double "The allowed value-type for this CV term."
> is_a: MS:1002484 ! peptide-level target-decoy threshold
> 
> [Term]
> id: MS:1002369
> name: protein group-level global FDR
> def: "Estimation of the global false discovery rate of protein groups." [PSI:PI]
> xref: value-type:xsd\:double "The allowed value-type for this CV term."
> is_a: MS:1002346 ! protein group-level result details
> is_a: MS:1002486 ! protein group-level target-decoy threshold
> 
> [Term]
> id: MS:1002370
> name: protein group-level local FDR
> def: "Estimation of the local false discovery rate of protein groups." [PSI:PI]
> xref: value-type:xsd\:double "The allowed value-type for this CV term."
> is_a: MS:1002346 ! protein group-level result details
> is_a: MS:1002486 ! protein group-level target-decoy threshold
> 
> [Term]
> id: MS:1002460
> name: protein group-level global FNR
> def: "Estimation of the global false negative rate of protein groups." [PSI:PI]
> is_a: MS:1002346 ! protein group-level result details
> relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive
> is_a: MS:1002486 ! protein group-level target-decoy threshold
> 
> 
> 
> New CV terms in version 3.65.0_rc2 of psi-ms.obo:
> =================================================
> [Term]
> id: MS:1002481
> name: higher energy beam-type collision-induced dissociation
> def: "A collision-induced dissociation process wherein the projectile ion has the translational energy higher than approximately 1000 eV." [PSI:MS]
> is_a: MS:1000422 ! beam-type collision-induced dissociation
> 
> [Term]
> id: MS:1002482
> name: statistical threshold
> def: "Estimated statistical threshold." [PSI:MS]
> is_a: MS:1001060 ! quality estimation method details
> 
> [Term]
> id: MS:1002483
> name: PSM-level statistical threshold
> def: "Estimated statistical threshold at PSM-level." [PSI:MS]
> is_a: MS:1002482 ! statistical threshold
> 
> [Term]
> id: MS:1002484
> name: peptide-level statistical threshold
> def: "Estimated statistical threshold at peptide-level." [PSI:MS]
> is_a: MS:1002482 ! statistical threshold
> 
> [Term]
> id: MS:1002485
> name: protein-level statistical threshold
> def: "Estimated statistical threshold at protein-level." [PSI:MS]
> is_a: MS:1002482 ! statistical threshold
> 
> [Term]
> id: MS:1002486
> name: protein group-level statistical threshold
> def: "Estimated statistical threshold at protein group-level." [PSI:PI]
> is_a: MS:1002482 ! statistical threshold
> 
> [Term]
> id: MS:1002487
> name: MassIVE dataset identifier
> def: "Dataset identifier issued by the MassIVE repository. A dataset can refer to either a single sample as part of a study, or all samples that are part of the study corresponding to a publication." [PSI:PI]
> is_a: MS:1000878 ! external reference identifier
> 
> [Term]
> id: MS:1002488
> name: MassIVE dataset URI
> def: "URI that allows the access to one dataset in the MassIVE repository. A dataset can refer to either a single sample as part of a study, or all samples that are part of the study corresponding to a publication." [PSI:PI]
> xref: value-type:xsd\:anyURI "The allowed value-type for this CV term."
> is_a: MS:1000878 ! external reference identifier
> 
> [Term]
> id: MS:1002489
> name: special processing
> def: "Details describing a special processing." [PSI:PI]
> relationship: part_of MS:1001000 ! spectrum interpretation
> 
> [Term]
> id: MS:1002490
> name: peptide-level scoring
> def: "Peptide-level scoring performed." [PSI:PI]
> is_a: MS:1002489 ! special processing
> 
> [Term]
> id: MS:1002491
> name: modification localization scoring
> def: "Modification localization scoring performed." [PSI:PI]
> is_a: MS:1002489 ! special processing
> 
> [Term]
> id: MS:1002492
> name: consensus scoring
> def: "Consensus multiple search engine approach performed." [PSI:PI]
> is_a: MS:1002489 ! special processing
> 
> [Term]
> id: MS:1002493
> name: sample pre-fractionation
> def: "Sample pre-fractionation performed." [PSI:PI]
> is_a: MS:1002489 ! special processing
> 
> [Term]
> id: MS:1002494
> name: cross-linking search
> def: "Cross-linking search performed." [PSI:PI]
> is_a: MS:1002489 ! special processing
> 
> [Term]
> id: MS:1002495
> name: no special processing
> def: "No special processing performed." [PSI:PI]
> is_a: MS:1002489 ! special processing
> 
> [Term]
> id: MS:1002496
> name: group PSMs by sequence
> def: "Group PSMs by distinct peptide sequence ignoring modifications." [PSI:PI]
> is_a: MS:1002345 ! PSM-level result details
> 
> [Term]
> id: MS:1002497
> name: group PSMs by sequence with modifications
> def: "Group PSMs by distinct peptide sequence with taking modifications into account." [PSI:PI]
> is_a: MS:1002345 ! PSM-level result details
> 
> [Term]
> id: MS:1002498
> name: group PSMs by sequence with modifications and charge
> def: "Group PSMs by distinct peptide sequence with taking modifications and charge into account." [PSI:PI]
> is_a: MS:1002345 ! PSM-level result details
> 
> [Term]
> id: MS:1002499
> name: peptide level score
> def: "Peptide level score." [PSI:PI]
> is_a: MS:1002358 ! search engine specific score for distinct peptides
> 
> [Term]
> id: MS:1002500
> name: peptide passes threshold
> def: "A Boolean attribute to determine whether the peptide has passed the threshold indicated in the file." [PSI:PI]
> xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
> is_a: MS:1001105 ! peptide result details
> 
> [Term]
> id: MS:1002501
> name: no PSM threshold
> def: "Indicating that no PSM threshold was used." [PSI:PI]
> is_a: MS:1002345 ! PSM-level result details
> 
> [Term]
> id: MS:1002502
> name: no peptide-level threshold
> def: "Indicating that no peptide-level threshold was used." [PSI:PI]
> is_a: MS:1001105 ! peptide result details
> 
> [Term]
> id: MS:1002503
> name: PSM is used for peptide-level scoring
> def: "Flags a PSM that it is used for peptide-level scoring." [PSI:PI]
> is_a: MS:1001105 ! peptide result details
> 
> [Term]
> id: MS:1002504
> name: order
> def: "The order of modifications to be referenced elsewhere in the document." [PSI:PI]
> xref: value-type:xsd\:integer "The allowed value-type for this CV term."
> is_a: MS:1001055 ! modification parameters
> 
> [Term]
> id: MS:1002505
> name: regular expression for modification localization scoring
> def: "([:digit:]+:[0|1]{1}.[:digit:]+:[:digit:]+[|:digit:]*:(true|false){1})." [PSI:PI]
> is_a: MS:1002479 ! regular expression
> 
> [Term]
> id: MS:1002506
> name: modification position score
> def: "Modification position score." [PSI:PI]
> is_a: MS:1001055 ! modification parameters
> 
> [Term]
> id: MS:1002507
> name: modification rescoring:false localization rate
> def: "Mod position score: false localization rate." [PSI:PI]
> xref: value-type:xsd\:string "The allowed value-type for this CV term."
> is_a: MS:1002506 ! modification position score
> relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring
> 
> [Term]
> id: MS:1002508
> name: cross-linking attribute
> def: "Cross-linking attribute." [PSI:PI]
> is_a: MS:1001105 ! peptide result details
> 
> [Term]
> id: MS:1002509
> name: cross-link donor
> def: "The Cross-linking donor, assigned according to the following rules: the export software SHOULD use the following rules to choose the cross-link donor as the: longer peptide, then higher peptide neutral mass, then alphabetical order." [PSI:PI]
> xref: value-type:xsd\:string "The allowed value-type for this CV term."
> is_a: MS:1002508 ! cross-linking attribute
> 
> [Term]
> id: MS:1002510
> name: cross-link receiver
> def: "Cross-linking receiver, assigned according to the following rules: the export software SHOULD use the following rules to choose the cross-link donor as the: longer peptide, then higher peptide neutral mass, then alphabetical order." [PSI:PI]
> xref: value-type:xsd\:string "The allowed value-type for this CV term."
> is_a: MS:1002508 ! cross-linking attribute
> 
> [Term]
> id: MS:1002511
> name: cross-link spectrum identification item
> def: "Cross-linked spectrum identification item." [PSI:PI]
> xref: value-type:xsd\:integer "The allowed value-type for this CV term."
> is_a: MS:1002508 ! cross-linking attribute
> 
> [Term]
> id: MS:1002512
> name: cross-linking score
> def: "Cross-linking scoring value." [PSI:PI]
> xref: value-type:xsd\:double "The allowed value-type for this CV term."
> is_a: MS:1001153 ! search engine specific score
> 
> Best Regards,
> Gerhard
> 
> -- 
> ---
> Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
> Bioinformatics / Biostatistics
> Medizinisches-Proteom-Center (MPC)
> Ruhr-Universität Bochum
> Zentrum für klinische Forschung I (ZKF I), E.049a
> Universitätsstraße 150
> D-44801 Bochum
> Phone:    +49(0)234/32-21006
> Fax:    +49(0)234/32-14554
> Email:    ger...@ru...
> Web:    http://www.medizinisches-proteom-center.de
> 
> <psi-ms_3.65.0_rc2.obo.zip>
> ------------------------------------------------------------------------------
> HPCC Systems Open Source Big Data Platform from LexisNexis Risk Solutions
> Find What Matters Most in Your Big Data with HPCC Systems
> Open Source. Fast. Scalable. Simple. Ideal for Dirty Data.
> Leverages Graph Analysis for Fast Processing & Easy Data Exploration
> http://p.sf.net/sfu/hpccsystems
> _______________________________________________
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> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev

[Psidev-ms-dev] Release candidate 3.65.0_rc2 of psi-ms.obo

[Gerhard M. <may...@ru...>]

Dear proteomics community,

attached you find the release candidate 3.65.0_rc2 of the psi-ms.obo file.

It contains a new "statistical threshold" term as parent of the
different thresholding mechanisms, two new terms for MassIVE and a bunch
of new terms for use in the coming mzIdentML version 1.2 (for peptide-level
scoring, modification localization re-scoring and cross-linking).

According to the CID terms we now have the following hierarchy:
collision-induced association (synonyms: CID, CAD, collision –activated 
association)
beam-type collision-induced dissociation (synonym: HCD)
higher-energy beam-type collision-induced dissociation
trap-type collision-induced dissociation



Changed CV terms in version 3.65.0_rc2 of psi-ms.obo:
=====================================================
************ Changed synonym to "collisionally activated dissociation"
************ instead of "collision activated dissociation"
************ in order to match the IUPAC recommendations
[Term]
id: MS:1000133
name: collision-induced dissociation
def: "The dissociation of an ion after collisional excitation. The term 
collisional-activated dissociation is not recommended." [PSI:MS]
synonym: "CID" EXACT []
synonym: "CAD" EXACT []
synonym: "collisionally activated dissociation" EXACT []
is_a: MS:1000044 ! dissociation method

************ Changed definition to
************ "... The term parent ion is deprecated."
************ in order to match the IUPAC recommendations
[Term]
id: MS:1000340
name: precursor ion
def: "An ion that reacts to form particular product ions. The reaction 
can be unimolecular dissociation, ion/molecule reaction, isomerization, 
or change in charge state. The term parent ion is not deprecated." [PSI:MS]
synonym: "parent ion" RELATED []
is_a: MS:1000506 ! ion role

************ Renamed to beam-type collision-induced dissociation
[Term]
id: MS:1000422
name: beam-type collision-induced dissociation
def: "A collision-induced dissociation process that occurs in a 
beam-type collision cell." [PSI:MS]
synonym: "HCD" EXACT []
is_a: MS:1000133 ! collision-induced dissociation

************ Added the def: tag
[Term]
id: MS:1002231
name: ([A-Fa-f0-9]{8}-([A-Fa-f0-9]{4}-){3}[A-Fa-f0-9]{12})
def: "Regular expressions for a GUID." [PSI:PI]
is_a: MS:1002479 ! regular expression

************ The following two terms are flagged as "UNDER DISCUSSION"
[Term]
id: MS:1002439
name: final PSM list UNDER DISCUSSION
def: "A flag on a list of PSMs (SpectrumIdentificationList) to indicate 
that this is the final set of identifications to be interpreted by 
consuming software. Amongst the set of SpectrumIdentificationList(s) 
that are flagged with the term, each spectrum must not be referenced 
from more than one SpectrumIdentificationResult." [PSI:PI]
is_a: MS:1002438 ! spectrum identification list result details

[Term]
id: MS:1002440
name: intermediate PSM list UNDER DISCUSSION
def: "A flag on a list of PSMs (SpectrumIdentificationList) to indicate 
that this is not the final set of identifications to be interpreted by 
consuming software. This term should be used when results are provided 
from multiple search engines for the results from each search engine 
before they are combined to give consensus identifications. Amongst the 
set of SpectrumIdentificationList(s) that are flagged with the term, 
each spectrum may be referenced from more than one 
SpectrumIdentificationResult." [PSI:PI]
is_a: MS:1002438 ! spectrum identification list result details

************ Added is_a relations for the
************ ... target-decoy thresholds to the following terms:
[Term]
id: MS:1001364
name: distinct peptide-level global FDR
def: "Estimation of the global false discovery rate for distinct 
peptides once redundant identifications of the same peptide have been 
removed (id est multiple PSMs have been collapsed to one entry)." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001105 ! peptide result details
is_a: MS:1002484 ! peptide-level target-decoy threshold
relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive

[Term]
id: MS:1001447
name: prot:FDR threshold
def: "False-discovery rate threshold for proteins." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002485 ! protein-level target-decoy threshold

[Term]
id: MS:1001448
name: pep:FDR threshold
def: "False-discovery rate threshold for peptides." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002484 ! peptide-level target-decoy threshold

[Term]
id: MS:1002369
name: protein group-level global FDR
def: "Estimation of the global false discovery rate of protein groups." 
[PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002346 ! protein group-level result details
is_a: MS:1002486 ! protein group-level target-decoy threshold

[Term]
id: MS:1002370
name: protein group-level local FDR
def: "Estimation of the local false discovery rate of protein groups." 
[PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002346 ! protein group-level result details
is_a: MS:1002486 ! protein group-level target-decoy threshold

[Term]
id: MS:1002460
name: protein group-level global FNR
def: "Estimation of the global false negative rate of protein groups." 
[PSI:PI]
is_a: MS:1002346 ! protein group-level result details
relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive
is_a: MS:1002486 ! protein group-level target-decoy threshold



New CV terms in version 3.65.0_rc2 of psi-ms.obo:
=================================================
[Term]
id: MS:1002481
name: higher energy beam-type collision-induced dissociation
def: "A collision-induced dissociation process wherein the projectile 
ion has the translational energy higher than approximately 1000 eV." 
[PSI:MS]
is_a: MS:1000422 ! beam-type collision-induced dissociation

[Term]
id: MS:1002482
name: statistical threshold
def: "Estimated statistical threshold." [PSI:MS]
is_a: MS:1001060 ! quality estimation method details

[Term]
id: MS:1002483
name: PSM-level statistical threshold
def: "Estimated statistical threshold at PSM-level." [PSI:MS]
is_a: MS:1002482 ! statistical threshold

[Term]
id: MS:1002484
name: peptide-level statistical threshold
def: "Estimated statistical threshold at peptide-level." [PSI:MS]
is_a: MS:1002482 ! statistical threshold

[Term]
id: MS:1002485
name: protein-level statistical threshold
def: "Estimated statistical threshold at protein-level." [PSI:MS]
is_a: MS:1002482 ! statistical threshold

[Term]
id: MS:1002486
name: protein group-level statistical threshold
def: "Estimated statistical threshold at protein group-level." [PSI:PI]
is_a: MS:1002482 ! statistical threshold

[Term]
id: MS:1002487
name: MassIVE dataset identifier
def: "Dataset identifier issued by the MassIVE repository. A dataset can 
refer to either a single sample as part of a study, or all samples that 
are part of the study corresponding to a publication." [PSI:PI]
is_a: MS:1000878 ! external reference identifier

[Term]
id: MS:1002488
name: MassIVE dataset URI
def: "URI that allows the access to one dataset in the MassIVE 
repository. A dataset can refer to either a single sample as part of a 
study, or all samples that are part of the study corresponding to a 
publication." [PSI:PI]
xref: value-type:xsd\:anyURI "The allowed value-type for this CV term."
is_a: MS:1000878 ! external reference identifier

[Term]
id: MS:1002489
name: special processing
def: "Details describing a special processing." [PSI:PI]
relationship: part_of MS:1001000 ! spectrum interpretation

[Term]
id: MS:1002490
name: peptide-level scoring
def: "Peptide-level scoring performed." [PSI:PI]
is_a: MS:1002489 ! special processing

[Term]
id: MS:1002491
name: modification localization scoring
def: "Modification localization scoring performed." [PSI:PI]
is_a: MS:1002489 ! special processing

[Term]
id: MS:1002492
name: consensus scoring
def: "Consensus multiple search engine approach performed." [PSI:PI]
is_a: MS:1002489 ! special processing

[Term]
id: MS:1002493
name: sample pre-fractionation
def: "Sample pre-fractionation performed." [PSI:PI]
is_a: MS:1002489 ! special processing

[Term]
id: MS:1002494
name: cross-linking search
def: "Cross-linking search performed." [PSI:PI]
is_a: MS:1002489 ! special processing

[Term]
id: MS:1002495
name: no special processing
def: "No special processing performed." [PSI:PI]
is_a: MS:1002489 ! special processing

[Term]
id: MS:1002496
name: group PSMs by sequence
def: "Group PSMs by distinct peptide sequence ignoring modifications." 
[PSI:PI]
is_a: MS:1002345 ! PSM-level result details

[Term]
id: MS:1002497
name: group PSMs by sequence with modifications
def: "Group PSMs by distinct peptide sequence with taking modifications 
into account." [PSI:PI]
is_a: MS:1002345 ! PSM-level result details

[Term]
id: MS:1002498
name: group PSMs by sequence with modifications and charge
def: "Group PSMs by distinct peptide sequence with taking modifications 
and charge into account." [PSI:PI]
is_a: MS:1002345 ! PSM-level result details

[Term]
id: MS:1002499
name: peptide level score
def: "Peptide level score." [PSI:PI]
is_a: MS:1002358 ! search engine specific score for distinct peptides

[Term]
id: MS:1002500
name: peptide passes threshold
def: "A Boolean attribute to determine whether the peptide has passed 
the threshold indicated in the file." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001105 ! peptide result details

[Term]
id: MS:1002501
name: no PSM threshold
def: "Indicating that no PSM threshold was used." [PSI:PI]
is_a: MS:1002345 ! PSM-level result details

[Term]
id: MS:1002502
name: no peptide-level threshold
def: "Indicating that no peptide-level threshold was used." [PSI:PI]
is_a: MS:1001105 ! peptide result details

[Term]
id: MS:1002503
name: PSM is used for peptide-level scoring
def: "Flags a PSM that it is used for peptide-level scoring." [PSI:PI]
is_a: MS:1001105 ! peptide result details

[Term]
id: MS:1002504
name: order
def: "The order of modifications to be referenced elsewhere in the 
document." [PSI:PI]
xref: value-type:xsd\:integer "The allowed value-type for this CV term."
is_a: MS:1001055 ! modification parameters

[Term]
id: MS:1002505
name: regular expression for modification localization scoring
def: 
"([:digit:]+:[0|1]{1}.[:digit:]+:[:digit:]+[|:digit:]*:(true|false){1})." [PSI:PI]
is_a: MS:1002479 ! regular expression

[Term]
id: MS:1002506
name: modification position score
def: "Modification position score." [PSI:PI]
is_a: MS:1001055 ! modification parameters

[Term]
id: MS:1002507
name: modification rescoring:false localization rate
def: "Mod position score: false localization rate." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002506 ! modification position score
relationship: has_regexp MS:1002505 ! regular expression for 
modification localization scoring

[Term]
id: MS:1002508
name: cross-linking attribute
def: "Cross-linking attribute." [PSI:PI]
is_a: MS:1001105 ! peptide result details

[Term]
id: MS:1002509
name: cross-link donor
def: "The Cross-linking donor, assigned according to the following 
rules: the export software SHOULD use the following rules to choose the 
cross-link donor as the: longer peptide, then higher peptide neutral 
mass, then alphabetical order." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002508 ! cross-linking attribute

[Term]
id: MS:1002510
name: cross-link receiver
def: "Cross-linking receiver, assigned according to the following rules: 
the export software SHOULD use the following rules to choose the 
cross-link donor as the: longer peptide, then higher peptide neutral 
mass, then alphabetical order." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002508 ! cross-linking attribute

[Term]
id: MS:1002511
name: cross-link spectrum identification item
def: "Cross-linked spectrum identification item." [PSI:PI]
xref: value-type:xsd\:integer "The allowed value-type for this CV term."
is_a: MS:1002508 ! cross-linking attribute

[Term]
id: MS:1002512
name: cross-linking score
def: "Cross-linking scoring value." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001153 ! search engine specific score

Best Regards,
Gerhard

-- 
---
Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
Bioinformatics / Biostatistics
Medizinisches-Proteom-Center (MPC)
Ruhr-Universität Bochum
Zentrum für klinische Forschung I (ZKF I), E.049a
Universitätsstraße 150
D-44801 Bochum
  
Phone:	+49(0)234/32-21006
Fax:	+49(0)234/32-14554
Email:	ger...@ru...
Web:	http://www.medizinisches-proteom-center.de

Re: [Psidev-ms-dev] [Psidev-ms-vocab] Release candidate 3.64.0_rc4 of psi-ms.obo

[Chambers, M. <mat...@gm...>]

Hi Henry,

Can you chime in on whether it really makes sense for SpectraST to be 
differentiating spectra based on QTOF or HCD? This seems to mixing 
concepts at different levels. Q[q]TOF is a fully specified instrument 
type, while HCD is a single activation mode that - as I understand it - 
creates essentially equivalent fragmentation to that of the [q] of 
Q[q]TOF. The main difference between QTOF and Q-Exactive (QqOrbi) is 
going to be resolution, not fragmentation. Different QTOFs will have 
wildly varying resolution, so putting them all in the same bucket for 
purposes other than fragmentation model doesn't make much sense to me. 
Also, different vendors have quite variable signal processing for 
filtering noise which affect comparisons between QTOFs and between QTOFs 
and Orbitraps.

If there's a good reason for software like SpectraST to differentiate 
QTOF from HCD Orbitrap in terms of fragmentation, then I might vote for 
plan B, so... what's the reason?

Thanks,
-Matt


On 5/27/2014 10:47 AM, Eric Deutsch wrote:
>
> Hi Pierre-Alain, I don't think I fully understand what you're saying, 
> but it seems clear that you're not in favor of what I'm proposing.
>
> So just to recap, the "plan A" proposal for mapping a few specific 
> instruments to dissociation terms is this:
>
> LTQ MS:1002472        name: trap-type collision-induced dissociation
>
> HCD Orbitrap     MS:1000422 name: beam-type collision-induced dissociation
>
> QTOF MS:1000422        name: beam-type collision-induced dissociation
>
> 4800 TOF/TOF MS:1002481        name: higher energy beam-type 
> collision-induced dissociation
>
> My "alternate B" proposal was:
>
> LTQ MS:1002472        name: trap-type collision-induced dissociation
>
> QTOF MS:1000422        name: beam-type collision-induced dissociation
>
> HCD Orbitrap     MS:100????        name: higher energy beam-type 
> collision-induced dissociation
>
> 4800 TOF/TOF MS:1002481        name: keV energy beam-type 
> collision-induced dissociation
>
> Although not completely clear, it seems that Pierre-Alain and Matt 
> favor A. And Eric and Wilfred favor B.
>
> First, is this a correct assessment?
>
> Second, would anyone else care to comment or show support for either A 
> or B?
>
> Thanks,
>
> Eric
>
> *From:*Binz Pierre-Alain [mailto:Pie...@ch... 
> <mailto:Pie...@ch...>]
> *Sent:* Tuesday, May 27, 2014 8:14 AM
> *To:* Mass spectrometry standard development
> *Subject:* Re: [Psidev-ms-dev] [Psidev-ms-vocab] Release candidate 
> 3.64.0_rc4 of psi-ms.obo
>
> Hi Eric,
>
> What if SpectraST would look into the instrumentConfiguration 
> element ? It should be able to make the difference. This has the 
> advantage that we do not need to invent additional terms just to match 
> with a specific software. And what if Spectrast once can make the 
> difference between ABSciex QTOF and Waters G2 (also a QTOF), or 
> between two CID conditions for one QTOF instrument (you should maybe 
> look at the activation element instead of creating yet other terms for 
> this ?
>
> Otherwise I beleive that we would need to create a number of child 
> terms to there trap-type and beam-type CIDs, where the nomenclature 
> and ontology might potentially be a bit vague.
>
> I understand that it does not simplify the parsing, but a) it 
> simplifies the CV, b) it potentially removes additional checks to 
> validate (do one need to check whether a activation/fragmentation term 
> does correspond to the instrument at all ?) and c) there is anyway a 
> need for software such as SpectraST to deal with ambiguity if the 
> precise term does not exist
>
> Cheers
>
> Pierre-Alain
>
> *De :*Eric Deutsch [mailto:ede...@sy...]
> *Envoyé :* mardi 27 mai 2014 16:40
> *À :* Mass spectrometry standard development
> *Cc :* Eric Deutsch
> *Objet :* Re: [Psidev-ms-dev] [Psidev-ms-vocab] Release candidate 
> 3.64.0_rc4 of psi-ms.obo
>
> Well, for example, the SpectraST software has different modes for HCD 
> and QTOF. If Orbi and QTOF data files are annotated the same way, then 
> it will be extremely difficult for SpectraST to know which mode to 
> set. It would have to resort to complex logic based on the instrument 
> model. It seems to me that if we make them two different terms, it 
> would be trivial for other software to treat them the same. However, 
> if we make it one term, it will be very burdensome for other software 
> that wants to differentiate them to treat them differently.
>
> Regards,
>
> Eric
>
> *From:*Chambers, Matthew [mailto:mat...@gm... 
> <mailto:mat...@gm...>]
> *Sent:* Friday, May 23, 2014 3:12 PM
> *To:* psi...@li... 
> <mailto:psi...@li...>
> *Subject:* Re: [Psidev-ms-dev] [Psidev-ms-vocab] Release candidate 
> 3.64.0_rc4 of psi-ms.obo
>
> Why would that dismay you? AFAIK, QTOF and HCD fragmentation are 
> essentially the same. I think Gerhard's approach is more in line with 
> IUPAC and the only drawback is confusion between Thermo's proprietary 
> name and the IUPAC term with similar semantics.
>
> -Matt
>
> On 5/23/2014 11:37 AM, Eric Deutsch wrote:
>
>
>     As are some others, I'm a bit dismayed that Thermo HCD and QTOF
>     are lumped into one.
>
>     Thanks,
>
>     Eric
>
>     -----Original Message-----
>     From: Gerhard Mayer [mailto:may...@ru... <mailto:may...@ru...>]
>     Sent: Friday, May 23, 2014 1:46 AM
>     To: psi...@li...
>     <mailto:psi...@li...>;
>     psi...@li...
>     <mailto:psi...@li...>
>     Cc: psi...@li...
>     <mailto:psi...@li...>
>     Subject: Re: [Psidev-ms-dev] [Psidev-ms-vocab] Release candidate
>     3.64.0_rc4 of psi-ms.obo
>
>     Dear proteomics community,
>
>     attached you find the release candidate 3.65.0_rc1 of the
>     psi-ms.obo file.
>
>     It contains a new "statistical threshold" term as parent of the
>
>     different thresholding mechanisms.
>
>     According to the CID terms we now have the following hierarchy:
>
>     collision-induced association (synonyms: CID, CAD, collision
>     --activated
>
>     association)
>
>     beam-type collision-induced dissociation (synonym: HCD)
>
>     higher-energy beam-type collision-induced dissociation
>
>     trap-type high-energy collision-induced dissociation
>
>     that would map to Matt's proposal and Wilfred's buckets as follows:
>
>     Am 23.05.2014 06:49, schrieb Wilfred Tang:
>
>     > I think the activation type should be described in broad buckets. I
>
>     > would guess (for example) that the various QTOF dissociations
>     (ABSciex
>
>     > QTOF, Agilent QTOF, Waters QTOF, etc.) would be more similar to one
>
>     > another than ABSciex QTOF vs ABSciex TOF/TOF for example. For
>     the sake
>
>     > of argument, I'll put down some broad buckets:
>
>     > - ion trap collisional dissociation
>
>     --> trap-type collision-induced dissociation (MS:1002472)
>
>     > - QTOF collisional dissociation
>
>     > - HCD collisional dissociation
>
>     --> beam-type collision-induced dissociation (MS:1000422)
>
>     > - TOF/TOF collisional dissociation
>
>     --> higher-energy beam-type collision-induced dissociation
>     (MS:1002481)
>
>     > Maybe QTOF collisional dissociation and HCD collisional
>     dissociation
>
>     > can be collapsed into one bucket. Does anyone know how similar
>     their
>
>     > fragmentations are?
>
>     >
>
>     > I don't think one should need to read the instrument name to figure
>
>     > out the activation type. Every new instrument introduction would
>     break
>
>     > things.
>
>     >
>
>     > Wilfred
>
>     Changed CV terms in version 3.65.0_rc1 of psi-ms.obo:
>
>     =====================================================
>
>     ************ Changed synonym to "collisionally activated dissociation"
>
>     ************ instead of "collision activated dissociation"
>
>     ************ in order to match the IUPAC recommendations
>
>     [Term]
>
>     id: MS:1000133
>
>     name: collision-induced dissociation
>
>     def: "The dissociation of an ion after collisional excitation. The
>     term
>
>     collisional-activated dissociation is not recommended." [PSI:MS]
>
>     synonym: "CID" EXACT []
>
>     synonym: "CAD" EXACT []
>
>     synonym: "collisionally activated dissociation" EXACT []
>
>     is_a: MS:1000044 ! dissociation method
>
>     ************ Renamed to beam-type collision-induced dissociation
>
>     [Term]
>
>     id: MS:1000422
>
>     name: beam-type collision-induced dissociation
>
>     def: "A collision-induced dissociation process that occurs in a
>
>     beam-type collision cell." [PSI:MS]
>
>     synonym: "HCD" EXACT []
>
>     is_a: MS:1000133 ! collision-induced dissociation
>
>
>     New CV terms in version 3.65.0_rc1 of psi-ms.obo:
>
>     =================================================
>
>     [Term]
>
>     id: MS:1002481
>
>     name: higher energy beam-type collision-induced dissociation
>
>     def: "A collision-induced dissociation process wherein the projectile
>
>     ion has the translational energy higher than approximately 1000 eV."
>
>     [PSI:MS]
>
>     is_a: MS:1000422 ! beam-type collision-induced dissociation
>
>
>     Best Regards,
>
>     Gerhard
>

Re: [Psidev-ms-dev] [Psidev-ms-vocab] Release candidate 3.64.0_rc4 of psi-ms.obo

[Wilfred T. <wt...@pr...>]

Sorry, forgot to reply to this. I'm fine with either plan A or plan B. The
key point for me is that there is a way to distinguish TOFTOF
fragmentation, and both plans address that.

Wilfred


On Tue, Jun 10, 2014 at 11:35 PM, Gerhard Mayer <may...@ru...> wrote:

>  Hi Eric,
>
> since Wilfred wrote in his mail from May 23rd:
>
> *... *
>
> *I think the activation type should be described in broad buckets. I would
> guess (for example) that the various QTOF dissociations (ABSciex QTOF,
> Agilent QTOF, Waters QTOF, etc.) would be more similar to one another than
> ABSciex QTOF vs ABSciex TOF/TOF for example. For the sake of argument, I'll
> put down some broad buckets: *
>
> *- ion trap collisional dissociation *
>
> *- QTOF collisional dissociation *
>
> *- HCD collisional dissociation *
>
> *- TOF/TOF collisional dissociation *
>
> *Maybe QTOF collisional dissociation and HCD collisional dissociation can
> be collapsed into one bucket. Does anyone know how similar their
> fragmentations are? ...*
>
>  I interpreted it, that he also voted to "plan A", which has one term for
> QTOF and HCD.
>
> Best regards,
> Gerhard
>
>
> Am 27.05.2014 17:47, schrieb Eric Deutsch:
>
>  Hi Pierre-Alain, I don’t think I fully understand what you’re saying,
> but it seems clear that you’re not in favor of what I’m proposing.
>
>
>
> So just to recap, the “plan A” proposal for mapping a few specific
> instruments to dissociation terms is this:
>
>
>
> LTQ                        MS:1002472        name: trap-type
> collision-induced dissociation
>
> HCD Orbitrap     MS:1000422        name: beam-type collision-induced
> dissociation
>
> QTOF                     MS:1000422        name: beam-type
> collision-induced dissociation
>
> 4800 TOF/TOF    MS:1002481        name: higher energy beam-type
> collision-induced dissociation
>
>  My “alternate B” proposal was:
>
>
>
> LTQ                        MS:1002472        name: trap-type
> collision-induced dissociation
>
> QTOF                     MS:1000422        name: beam-type
> collision-induced dissociation
>
> HCD Orbitrap     MS:100????        name: higher energy beam-type
> collision-induced dissociation
>
> 4800 TOF/TOF    MS:1002481        name: keV energy beam-type
> collision-induced dissociation
>
>
>
> Although not completely clear, it seems that Pierre-Alain and Matt favor
> A. And Eric and Wilfred favor B.
>
>
>
> First, is this a correct assessment?
>
>
>
> Second, would anyone else care to comment or show support for either A or
> B?
>
>
>
> Thanks,
>
> Eric
>
>
>
>
>
>
>
> *From:* Binz Pierre-Alain [mailto:Pie...@ch...]
> *Sent:* Tuesday, May 27, 2014 8:14 AM
> *To:* Mass spectrometry standard development
> *Subject:* Re: [Psidev-ms-dev] [Psidev-ms-vocab] Release candidate
> 3.64.0_rc4 of psi-ms.obo
>
>
>
> Hi Eric,
>
>
>
> What if SpectraST would look into the instrumentConfiguration element ? It
> should be able to make the difference. This has the advantage that we do
> not need to invent additional terms just to match with a specific software.
> And what if Spectrast once can make the difference between ABSciex QTOF and
> Waters G2 (also a QTOF), or between two CID conditions for one QTOF
> instrument (you should maybe look at the activation element instead of
> creating yet other terms for this ?
>
> Otherwise I beleive that we would need to create a number of child terms
> to there trap-type and beam-type CIDs, where the nomenclature and ontology
> might potentially be a bit vague.
>
> I understand that it does not simplify the parsing, but a) it simplifies
> the CV, b) it potentially removes additional checks to validate (do one
> need to check whether a activation/fragmentation term does correspond to
> the instrument at all ?) and c) there is anyway a need for software such as
> SpectraST to deal with ambiguity if the precise term does not exist
>
>
>
> Cheers
>
> Pierre-Alain
>
>
>
>
>
>
>
>
>
> *De :* Eric Deutsch [mailto:ede...@sy...
> <ede...@sy...>]
> *Envoyé :* mardi 27 mai 2014 16:40
> *À :* Mass spectrometry standard development
> *Cc :* Eric Deutsch
> *Objet :* Re: [Psidev-ms-dev] [Psidev-ms-vocab] Release candidate
> 3.64.0_rc4 of psi-ms.obo
>
>
>
> Well, for example, the SpectraST software has different modes for HCD and
> QTOF. If Orbi and QTOF data files are annotated the same way, then it will
> be extremely difficult for SpectraST to know which mode to set. It would
> have to resort to complex logic based on the instrument model. It seems to
> me that if we make them two different terms, it would be trivial for other
> software to treat them the same. However, if we make it one term, it will
> be very burdensome for other software that wants to differentiate them to
> treat them differently.
>
>
>
> Regards,
>
> Eric
>
>
>
>
>
> *From:* Chambers, Matthew [mailto:mat...@gm...]
> *Sent:* Friday, May 23, 2014 3:12 PM
> *To:* psi...@li...
> *Subject:* Re: [Psidev-ms-dev] [Psidev-ms-vocab] Release candidate
> 3.64.0_rc4 of psi-ms.obo
>
>
>
> Why would that dismay you? AFAIK, QTOF and HCD fragmentation are
> essentially the same. I think Gerhard's approach is more in line with IUPAC
> and the only drawback is confusion between Thermo's proprietary name and
> the IUPAC term with similar semantics.
>
> -Matt
>
> On 5/23/2014 11:37 AM, Eric Deutsch wrote:
>
>  Hi Gerhard, thank you for pushing this forward. You wrote:
>
>
>
> trap-type high-energy collision-induced dissociation
>
>
>
> Is that correct? OR should it just be:
>
>
>
> trap-type collision-induced dissociation
>
>
>
> ?
>
>
>
> I still a little confused what we will tag the various instruments with.
> What will be the recommended for acquisition in these instrument modes?
> This?
>
>
>
> LTQ                        MS:1002472        name: trap-type
> collision-induced dissociation
>
> HCD Orbitrap     MS:1000422        name: beam-type collision-induced
> dissociation
>
> QTOF                     MS:1000422        name: beam-type
> collision-induced dissociation
>
> 4800 TOF/TOF    MS:1002481        name: higher energy beam-type
> collision-induced dissociation
>
>
>
> As are some others, I'm a bit dismayed that Thermo HCD and QTOF are lumped
> into one.
>
>
>
> Can we just rename 2481 to higher energy beam-type collision-induced
> dissociation
>
> I feel the “er” will just serve to confuse with HCD more, and seems
> unnecessary.
>
>
>
> I didn’t follow all the discussion. Was my proposal for this:
>
>
>
> LTQ                        MS:1002472        name: trap-type
> collision-induced dissociation
>
> HCD Orbitrap     MS:100????        name: higher energy beam-type
> collision-induced dissociation
>
> QTOF                     MS:1000422        name: beam-type
> collision-induced dissociation
>
> 4800 TOF/TOF    MS:1002481        name: keV energy beam-type
> collision-induced dissociation
>
>
>
> voted down?
>
>
>
> Thanks,
>
> Eric
>
>
>
>
>
>
>
> -----Original Message-----
> From: Gerhard Mayer [mailto:may...@ru...]
> Sent: Friday, May 23, 2014 1:46 AM
> To: psi...@li...;
> psi...@li...
> Cc: psi...@li...
> Subject: Re: [Psidev-ms-dev] [Psidev-ms-vocab] Release candidate
> 3.64.0_rc4 of psi-ms.obo
>
>
>
> Dear proteomics community,
>
>
>
> attached you find the release candidate 3.65.0_rc1 of the psi-ms.obo file.
>
>
>
> It contains a new "statistical threshold" term as parent of the
>
> different thresholding mechanisms.
>
>
>
> According to the CID terms we now have the following hierarchy:
>
> collision-induced association (synonyms: CID, CAD, collision –activated
>
> association)
>
> beam-type collision-induced dissociation (synonym: HCD)
>
> higher-energy beam-type collision-induced dissociation
>
> trap-type high-energy collision-induced dissociation
>
>
>
> that would map to Matt's proposal and Wilfred's buckets as follows:
>
>
>
> Am 23.05.2014 06:49, schrieb Wilfred Tang:
>
> > I think the activation type should be described in broad buckets. I
>
> > would guess (for example) that the various QTOF dissociations (ABSciex
>
> > QTOF, Agilent QTOF, Waters QTOF, etc.) would be more similar to one
>
> > another than ABSciex QTOF vs ABSciex TOF/TOF for example. For the sake
>
> > of argument, I'll put down some broad buckets:
>
> > - ion trap collisional dissociation
>
> --> trap-type collision-induced dissociation (MS:1002472)
>
> > - QTOF collisional dissociation
>
> > - HCD collisional dissociation
>
> --> beam-type collision-induced dissociation (MS:1000422)
>
> > - TOF/TOF collisional dissociation
>
> --> higher-energy beam-type collision-induced dissociation (MS:1002481)
>
> > Maybe QTOF collisional dissociation and HCD collisional dissociation
>
> > can be collapsed into one bucket. Does anyone know how similar their
>
> > fragmentations are?
>
> >
>
> > I don't think one should need to read the instrument name to figure
>
> > out the activation type. Every new instrument introduction would break
>
> > things.
>
> >
>
> > Wilfred
>
>
>
> Changed CV terms in version 3.65.0_rc1 of psi-ms.obo:
>
> =====================================================
>
> ************ Changed synonym to "collisionally activated dissociation"
>
> ************ instead of "collision activated dissociation"
>
> ************ in order to match the IUPAC recommendations
>
> [Term]
>
> id: MS:1000133
>
> name: collision-induced dissociation
>
> def: "The dissociation of an ion after collisional excitation. The term
>
> collisional-activated dissociation is not recommended." [PSI:MS]
>
> synonym: "CID" EXACT []
>
> synonym: "CAD" EXACT []
>
> synonym: "collisionally activated dissociation" EXACT []
>
> is_a: MS:1000044 ! dissociation method
>
>
>
> ************ Changed definition to
>
> ************ "... The term parent ion is deprecated."
>
> ************ in order to match the IUPAC recommendations
>
> [Term]
>
> id: MS:1000340
>
> name: precursor ion
>
> def: "An ion that reacts to form particular product ions. The reaction
>
> can be unimolecular dissociation, ion/molecule reaction, isomerization,
>
> or change in charge state. The term parent ion is not deprecated." [PSI:MS]
>
> synonym: "parent ion" RELATED []
>
> is_a: MS:1000506 ! ion role
>
>
>
> ************ Renamed to beam-type collision-induced dissociation
>
> [Term]
>
> id: MS:1000422
>
> name: beam-type collision-induced dissociation
>
> def: "A collision-induced dissociation process that occurs in a
>
> beam-type collision cell." [PSI:MS]
>
> synonym: "HCD" EXACT []
>
> is_a: MS:1000133 ! collision-induced dissociation
>
>
>
> ************ The following two terms are flagged as "UNDER DISCUSSION"
>
> [Term]
>
> id: MS:1002439
>
> name: final PSM list UNDER DISCUSSION
>
> def: "A flag on a list of PSMs (SpectrumIdentificationList) to indicate
>
> that this is the final set of identifications to be interpreted by
>
> consuming software. Amongst the set of SpectrumIdentificationList(s)
>
> that are flagged with the term, each spectrum must not be referenced
>
> from more than one SpectrumIdentificationResult." [PSI:PI]
>
> is_a: MS:1002438 ! spectrum identification list result details
>
>
>
> [Term]
>
> id: MS:1002440
>
> name: intermediate PSM list UNDER DISCUSSION
>
> def: "A flag on a list of PSMs (SpectrumIdentificationList) to indicate
>
> that this is not the final set of identifications to be interpreted by
>
> consuming software. This term should be used when results are provided
>
> from multiple search engines for the results from each search engine
>
> before they are combined to give consensus identifications. Amongst the
>
> set of SpectrumIdentificationList(s) that are flagged with the term,
>
> each spectrum may be referenced from more than one
>
> SpectrumIdentificationResult." [PSI:PI]
>
> is_a: MS:1002438 ! spectrum identification list result details
>
>
>
>
>
>
>
> New CV terms in version 3.65.0_rc1 of psi-ms.obo:
>
> =================================================
>
> [Term]
>
> id: MS:1002481
>
> name: higher energy beam-type collision-induced dissociation
>
> def: "A collision-induced dissociation process wherein the projectile
>
> ion has the translational energy higher than approximately 1000 eV."
>
> [PSI:MS]
>
> is_a: MS:1000422 ! beam-type collision-induced dissociation
>
>
>
> [Term]
>
> id: MS:1002482
>
> name: statistical threshold
>
> def: "Estimated statistical threshold." [PSI:MS]
>
> is_a: MS:1001060 ! quality estimation method details
>
>
>
> [Term]
>
> id: MS:1002483
>
> name: PSM-level statistical threshold
>
> def: "Estimated statistical threshold at PSM-level." [PSI:MS]
>
> is_a: MS:1002482 ! statistical threshold
>
>
>
> [Term]
>
> id: MS:1002484
>
> name: peptide-level statistical threshold
>
> def: "Estimated statistical threshold at peptide-level." [PSI:MS]
>
> is_a: MS:1002482 ! statistical threshold
>
>
>
> [Term]
>
> id: MS:1002485
>
> name: protein or protein group-level statistical threshold
>
> def: "Estimated statistical threshold at protein-level." [PSI:MS]
>
> is_a: MS:1002482 ! statistical threshold
>
>
>
> Best Regards,
>
> Gerhard
>
>
>
> --
>
> ---
>
> Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
>
> Bioinformatics / Biostatistics
>
> Medizinisches-Proteom-Center (MPC)
>
> Ruhr-Universität Bochum
>
> Zentrum für klinische Forschung I (ZKF I), E.049a
>
> Universitätsstraße 150
>
> D-44801 Bochum
>
>
>
> Phone: +49(0)234/32-21006
>
> Fax:        +49(0)234/32-14554
>
> Email:    ger...@ru...
>
> Web:     http://www.medizinisches-proteom-center.de
>
>
>
>
>
> ------------------------------------------------------------------------------
>
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>
>
> --
> ---
> Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
> Bioinformatics / Biostatistics
> Medizinisches-Proteom-Center (MPC)
> Ruhr-Universität Bochum
> Zentrum für klinische Forschung I (ZKF I), E.049a
> Universitätsstraße 150
> D-44801 Bochum
>
> Phone:	+49(0)234/32-21006
> Fax:	+49(0)234/32-14554
> Email:	ger...@ru...
> Web:	http://www.medizinisches-proteom-center.de
>
>
>
> ------------------------------------------------------------------------------
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[Psidev-ms-dev] Release candidate 3.65.0_rc1 of psi-ms.obo

[Gerhard M. <may...@ru...>]

Dear proteomics community,

attached you find the release candidate 3.65.0_rc1 of the psi-ms.obo file.

It contains a new "statistical threshold" term as parent of the
different thresholding mechanisms and two new terms for MassIVE.

According to the CID terms we now have the following hierarchy:
collision-induced association (synonyms: CID, CAD, collision –activated 
association)
beam-type collision-induced dissociation (synonym: HCD)
higher-energy beam-type collision-induced dissociation
trap-type collision-induced dissociation


Changed CV terms in version 3.65.0_rc1 of psi-ms.obo:
=====================================================
************ Changed synonym to "collisionally activated dissociation"
************ instead of "collision activated dissociation"
************ in order to match the IUPAC recommendations
[Term]
id: MS:1000133
name: collision-induced dissociation
def: "The dissociation of an ion after collisional excitation. The term 
collisional-activated dissociation is not recommended." [PSI:MS]
synonym: "CID" EXACT []
synonym: "CAD" EXACT []
synonym: "collisionally activated dissociation" EXACT []
is_a: MS:1000044 ! dissociation method

************ Changed definition to
************ "... The term parent ion is deprecated."
************ in order to match the IUPAC recommendations
[Term]
id: MS:1000340
name: precursor ion
def: "An ion that reacts to form particular product ions. The reaction 
can be unimolecular dissociation, ion/molecule reaction, isomerization, 
or change in charge state. The term parent ion is not deprecated." [PSI:MS]
synonym: "parent ion" RELATED []
is_a: MS:1000506 ! ion role

************ Renamed to beam-type collision-induced dissociation
[Term]
id: MS:1000422
name: beam-type collision-induced dissociation
def: "A collision-induced dissociation process that occurs in a 
beam-type collision cell." [PSI:MS]
synonym: "HCD" EXACT []
is_a: MS:1000133 ! collision-induced dissociation

************ The following two terms are flagged as "UNDER DISCUSSION"
[Term]
id: MS:1002439
name: final PSM list UNDER DISCUSSION
def: "A flag on a list of PSMs (SpectrumIdentificationList) to indicate 
that this is the final set of identifications to be interpreted by 
consuming software. Amongst the set of SpectrumIdentificationList(s) 
that are flagged with the term, each spectrum must not be referenced 
from more than one SpectrumIdentificationResult." [PSI:PI]
is_a: MS:1002438 ! spectrum identification list result details

[Term]
id: MS:1002440
name: intermediate PSM list UNDER DISCUSSION
def: "A flag on a list of PSMs (SpectrumIdentificationList) to indicate 
that this is not the final set of identifications to be interpreted by 
consuming software. This term should be used when results are provided 
from multiple search engines for the results from each search engine 
before they are combined to give consensus identifications. Amongst the 
set of SpectrumIdentificationList(s) that are flagged with the term, 
each spectrum may be referenced from more than one 
SpectrumIdentificationResult." [PSI:PI]
is_a: MS:1002438 ! spectrum identification list result details


New CV terms in version 3.65.0_rc1 of psi-ms.obo:
=================================================
[Term]
id: MS:1002481
name: higher energy beam-type collision-induced dissociation
def: "A collision-induced dissociation process wherein the projectile 
ion has the translational energy higher than approximately 1000 eV." 
[PSI:MS]
is_a: MS:1000422 ! beam-type collision-induced dissociation

[Term]
id: MS:1002482
name: statistical threshold
def: "Estimated statistical threshold." [PSI:PI]
is_a: MS:1001060 ! quality estimation method details

[Term]
id: MS:1002483
name: PSM-level statistical threshold
def: "Estimated statistical threshold at PSM-level." [PSI:PI]
is_a: MS:1002482 ! statistical threshold

[Term]
id: MS:1002484
name: peptide-level statistical threshold
def: "Estimated statistical threshold at peptide-level." [PSI:PI]
is_a: MS:1002482 ! statistical threshold

[Term]
id: MS:1002485
name: protein-level statistical threshold
def: "Estimated statistical threshold at protein-level." [PSI:PI]
is_a: MS:1002482 ! statistical threshold

[Term]
id: MS:1002486
name: protein group-level statistical threshold
def: "Estimated statistical threshold at protein group-level." [PSI:PI]
is_a: MS:1002482 ! statistical threshold

[Term]
id: MS:1002487
name: MassIVE dataset identifier
def: "Dataset identifier issued by the MassIVE repository. A dataset can 
refer to either a single sample as part of a study, or all samples that 
are part of the study corresponding to a publication." [PSI:PI]
is_a: MS:1000878 ! external reference identifier

[Term]
id: MS:1002488
name: MassIVE dataset URI
def: "URI that allows the access to one dataset in the MassIVE 
repository. A dataset can refer to either a single sample as part of a 
study, or all samples that are part of the study corresponding to a 
publication." [PSI:PI]
xref: value-type:xsd\:anyURI "The allowed value-type for this CV term."
is_a: MS:1000878 ! external reference identifier

Best Regards,
Gerhard

-- 
---
Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
Bioinformatics / Biostatistics
Medizinisches-Proteom-Center (MPC)
Ruhr-Universität Bochum
Zentrum für klinische Forschung I (ZKF I), E.049a
Universitätsstraße 150
D-44801 Bochum
  
Phone:	+49(0)234/32-21006
Fax:	+49(0)234/32-14554
Email:	ger...@ru...
Web:	http://www.medizinisches-proteom-center.de

Re: [Psidev-ms-dev] [Psidev-ms-vocab] Release candidate 3.64.0_rc4 of psi-ms.obo

[Gerhard M. <may...@ru...>]

Hi Eric,

since Wilfred wrote in his mail from May 23rd:
/...
/
/I think the activation type should be described in broad buckets. I 
would guess (for example) that the various QTOF dissociations (ABSciex 
QTOF, Agilent QTOF, Waters QTOF, etc.) would be more similar to one 
another than ABSciex QTOF vs ABSciex TOF/TOF for example. For the sake 
of argument, I'll put down some broad buckets:
/
/- ion trap collisional dissociation
/
/- QTOF collisional dissociation
/
/- HCD collisional dissociation
/
//
/- TOF/TOF collisional dissociation
/
/Maybe QTOF collisional dissociation and HCD collisional dissociation 
can be collapsed into one bucket. Does anyone know how similar their 
fragmentations are?
.../

I interpreted it, that he also voted to "plan A", which has one term for 
QTOF and HCD.

Best regards,
Gerhard


Am 27.05.2014 17:47, schrieb Eric Deutsch:
>
> Hi Pierre-Alain, I don't think I fully understand what you're saying, 
> but it seems clear that you're not in favor of what I'm proposing.
>
> So just to recap, the "plan A" proposal for mapping a few specific 
> instruments to dissociation terms is this:
>
> LTQ MS:1002472        name: trap-type collision-induced dissociation
>
> HCD Orbitrap     MS:1000422 name: beam-type collision-induced dissociation
>
> QTOF MS:1000422        name: beam-type collision-induced dissociation
>
> 4800 TOF/TOF MS:1002481        name: higher energy beam-type 
> collision-induced dissociation
>
> My "alternate B" proposal was:
>
> LTQ MS:1002472        name: trap-type collision-induced dissociation
>
> QTOF MS:1000422        name: beam-type collision-induced dissociation
>
> HCD Orbitrap     MS:100????        name: higher energy beam-type 
> collision-induced dissociation
>
> 4800 TOF/TOF MS:1002481        name: keV energy beam-type 
> collision-induced dissociation
>
> Although not completely clear, it seems that Pierre-Alain and Matt 
> favor A. And Eric and Wilfred favor B.
>
> First, is this a correct assessment?
>
> Second, would anyone else care to comment or show support for either A 
> or B?
>
> Thanks,
>
> Eric
>
> *From:*Binz Pierre-Alain [mailto:Pie...@ch... 
> <mailto:Pie...@ch...>]
> *Sent:* Tuesday, May 27, 2014 8:14 AM
> *To:* Mass spectrometry standard development
> *Subject:* Re: [Psidev-ms-dev] [Psidev-ms-vocab] Release candidate 
> 3.64.0_rc4 of psi-ms.obo
>
> Hi Eric,
>
> What if SpectraST would look into the instrumentConfiguration 
> element ? It should be able to make the difference. This has the 
> advantage that we do not need to invent additional terms just to match 
> with a specific software. And what if Spectrast once can make the 
> difference between ABSciex QTOF and Waters G2 (also a QTOF), or 
> between two CID conditions for one QTOF instrument (you should maybe 
> look at the activation element instead of creating yet other terms for 
> this ?
>
> Otherwise I beleive that we would need to create a number of child 
> terms to there trap-type and beam-type CIDs, where the nomenclature 
> and ontology might potentially be a bit vague.
>
> I understand that it does not simplify the parsing, but a) it 
> simplifies the CV, b) it potentially removes additional checks to 
> validate (do one need to check whether a activation/fragmentation term 
> does correspond to the instrument at all ?) and c) there is anyway a 
> need for software such as SpectraST to deal with ambiguity if the 
> precise term does not exist
>
> Cheers
>
> Pierre-Alain
>
> *De :*Eric Deutsch [mailto:ede...@sy...]
> *Envoyé :* mardi 27 mai 2014 16:40
> *À :* Mass spectrometry standard development
> *Cc :* Eric Deutsch
> *Objet :* Re: [Psidev-ms-dev] [Psidev-ms-vocab] Release candidate 
> 3.64.0_rc4 of psi-ms.obo
>
> Well, for example, the SpectraST software has different modes for HCD 
> and QTOF. If Orbi and QTOF data files are annotated the same way, then 
> it will be extremely difficult for SpectraST to know which mode to 
> set. It would have to resort to complex logic based on the instrument 
> model. It seems to me that if we make them two different terms, it 
> would be trivial for other software to treat them the same. However, 
> if we make it one term, it will be very burdensome for other software 
> that wants to differentiate them to treat them differently.
>
> Regards,
>
> Eric
>
> *From:*Chambers, Matthew [mailto:mat...@gm... 
> <mailto:mat...@gm...>]
> *Sent:* Friday, May 23, 2014 3:12 PM
> *To:* psi...@li... 
> <mailto:psi...@li...>
> *Subject:* Re: [Psidev-ms-dev] [Psidev-ms-vocab] Release candidate 
> 3.64.0_rc4 of psi-ms.obo
>
> Why would that dismay you? AFAIK, QTOF and HCD fragmentation are 
> essentially the same. I think Gerhard's approach is more in line with 
> IUPAC and the only drawback is confusion between Thermo's proprietary 
> name and the IUPAC term with similar semantics.
>
> -Matt
>
> On 5/23/2014 11:37 AM, Eric Deutsch wrote:
>
>     Hi Gerhard, thank you for pushing this forward. You wrote:
>
>     trap-type high-energy collision-induced dissociation
>
>     Is that correct? OR should it just be:
>
>     trap-type collision-induced dissociation
>
>     ?
>
>     I still a little confused what we will tag the various instruments
>     with. What will be the recommended for acquisition in these
>     instrument modes? This?
>
>     LTQ                        MS:1002472        name: trap-type
>     collision-induced dissociation
>
>     HCD Orbitrap     MS:1000422        name: beam-type
>     collision-induced dissociation
>
>     QTOF MS:1000422        name: beam-type collision-induced dissociation
>
>     4800 TOF/TOF    MS:1002481        name: higher energy beam-type
>     collision-induced dissociation
>
>     As are some others, I'm a bit dismayed that Thermo HCD and QTOF
>     are lumped into one.
>
>     Can we just rename 2481 to higher energy beam-type
>     collision-induced dissociation
>
>     I feel the "er" will just serve to confuse with HCD more, and
>     seems unnecessary.
>
>     I didn't follow all the discussion. Was my proposal for this:
>
>     LTQ MS:1002472        name: trap-type collision-induced dissociation
>
>     HCD Orbitrap     MS:100????        name: higher energy beam-type
>     collision-induced dissociation
>
>     QTOF MS:1000422        name: beam-type collision-induced dissociation
>
>     4800 TOF/TOF    MS:1002481        name: keV energy beam-type
>     collision-induced dissociation
>
>     voted down?
>
>     Thanks,
>
>     Eric
>
>     -----Original Message-----
>     From: Gerhard Mayer [mailto:may...@ru... <mailto:may...@ru...>]
>     Sent: Friday, May 23, 2014 1:46 AM
>     To: psi...@li...
>     <mailto:psi...@li...>;
>     psi...@li...
>     <mailto:psi...@li...>
>     Cc: psi...@li...
>     <mailto:psi...@li...>
>     Subject: Re: [Psidev-ms-dev] [Psidev-ms-vocab] Release candidate
>     3.64.0_rc4 of psi-ms.obo
>
>     Dear proteomics community,
>
>     attached you find the release candidate 3.65.0_rc1 of the
>     psi-ms.obo file.
>
>     It contains a new "statistical threshold" term as parent of the
>
>     different thresholding mechanisms.
>
>     According to the CID terms we now have the following hierarchy:
>
>     collision-induced association (synonyms: CID, CAD, collision
>     --activated
>
>     association)
>
>     beam-type collision-induced dissociation (synonym: HCD)
>
>     higher-energy beam-type collision-induced dissociation
>
>     trap-type high-energy collision-induced dissociation
>
>     that would map to Matt's proposal and Wilfred's buckets as follows:
>
>     Am 23.05.2014 06:49, schrieb Wilfred Tang:
>
>     > I think the activation type should be described in broad buckets. I
>
>     > would guess (for example) that the various QTOF dissociations
>     (ABSciex
>
>     > QTOF, Agilent QTOF, Waters QTOF, etc.) would be more similar to one
>
>     > another than ABSciex QTOF vs ABSciex TOF/TOF for example. For
>     the sake
>
>     > of argument, I'll put down some broad buckets:
>
>     > - ion trap collisional dissociation
>
>     --> trap-type collision-induced dissociation (MS:1002472)
>
>     > - QTOF collisional dissociation
>
>     > - HCD collisional dissociation
>
>     --> beam-type collision-induced dissociation (MS:1000422)
>
>     > - TOF/TOF collisional dissociation
>
>     --> higher-energy beam-type collision-induced dissociation
>     (MS:1002481)
>
>     > Maybe QTOF collisional dissociation and HCD collisional
>     dissociation
>
>     > can be collapsed into one bucket. Does anyone know how similar
>     their
>
>     > fragmentations are?
>
>     >
>
>     > I don't think one should need to read the instrument name to figure
>
>     > out the activation type. Every new instrument introduction would
>     break
>
>     > things.
>
>     >
>
>     > Wilfred
>
>     Changed CV terms in version 3.65.0_rc1 of psi-ms.obo:
>
>     =====================================================
>
>     ************ Changed synonym to "collisionally activated dissociation"
>
>     ************ instead of "collision activated dissociation"
>
>     ************ in order to match the IUPAC recommendations
>
>     [Term]
>
>     id: MS:1000133
>
>     name: collision-induced dissociation
>
>     def: "The dissociation of an ion after collisional excitation. The
>     term
>
>     collisional-activated dissociation is not recommended." [PSI:MS]
>
>     synonym: "CID" EXACT []
>
>     synonym: "CAD" EXACT []
>
>     synonym: "collisionally activated dissociation" EXACT []
>
>     is_a: MS:1000044 ! dissociation method
>
>     ************ Changed definition to
>
>     ************ "... The term parent ion is deprecated."
>
>     ************ in order to match the IUPAC recommendations
>
>     [Term]
>
>     id: MS:1000340
>
>     name: precursor ion
>
>     def: "An ion that reacts to form particular product ions. The
>     reaction
>
>     can be unimolecular dissociation, ion/molecule reaction,
>     isomerization,
>
>     or change in charge state. The term parent ion is not deprecated."
>     [PSI:MS]
>
>     synonym: "parent ion" RELATED []
>
>     is_a: MS:1000506 ! ion role
>
>     ************ Renamed to beam-type collision-induced dissociation
>
>     [Term]
>
>     id: MS:1000422
>
>     name: beam-type collision-induced dissociation
>
>     def: "A collision-induced dissociation process that occurs in a
>
>     beam-type collision cell." [PSI:MS]
>
>     synonym: "HCD" EXACT []
>
>     is_a: MS:1000133 ! collision-induced dissociation
>
>     ************ The following two terms are flagged as "UNDER DISCUSSION"
>
>     [Term]
>
>     id: MS:1002439
>
>     name: final PSM list UNDER DISCUSSION
>
>     def: "A flag on a list of PSMs (SpectrumIdentificationList) to
>     indicate
>
>     that this is the final set of identifications to be interpreted by
>
>     consuming software. Amongst the set of SpectrumIdentificationList(s)
>
>     that are flagged with the term, each spectrum must not be referenced
>
>     from more than one SpectrumIdentificationResult." [PSI:PI]
>
>     is_a: MS:1002438 ! spectrum identification list result details
>
>     [Term]
>
>     id: MS:1002440
>
>     name: intermediate PSM list UNDER DISCUSSION
>
>     def: "A flag on a list of PSMs (SpectrumIdentificationList) to
>     indicate
>
>     that this is not the final set of identifications to be
>     interpreted by
>
>     consuming software. This term should be used when results are
>     provided
>
>     from multiple search engines for the results from each search engine
>
>     before they are combined to give consensus identifications.
>     Amongst the
>
>     set of SpectrumIdentificationList(s) that are flagged with the term,
>
>     each spectrum may be referenced from more than one
>
>     SpectrumIdentificationResult." [PSI:PI]
>
>     is_a: MS:1002438 ! spectrum identification list result details
>
>     New CV terms in version 3.65.0_rc1 of psi-ms.obo:
>
>     =================================================
>
>     [Term]
>
>     id: MS:1002481
>
>     name: higher energy beam-type collision-induced dissociation
>
>     def: "A collision-induced dissociation process wherein the projectile
>
>     ion has the translational energy higher than approximately 1000 eV."
>
>     [PSI:MS]
>
>     is_a: MS:1000422 ! beam-type collision-induced dissociation
>
>     [Term]
>
>     id: MS:1002482
>
>     name: statistical threshold
>
>     def: "Estimated statistical threshold." [PSI:MS]
>
>     is_a: MS:1001060 ! quality estimation method details
>
>     [Term]
>
>     id: MS:1002483
>
>     name: PSM-level statistical threshold
>
>     def: "Estimated statistical threshold at PSM-level." [PSI:MS]
>
>     is_a: MS:1002482 ! statistical threshold
>
>     [Term]
>
>     id: MS:1002484
>
>     name: peptide-level statistical threshold
>
>     def: "Estimated statistical threshold at peptide-level." [PSI:MS]
>
>     is_a: MS:1002482 ! statistical threshold
>
>     [Term]
>
>     id: MS:1002485
>
>     name: protein or protein group-level statistical threshold
>
>     def: "Estimated statistical threshold at protein-level." [PSI:MS]
>
>     is_a: MS:1002482 ! statistical threshold
>
>     Best Regards,
>
>     Gerhard
>
>     -- 
>
>     ---
>
>     Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
>
>     Bioinformatics / Biostatistics
>
>     Medizinisches-Proteom-Center (MPC)
>
>     Ruhr-Universität Bochum
>
>     Zentrum für klinische Forschung I (ZKF I), E.049a
>
>     Universitätsstraße 150
>
>     D-44801 Bochum
>
>     Phone: +49(0)234/32-21006
>
>     Fax: +49(0)234/32-14554
>
>     Email: ger...@ru... <mailto:ger...@ru...>
>
>     Web: http://www.medizinisches-proteom-center.de
>
>     ------------------------------------------------------------------------------
>
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-- 
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Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
Bioinformatics / Biostatistics
Medizinisches-Proteom-Center (MPC)
Ruhr-Universität Bochum
Zentrum für klinische Forschung I (ZKF I), E.049a
Universitätsstraße 150
D-44801 Bochum
  
Phone:	+49(0)234/32-21006
Fax:	+49(0)234/32-14554
Email:	ger...@ru...
Web:	http://www.medizinisches-proteom-center.de

Re: [Psidev-ms-dev] [Psidev-ms-vocab] Release candidate 3.64.0_rc4 of psi-ms.obo

[Eric D. <ede...@sy...>]

Hi Pierre-Alain, I don’t think I fully understand what you’re saying, but
it seems clear that you’re not in favor of what I’m proposing.



So just to recap, the “plan A” proposal for mapping a few specific
instruments to dissociation terms is this:



LTQ                        MS:1002472        name: trap-type
collision-induced dissociation

HCD Orbitrap     MS:1000422        name: beam-type collision-induced
dissociation

QTOF                     MS:1000422        name: beam-type
collision-induced dissociation

4800 TOF/TOF    MS:1002481        name: higher energy beam-type
collision-induced dissociation

My “alternate B” proposal was:



LTQ                        MS:1002472        name: trap-type
collision-induced dissociation

QTOF                     MS:1000422        name: beam-type
collision-induced dissociation

HCD Orbitrap     MS:100????        name: higher energy beam-type
collision-induced dissociation

4800 TOF/TOF    MS:1002481        name: keV energy beam-type
collision-induced dissociation



Although not completely clear, it seems that Pierre-Alain and Matt favor A.
And Eric and Wilfred favor B.



First, is this a correct assessment?



Second, would anyone else care to comment or show support for either A or B?



Thanks,

Eric







*From:* Binz Pierre-Alain [mailto:Pie...@ch...]
*Sent:* Tuesday, May 27, 2014 8:14 AM
*To:* Mass spectrometry standard development
*Subject:* Re: [Psidev-ms-dev] [Psidev-ms-vocab] Release candidate
3.64.0_rc4 of psi-ms.obo



Hi Eric,



What if SpectraST would look into the instrumentConfiguration element ? It
should be able to make the difference. This has the advantage that we do
not need to invent additional terms just to match with a specific software.
And what if Spectrast once can make the difference between ABSciex QTOF and
Waters G2 (also a QTOF), or between two CID conditions for one QTOF
instrument (you should maybe look at the activation element instead of
creating yet other terms for this ?

Otherwise I beleive that we would need to create a number of child terms to
there trap-type and beam-type CIDs, where the nomenclature and ontology
might potentially be a bit vague.

I understand that it does not simplify the parsing, but a) it simplifies
the CV, b) it potentially removes additional checks to validate (do one
need to check whether a activation/fragmentation term does correspond to
the instrument at all ?) and c) there is anyway a need for software such as
SpectraST to deal with ambiguity if the precise term does not exist



Cheers

Pierre-Alain









*De :* Eric Deutsch
[mailto:ede...@sy...<ede...@sy...>]

*Envoyé :* mardi 27 mai 2014 16:40
*À :* Mass spectrometry standard development
*Cc :* Eric Deutsch
*Objet :* Re: [Psidev-ms-dev] [Psidev-ms-vocab] Release candidate
3.64.0_rc4 of psi-ms.obo



Well, for example, the SpectraST software has different modes for HCD and
QTOF. If Orbi and QTOF data files are annotated the same way, then it will
be extremely difficult for SpectraST to know which mode to set. It would
have to resort to complex logic based on the instrument model. It seems to
me that if we make them two different terms, it would be trivial for other
software to treat them the same. However, if we make it one term, it will
be very burdensome for other software that wants to differentiate them to
treat them differently.



Regards,

Eric





*From:* Chambers, Matthew [mailto:mat...@gm...]
*Sent:* Friday, May 23, 2014 3:12 PM
*To:* psi...@li...
*Subject:* Re: [Psidev-ms-dev] [Psidev-ms-vocab] Release candidate
3.64.0_rc4 of psi-ms.obo



Why would that dismay you? AFAIK, QTOF and HCD fragmentation are
essentially the same. I think Gerhard's approach is more in line with IUPAC
and the only drawback is confusion between Thermo's proprietary name and
the IUPAC term with similar semantics.

-Matt

On 5/23/2014 11:37 AM, Eric Deutsch wrote:

Hi Gerhard, thank you for pushing this forward. You wrote:



trap-type high-energy collision-induced dissociation



Is that correct? OR should it just be:



trap-type collision-induced dissociation



?



I still a little confused what we will tag the various instruments with.
What will be the recommended for acquisition in these instrument modes?
This?



LTQ                        MS:1002472        name: trap-type
collision-induced dissociation

HCD Orbitrap     MS:1000422        name: beam-type collision-induced
dissociation

QTOF                     MS:1000422        name: beam-type
collision-induced dissociation

4800 TOF/TOF    MS:1002481        name: higher energy beam-type
collision-induced dissociation



As are some others, I'm a bit dismayed that Thermo HCD and QTOF are lumped
into one.



Can we just rename 2481 to higher energy beam-type collision-induced
dissociation

I feel the “er” will just serve to confuse with HCD more, and seems
unnecessary.



I didn’t follow all the discussion. Was my proposal for this:



LTQ                        MS:1002472        name: trap-type
collision-induced dissociation

HCD Orbitrap     MS:100????        name: higher energy beam-type
collision-induced dissociation

QTOF                     MS:1000422        name: beam-type
collision-induced dissociation

4800 TOF/TOF    MS:1002481        name: keV energy beam-type
collision-induced dissociation



voted down?



Thanks,

Eric







-----Original Message-----
From: Gerhard Mayer [mailto:may...@ru...]
Sent: Friday, May 23, 2014 1:46 AM
To: psi...@li...;
psi...@li...
Cc: psi...@li...
Subject: Re: [Psidev-ms-dev] [Psidev-ms-vocab] Release candidate 3.64.0_rc4
of psi-ms.obo



Dear proteomics community,



attached you find the release candidate 3.65.0_rc1 of the psi-ms.obo file.



It contains a new "statistical threshold" term as parent of the

different thresholding mechanisms.



According to the CID terms we now have the following hierarchy:

collision-induced association (synonyms: CID, CAD, collision –activated

association)

beam-type collision-induced dissociation (synonym: HCD)

higher-energy beam-type collision-induced dissociation

trap-type high-energy collision-induced dissociation



that would map to Matt's proposal and Wilfred's buckets as follows:



Am 23.05.2014 06:49, schrieb Wilfred Tang:

> I think the activation type should be described in broad buckets. I

> would guess (for example) that the various QTOF dissociations (ABSciex

> QTOF, Agilent QTOF, Waters QTOF, etc.) would be more similar to one

> another than ABSciex QTOF vs ABSciex TOF/TOF for example. For the sake

> of argument, I'll put down some broad buckets:

> - ion trap collisional dissociation

--> trap-type collision-induced dissociation (MS:1002472)

> - QTOF collisional dissociation

> - HCD collisional dissociation

--> beam-type collision-induced dissociation (MS:1000422)

> - TOF/TOF collisional dissociation

--> higher-energy beam-type collision-induced dissociation (MS:1002481)

> Maybe QTOF collisional dissociation and HCD collisional dissociation

> can be collapsed into one bucket. Does anyone know how similar their

> fragmentations are?

>

> I don't think one should need to read the instrument name to figure

> out the activation type. Every new instrument introduction would break

> things.

>

> Wilfred



Changed CV terms in version 3.65.0_rc1 of psi-ms.obo:

=====================================================

************ Changed synonym to "collisionally activated dissociation"

************ instead of "collision activated dissociation"

************ in order to match the IUPAC recommendations

[Term]

id: MS:1000133

name: collision-induced dissociation

def: "The dissociation of an ion after collisional excitation. The term

collisional-activated dissociation is not recommended." [PSI:MS]

synonym: "CID" EXACT []

synonym: "CAD" EXACT []

synonym: "collisionally activated dissociation" EXACT []

is_a: MS:1000044 ! dissociation method



************ Changed definition to

************ "... The term parent ion is deprecated."

************ in order to match the IUPAC recommendations

[Term]

id: MS:1000340

name: precursor ion

def: "An ion that reacts to form particular product ions. The reaction

can be unimolecular dissociation, ion/molecule reaction, isomerization,

or change in charge state. The term parent ion is not deprecated." [PSI:MS]

synonym: "parent ion" RELATED []

is_a: MS:1000506 ! ion role



************ Renamed to beam-type collision-induced dissociation

[Term]

id: MS:1000422

name: beam-type collision-induced dissociation

def: "A collision-induced dissociation process that occurs in a

beam-type collision cell." [PSI:MS]

synonym: "HCD" EXACT []

is_a: MS:1000133 ! collision-induced dissociation



************ The following two terms are flagged as "UNDER DISCUSSION"

[Term]

id: MS:1002439

name: final PSM list UNDER DISCUSSION

def: "A flag on a list of PSMs (SpectrumIdentificationList) to indicate

that this is the final set of identifications to be interpreted by

consuming software. Amongst the set of SpectrumIdentificationList(s)

that are flagged with the term, each spectrum must not be referenced

from more than one SpectrumIdentificationResult." [PSI:PI]

is_a: MS:1002438 ! spectrum identification list result details



[Term]

id: MS:1002440

name: intermediate PSM list UNDER DISCUSSION

def: "A flag on a list of PSMs (SpectrumIdentificationList) to indicate

that this is not the final set of identifications to be interpreted by

consuming software. This term should be used when results are provided

from multiple search engines for the results from each search engine

before they are combined to give consensus identifications. Amongst the

set of SpectrumIdentificationList(s) that are flagged with the term,

each spectrum may be referenced from more than one

SpectrumIdentificationResult." [PSI:PI]

is_a: MS:1002438 ! spectrum identification list result details







New CV terms in version 3.65.0_rc1 of psi-ms.obo:

=================================================

[Term]

id: MS:1002481

name: higher energy beam-type collision-induced dissociation

def: "A collision-induced dissociation process wherein the projectile

ion has the translational energy higher than approximately 1000 eV."

[PSI:MS]

is_a: MS:1000422 ! beam-type collision-induced dissociation



[Term]

id: MS:1002482

name: statistical threshold

def: "Estimated statistical threshold." [PSI:MS]

is_a: MS:1001060 ! quality estimation method details



[Term]

id: MS:1002483

name: PSM-level statistical threshold

def: "Estimated statistical threshold at PSM-level." [PSI:MS]

is_a: MS:1002482 ! statistical threshold



[Term]

id: MS:1002484

name: peptide-level statistical threshold

def: "Estimated statistical threshold at peptide-level." [PSI:MS]

is_a: MS:1002482 ! statistical threshold



[Term]

id: MS:1002485

name: protein or protein group-level statistical threshold

def: "Estimated statistical threshold at protein-level." [PSI:MS]

is_a: MS:1002482 ! statistical threshold



Best Regards,

Gerhard



-- 

---

Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer

Bioinformatics / Biostatistics

Medizinisches-Proteom-Center (MPC)

Ruhr-Universität Bochum

Zentrum für klinische Forschung I (ZKF I), E.049a

Universitätsstraße 150

D-44801 Bochum



Phone: +49(0)234/32-21006

Fax:        +49(0)234/32-14554

Email:    ger...@ru...

Web:     http://www.medizinisches-proteom-center.de





------------------------------------------------------------------------------

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Instantly run your Selenium tests across 300+ browser/OS combos.

Get unparalleled scalability from the best Selenium testing platform available

Simple to use. Nothing to install. Get started now for free."

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_______________________________________________

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Re: [Psidev-ms-dev] [Psidev-ms-vocab] Release candidate 3.64.0_rc4 of psi-ms.obo

[Binz Pierre-A. <Pie...@ch...>]

Hi Eric,

What if SpectraST would look into the instrumentConfiguration element ? It should be able to make the difference. This has the advantage that we do not need to invent additional terms just to match with a specific software. And what if Spectrast once can make the difference between ABSciex QTOF and Waters G2 (also a QTOF), or between two CID conditions for one QTOF instrument (you should maybe look at the activation element instead of creating yet other terms for this ?
Otherwise I beleive that we would need to create a number of child terms to there trap-type and beam-type CIDs, where the nomenclature and ontology might potentially be a bit vague.
I understand that it does not simplify the parsing, but a) it simplifies the CV, b) it potentially removes additional checks to validate (do one need to check whether a activation/fragmentation term does correspond to the instrument at all ?) and c) there is anyway a need for software such as SpectraST to deal with ambiguity if the precise term does not exist

Cheers
Pierre-Alain




De : Eric Deutsch [mailto:ede...@sy...]
Envoyé : mardi 27 mai 2014 16:40
À : Mass spectrometry standard development
Cc : Eric Deutsch
Objet : Re: [Psidev-ms-dev] [Psidev-ms-vocab] Release candidate 3.64.0_rc4 of psi-ms.obo

Well, for example, the SpectraST software has different modes for HCD and QTOF. If Orbi and QTOF data files are annotated the same way, then it will be extremely difficult for SpectraST to know which mode to set. It would have to resort to complex logic based on the instrument model. It seems to me that if we make them two different terms, it would be trivial for other software to treat them the same. However, if we make it one term, it will be very burdensome for other software that wants to differentiate them to treat them differently.

Regards,
Eric


From: Chambers, Matthew [mailto:mat...@gm...<mailto:mat...@gm...>]
Sent: Friday, May 23, 2014 3:12 PM
To: psi...@li...<mailto:psi...@li...>
Subject: Re: [Psidev-ms-dev] [Psidev-ms-vocab] Release candidate 3.64.0_rc4 of psi-ms.obo

Why would that dismay you? AFAIK, QTOF and HCD fragmentation are essentially the same. I think Gerhard's approach is more in line with IUPAC and the only drawback is confusion between Thermo's proprietary name and the IUPAC term with similar semantics.

-Matt
On 5/23/2014 11:37 AM, Eric Deutsch wrote:

Hi Gerhard, thank you for pushing this forward. You wrote:



trap-type high-energy collision-induced dissociation



Is that correct? OR should it just be:



trap-type collision-induced dissociation



?



I still a little confused what we will tag the various instruments with. What will be the recommended for acquisition in these instrument modes? This?



LTQ                        MS:1002472        name: trap-type collision-induced dissociation

HCD Orbitrap     MS:1000422        name: beam-type collision-induced dissociation

QTOF                     MS:1000422        name: beam-type collision-induced dissociation

4800 TOF/TOF    MS:1002481        name: higher energy beam-type collision-induced dissociation



As are some others, I'm a bit dismayed that Thermo HCD and QTOF are lumped into one.



Can we just rename 2481 to higher energy beam-type collision-induced dissociation

I feel the “er” will just serve to confuse with HCD more, and seems unnecessary.



I didn’t follow all the discussion. Was my proposal for this:



LTQ                        MS:1002472        name: trap-type collision-induced dissociation

HCD Orbitrap     MS:100????        name: higher energy beam-type collision-induced dissociation

QTOF                     MS:1000422        name: beam-type collision-induced dissociation

4800 TOF/TOF    MS:1002481        name: keV energy beam-type collision-induced dissociation



voted down?



Thanks,

Eric







-----Original Message-----
From: Gerhard Mayer [mailto:may...@ru...<mailto:may...@ru...>]
Sent: Friday, May 23, 2014 1:46 AM
To: psi...@li...<mailto:psi...@li...>; psi...@li...<mailto:psi...@li...>
Cc: psi...@li...<mailto:psi...@li...>
Subject: Re: [Psidev-ms-dev] [Psidev-ms-vocab] Release candidate 3.64.0_rc4 of psi-ms.obo



Dear proteomics community,



attached you find the release candidate 3.65.0_rc1 of the psi-ms.obo file.



It contains a new "statistical threshold" term as parent of the

different thresholding mechanisms.



According to the CID terms we now have the following hierarchy:

collision-induced association (synonyms: CID, CAD, collision –activated

association)

beam-type collision-induced dissociation (synonym: HCD)

higher-energy beam-type collision-induced dissociation

trap-type high-energy collision-induced dissociation



that would map to Matt's proposal and Wilfred's buckets as follows:



Am 23.05.2014 06:49, schrieb Wilfred Tang:

> I think the activation type should be described in broad buckets. I

> would guess (for example) that the various QTOF dissociations (ABSciex

> QTOF, Agilent QTOF, Waters QTOF, etc.) would be more similar to one

> another than ABSciex QTOF vs ABSciex TOF/TOF for example. For the sake

> of argument, I'll put down some broad buckets:

> - ion trap collisional dissociation

--> trap-type collision-induced dissociation (MS:1002472)

> - QTOF collisional dissociation

> - HCD collisional dissociation

--> beam-type collision-induced dissociation (MS:1000422)

> - TOF/TOF collisional dissociation

--> higher-energy beam-type collision-induced dissociation (MS:1002481)

> Maybe QTOF collisional dissociation and HCD collisional dissociation

> can be collapsed into one bucket. Does anyone know how similar their

> fragmentations are?

>

> I don't think one should need to read the instrument name to figure

> out the activation type. Every new instrument introduction would break

> things.

>

> Wilfred



Changed CV terms in version 3.65.0_rc1 of psi-ms.obo:

=====================================================

************ Changed synonym to "collisionally activated dissociation"

************ instead of "collision activated dissociation"

************ in order to match the IUPAC recommendations

[Term]

id: MS:1000133

name: collision-induced dissociation

def: "The dissociation of an ion after collisional excitation. The term

collisional-activated dissociation is not recommended." [PSI:MS]

synonym: "CID" EXACT []

synonym: "CAD" EXACT []

synonym: "collisionally activated dissociation" EXACT []

is_a: MS:1000044 ! dissociation method



************ Changed definition to

************ "... The term parent ion is deprecated."

************ in order to match the IUPAC recommendations

[Term]

id: MS:1000340

name: precursor ion

def: "An ion that reacts to form particular product ions. The reaction

can be unimolecular dissociation, ion/molecule reaction, isomerization,

or change in charge state. The term parent ion is not deprecated." [PSI:MS]

synonym: "parent ion" RELATED []

is_a: MS:1000506 ! ion role



************ Renamed to beam-type collision-induced dissociation

[Term]

id: MS:1000422

name: beam-type collision-induced dissociation

def: "A collision-induced dissociation process that occurs in a

beam-type collision cell." [PSI:MS]

synonym: "HCD" EXACT []

is_a: MS:1000133 ! collision-induced dissociation



************ The following two terms are flagged as "UNDER DISCUSSION"

[Term]

id: MS:1002439

name: final PSM list UNDER DISCUSSION

def: "A flag on a list of PSMs (SpectrumIdentificationList) to indicate

that this is the final set of identifications to be interpreted by

consuming software. Amongst the set of SpectrumIdentificationList(s)

that are flagged with the term, each spectrum must not be referenced

from more than one SpectrumIdentificationResult." [PSI:PI]

is_a: MS:1002438 ! spectrum identification list result details



[Term]

id: MS:1002440

name: intermediate PSM list UNDER DISCUSSION

def: "A flag on a list of PSMs (SpectrumIdentificationList) to indicate

that this is not the final set of identifications to be interpreted by

consuming software. This term should be used when results are provided

from multiple search engines for the results from each search engine

before they are combined to give consensus identifications. Amongst the

set of SpectrumIdentificationList(s) that are flagged with the term,

each spectrum may be referenced from more than one

SpectrumIdentificationResult." [PSI:PI]

is_a: MS:1002438 ! spectrum identification list result details







New CV terms in version 3.65.0_rc1 of psi-ms.obo:

=================================================

[Term]

id: MS:1002481

name: higher energy beam-type collision-induced dissociation

def: "A collision-induced dissociation process wherein the projectile

ion has the translational energy higher than approximately 1000 eV."

[PSI:MS]

is_a: MS:1000422 ! beam-type collision-induced dissociation



[Term]

id: MS:1002482

name: statistical threshold

def: "Estimated statistical threshold." [PSI:MS]

is_a: MS:1001060 ! quality estimation method details



[Term]

id: MS:1002483

name: PSM-level statistical threshold

def: "Estimated statistical threshold at PSM-level." [PSI:MS]

is_a: MS:1002482 ! statistical threshold



[Term]

id: MS:1002484

name: peptide-level statistical threshold

def: "Estimated statistical threshold at peptide-level." [PSI:MS]

is_a: MS:1002482 ! statistical threshold



[Term]

id: MS:1002485

name: protein or protein group-level statistical threshold

def: "Estimated statistical threshold at protein-level." [PSI:MS]

is_a: MS:1002482 ! statistical threshold



Best Regards,

Gerhard



--

---

Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer

Bioinformatics / Biostatistics

Medizinisches-Proteom-Center (MPC)

Ruhr-Universität Bochum

Zentrum für klinische Forschung I (ZKF I), E.049a

Universitätsstraße 150

D-44801 Bochum



Phone: +49(0)234/32-21006

Fax:        +49(0)234/32-14554

Email:    ger...@ru...<mailto:ger...@ru...>

Web:     http://www.medizinisches-proteom-center.de





------------------------------------------------------------------------------

"Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE

Instantly run your Selenium tests across 300+ browser/OS combos.

Get unparalleled scalability from the best Selenium testing platform available

Simple to use. Nothing to install. Get started now for free."

http://p.sf.net/sfu/SauceLabs



_______________________________________________

Psidev-ms-dev mailing list

Psi...@li...<mailto:Psi...@li...>



https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev

Re: [Psidev-ms-dev] [Psidev-ms-vocab] Release candidate 3.64.0_rc4 of psi-ms.obo

[Eric D. <ede...@sy...>]

Well, for example, the SpectraST software has different modes for HCD and
QTOF. If Orbi and QTOF data files are annotated the same way, then it will
be extremely difficult for SpectraST to know which mode to set. It would
have to resort to complex logic based on the instrument model. It seems to
me that if we make them two different terms, it would be trivial for other
software to treat them the same. However, if we make it one term, it will
be very burdensome for other software that wants to differentiate them to
treat them differently.



Regards,

Eric





*From:* Chambers, Matthew [mailto:mat...@gm...]
*Sent:* Friday, May 23, 2014 3:12 PM
*To:* psi...@li...
*Subject:* Re: [Psidev-ms-dev] [Psidev-ms-vocab] Release candidate
3.64.0_rc4 of psi-ms.obo



Why would that dismay you? AFAIK, QTOF and HCD fragmentation are
essentially the same. I think Gerhard's approach is more in line with IUPAC
and the only drawback is confusion between Thermo's proprietary name and
the IUPAC term with similar semantics.

-Matt

On 5/23/2014 11:37 AM, Eric Deutsch wrote:

Hi Gerhard, thank you for pushing this forward. You wrote:



trap-type high-energy collision-induced dissociation



Is that correct? OR should it just be:



trap-type collision-induced dissociation



?



I still a little confused what we will tag the various instruments with.
What will be the recommended for acquisition in these instrument modes?
This?



LTQ                        MS:1002472        name: trap-type
collision-induced dissociation

HCD Orbitrap     MS:1000422        name: beam-type collision-induced
dissociation

QTOF                     MS:1000422        name: beam-type
collision-induced dissociation

4800 TOF/TOF    MS:1002481        name: higher energy beam-type
collision-induced dissociation



As are some others, I'm a bit dismayed that Thermo HCD and QTOF are lumped
into one.



Can we just rename 2481 to higher energy beam-type collision-induced
dissociation

I feel the “er” will just serve to confuse with HCD more, and seems
unnecessary.



I didn’t follow all the discussion. Was my proposal for this:



LTQ                        MS:1002472        name: trap-type
collision-induced dissociation

HCD Orbitrap     MS:100????        name: higher energy beam-type
collision-induced dissociation

QTOF                     MS:1000422        name: beam-type
collision-induced dissociation

4800 TOF/TOF    MS:1002481        name: keV energy beam-type
collision-induced dissociation



voted down?



Thanks,

Eric







-----Original Message-----
From: Gerhard Mayer [mailto:may...@ru...]
Sent: Friday, May 23, 2014 1:46 AM
To: psi...@li...;
psi...@li...
Cc: psi...@li...
Subject: Re: [Psidev-ms-dev] [Psidev-ms-vocab] Release candidate 3.64.0_rc4
of psi-ms.obo



Dear proteomics community,



attached you find the release candidate 3.65.0_rc1 of the psi-ms.obo file.



It contains a new "statistical threshold" term as parent of the

different thresholding mechanisms.



According to the CID terms we now have the following hierarchy:

collision-induced association (synonyms: CID, CAD, collision –activated

association)

beam-type collision-induced dissociation (synonym: HCD)

higher-energy beam-type collision-induced dissociation

trap-type high-energy collision-induced dissociation



that would map to Matt's proposal and Wilfred's buckets as follows:



Am 23.05.2014 06:49, schrieb Wilfred Tang:

> I think the activation type should be described in broad buckets. I

> would guess (for example) that the various QTOF dissociations (ABSciex

> QTOF, Agilent QTOF, Waters QTOF, etc.) would be more similar to one

> another than ABSciex QTOF vs ABSciex TOF/TOF for example. For the sake

> of argument, I'll put down some broad buckets:

> - ion trap collisional dissociation

--> trap-type collision-induced dissociation (MS:1002472)

> - QTOF collisional dissociation

> - HCD collisional dissociation

--> beam-type collision-induced dissociation (MS:1000422)

> - TOF/TOF collisional dissociation

--> higher-energy beam-type collision-induced dissociation (MS:1002481)

> Maybe QTOF collisional dissociation and HCD collisional dissociation

> can be collapsed into one bucket. Does anyone know how similar their

> fragmentations are?

>

> I don't think one should need to read the instrument name to figure

> out the activation type. Every new instrument introduction would break

> things.

>

> Wilfred



Changed CV terms in version 3.65.0_rc1 of psi-ms.obo:

=====================================================

************ Changed synonym to "collisionally activated dissociation"

************ instead of "collision activated dissociation"

************ in order to match the IUPAC recommendations

[Term]

id: MS:1000133

name: collision-induced dissociation

def: "The dissociation of an ion after collisional excitation. The term

collisional-activated dissociation is not recommended." [PSI:MS]

synonym: "CID" EXACT []

synonym: "CAD" EXACT []

synonym: "collisionally activated dissociation" EXACT []

is_a: MS:1000044 ! dissociation method



************ Changed definition to

************ "... The term parent ion is deprecated."

************ in order to match the IUPAC recommendations

[Term]

id: MS:1000340

name: precursor ion

def: "An ion that reacts to form particular product ions. The reaction

can be unimolecular dissociation, ion/molecule reaction, isomerization,

or change in charge state. The term parent ion is not deprecated." [PSI:MS]

synonym: "parent ion" RELATED []

is_a: MS:1000506 ! ion role



************ Renamed to beam-type collision-induced dissociation

[Term]

id: MS:1000422

name: beam-type collision-induced dissociation

def: "A collision-induced dissociation process that occurs in a

beam-type collision cell." [PSI:MS]

synonym: "HCD" EXACT []

is_a: MS:1000133 ! collision-induced dissociation



************ The following two terms are flagged as "UNDER DISCUSSION"

[Term]

id: MS:1002439

name: final PSM list UNDER DISCUSSION

def: "A flag on a list of PSMs (SpectrumIdentificationList) to indicate

that this is the final set of identifications to be interpreted by

consuming software. Amongst the set of SpectrumIdentificationList(s)

that are flagged with the term, each spectrum must not be referenced

from more than one SpectrumIdentificationResult." [PSI:PI]

is_a: MS:1002438 ! spectrum identification list result details



[Term]

id: MS:1002440

name: intermediate PSM list UNDER DISCUSSION

def: "A flag on a list of PSMs (SpectrumIdentificationList) to indicate

that this is not the final set of identifications to be interpreted by

consuming software. This term should be used when results are provided

from multiple search engines for the results from each search engine

before they are combined to give consensus identifications. Amongst the

set of SpectrumIdentificationList(s) that are flagged with the term,

each spectrum may be referenced from more than one

SpectrumIdentificationResult." [PSI:PI]

is_a: MS:1002438 ! spectrum identification list result details







New CV terms in version 3.65.0_rc1 of psi-ms.obo:

=================================================

[Term]

id: MS:1002481

name: higher energy beam-type collision-induced dissociation

def: "A collision-induced dissociation process wherein the projectile

ion has the translational energy higher than approximately 1000 eV."

[PSI:MS]

is_a: MS:1000422 ! beam-type collision-induced dissociation



[Term]

id: MS:1002482

name: statistical threshold

def: "Estimated statistical threshold." [PSI:MS]

is_a: MS:1001060 ! quality estimation method details



[Term]

id: MS:1002483

name: PSM-level statistical threshold

def: "Estimated statistical threshold at PSM-level." [PSI:MS]

is_a: MS:1002482 ! statistical threshold



[Term]

id: MS:1002484

name: peptide-level statistical threshold

def: "Estimated statistical threshold at peptide-level." [PSI:MS]

is_a: MS:1002482 ! statistical threshold



[Term]

id: MS:1002485

name: protein or protein group-level statistical threshold

def: "Estimated statistical threshold at protein-level." [PSI:MS]

is_a: MS:1002482 ! statistical threshold



Best Regards,

Gerhard



-- 

---

Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer

Bioinformatics / Biostatistics

Medizinisches-Proteom-Center (MPC)

Ruhr-Universität Bochum

Zentrum für klinische Forschung I (ZKF I), E.049a

Universitätsstraße 150

D-44801 Bochum



Phone: +49(0)234/32-21006

Fax:        +49(0)234/32-14554

Email:    ger...@ru...

Web:     http://www.medizinisches-proteom-center.de






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Re: [Psidev-ms-dev] [Psidev-ms-vocab] Release candidate 3.64.0_rc4 of psi-ms.obo

[Chambers, M. <mat...@gm...>]

Why would that dismay you? AFAIK, QTOF and HCD fragmentation are 
essentially the same. I think Gerhard's approach is more in line with 
IUPAC and the only drawback is confusion between Thermo's proprietary 
name and the IUPAC term with similar semantics.

-Matt


On 5/23/2014 11:37 AM, Eric Deutsch wrote:
>
> Hi Gerhard, thank you for pushing this forward. You wrote:
>
> trap-type high-energy collision-induced dissociation
>
> Is that correct? OR should it just be:
>
> trap-type collision-induced dissociation
>
> ?
>
> I still a little confused what we will tag the various instruments 
> with. What will be the recommended for acquisition in these instrument 
> modes? This?
>
> LTQ MS:1002472        name: trap-type collision-induced dissociation
>
> HCD Orbitrap     MS:1000422        name: beam-type collision-induced 
> dissociation
>
> QTOF MS:1000422        name: beam-type collision-induced dissociation
>
> 4800 TOF/TOF    MS:1002481        name: higher energy beam-type 
> collision-induced dissociation
>
> As are some others, I'm a bit dismayed that Thermo HCD and QTOF are 
> lumped into one.
>
> Can we just rename 2481 to higher energy beam-type collision-induced 
> dissociation
>
> I feel the "er" will just serve to confuse with HCD more, and seems 
> unnecessary.
>
> I didn't follow all the discussion. Was my proposal for this:
>
> LTQ MS:1002472        name: trap-type collision-induced dissociation
>
> HCD Orbitrap     MS:100????        name: higher energy beam-type 
> collision-induced dissociation
>
> QTOF MS:1000422        name: beam-type collision-induced dissociation
>
> 4800 TOF/TOF    MS:1002481        name: keV energy beam-type 
> collision-induced dissociation
>
> voted down?
>
> Thanks,
>
> Eric
>
> -----Original Message-----
> From: Gerhard Mayer [mailto:may...@ru... <mailto:may...@ru...>]
> Sent: Friday, May 23, 2014 1:46 AM
> To: psi...@li... 
> <mailto:psi...@li...>; 
> psi...@li... 
> <mailto:psi...@li...>
> Cc: psi...@li... 
> <mailto:psi...@li...>
> Subject: Re: [Psidev-ms-dev] [Psidev-ms-vocab] Release candidate 
> 3.64.0_rc4 of psi-ms.obo
>
> Dear proteomics community,
>
> attached you find the release candidate 3.65.0_rc1 of the psi-ms.obo file.
>
> It contains a new "statistical threshold" term as parent of the
>
> different thresholding mechanisms.
>
> According to the CID terms we now have the following hierarchy:
>
> collision-induced association (synonyms: CID, CAD, collision --activated
>
> association)
>
> beam-type collision-induced dissociation (synonym: HCD)
>
> higher-energy beam-type collision-induced dissociation
>
> trap-type high-energy collision-induced dissociation
>
> that would map to Matt's proposal and Wilfred's buckets as follows:
>
> Am 23.05.2014 06:49, schrieb Wilfred Tang:
>
> > I think the activation type should be described in broad buckets. I
>
> > would guess (for example) that the various QTOF dissociations (ABSciex
>
> > QTOF, Agilent QTOF, Waters QTOF, etc.) would be more similar to one
>
> > another than ABSciex QTOF vs ABSciex TOF/TOF for example. For the sake
>
> > of argument, I'll put down some broad buckets:
>
> > - ion trap collisional dissociation
>
> --> trap-type collision-induced dissociation (MS:1002472)
>
> > - QTOF collisional dissociation
>
> > - HCD collisional dissociation
>
> --> beam-type collision-induced dissociation (MS:1000422)
>
> > - TOF/TOF collisional dissociation
>
> --> higher-energy beam-type collision-induced dissociation (MS:1002481)
>
> > Maybe QTOF collisional dissociation and HCD collisional dissociation
>
> > can be collapsed into one bucket. Does anyone know how similar their
>
> > fragmentations are?
>
> >
>
> > I don't think one should need to read the instrument name to figure
>
> > out the activation type. Every new instrument introduction would break
>
> > things.
>
> >
>
> > Wilfred
>
> Changed CV terms in version 3.65.0_rc1 of psi-ms.obo:
>
> =====================================================
>
> ************ Changed synonym to "collisionally activated dissociation"
>
> ************ instead of "collision activated dissociation"
>
> ************ in order to match the IUPAC recommendations
>
> [Term]
>
> id: MS:1000133
>
> name: collision-induced dissociation
>
> def: "The dissociation of an ion after collisional excitation. The term
>
> collisional-activated dissociation is not recommended." [PSI:MS]
>
> synonym: "CID" EXACT []
>
> synonym: "CAD" EXACT []
>
> synonym: "collisionally activated dissociation" EXACT []
>
> is_a: MS:1000044 ! dissociation method
>
> ************ Changed definition to
>
> ************ "... The term parent ion is deprecated."
>
> ************ in order to match the IUPAC recommendations
>
> [Term]
>
> id: MS:1000340
>
> name: precursor ion
>
> def: "An ion that reacts to form particular product ions. The reaction
>
> can be unimolecular dissociation, ion/molecule reaction, isomerization,
>
> or change in charge state. The term parent ion is not deprecated." 
> [PSI:MS]
>
> synonym: "parent ion" RELATED []
>
> is_a: MS:1000506 ! ion role
>
> ************ Renamed to beam-type collision-induced dissociation
>
> [Term]
>
> id: MS:1000422
>
> name: beam-type collision-induced dissociation
>
> def: "A collision-induced dissociation process that occurs in a
>
> beam-type collision cell." [PSI:MS]
>
> synonym: "HCD" EXACT []
>
> is_a: MS:1000133 ! collision-induced dissociation
>
> ************ The following two terms are flagged as "UNDER DISCUSSION"
>
> [Term]
>
> id: MS:1002439
>
> name: final PSM list UNDER DISCUSSION
>
> def: "A flag on a list of PSMs (SpectrumIdentificationList) to indicate
>
> that this is the final set of identifications to be interpreted by
>
> consuming software. Amongst the set of SpectrumIdentificationList(s)
>
> that are flagged with the term, each spectrum must not be referenced
>
> from more than one SpectrumIdentificationResult." [PSI:PI]
>
> is_a: MS:1002438 ! spectrum identification list result details
>
> [Term]
>
> id: MS:1002440
>
> name: intermediate PSM list UNDER DISCUSSION
>
> def: "A flag on a list of PSMs (SpectrumIdentificationList) to indicate
>
> that this is not the final set of identifications to be interpreted by
>
> consuming software. This term should be used when results are provided
>
> from multiple search engines for the results from each search engine
>
> before they are combined to give consensus identifications. Amongst the
>
> set of SpectrumIdentificationList(s) that are flagged with the term,
>
> each spectrum may be referenced from more than one
>
> SpectrumIdentificationResult." [PSI:PI]
>
> is_a: MS:1002438 ! spectrum identification list result details
>
> New CV terms in version 3.65.0_rc1 of psi-ms.obo:
>
> =================================================
>
> [Term]
>
> id: MS:1002481
>
> name: higher energy beam-type collision-induced dissociation
>
> def: "A collision-induced dissociation process wherein the projectile
>
> ion has the translational energy higher than approximately 1000 eV."
>
> [PSI:MS]
>
> is_a: MS:1000422 ! beam-type collision-induced dissociation
>
> [Term]
>
> id: MS:1002482
>
> name: statistical threshold
>
> def: "Estimated statistical threshold." [PSI:MS]
>
> is_a: MS:1001060 ! quality estimation method details
>
> [Term]
>
> id: MS:1002483
>
> name: PSM-level statistical threshold
>
> def: "Estimated statistical threshold at PSM-level." [PSI:MS]
>
> is_a: MS:1002482 ! statistical threshold
>
> [Term]
>
> id: MS:1002484
>
> name: peptide-level statistical threshold
>
> def: "Estimated statistical threshold at peptide-level." [PSI:MS]
>
> is_a: MS:1002482 ! statistical threshold
>
> [Term]
>
> id: MS:1002485
>
> name: protein or protein group-level statistical threshold
>
> def: "Estimated statistical threshold at protein-level." [PSI:MS]
>
> is_a: MS:1002482 ! statistical threshold
>
> Best Regards,
>
> Gerhard
>
> -- 
>
> ---
>
> Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
>
> Bioinformatics / Biostatistics
>
> Medizinisches-Proteom-Center (MPC)
>
> Ruhr-Universität Bochum
>
> Zentrum für klinische Forschung I (ZKF I), E.049a
>
> Universitätsstraße 150
>
> D-44801 Bochum
>
> Phone: +49(0)234/32-21006
>
> Fax:        +49(0)234/32-14554
>
> Email: ger...@ru... <mailto:ger...@ru...>
>
> Web: http://www.medizinisches-proteom-center.de
>
>
>
> ------------------------------------------------------------------------------
> "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
> Instantly run your Selenium tests across 300+ browser/OS combos.
> Get unparalleled scalability from the best Selenium testing platform available
> Simple to use. Nothing to install. Get started now for free."
> http://p.sf.net/sfu/SauceLabs
>
>
> _______________________________________________
> Psidev-ms-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev

Re: [Psidev-ms-dev] [Psidev-ms-vocab] Release candidate 3.64.0_rc4 of psi-ms.obo

[Eric D. <ede...@sy...>]

Hi Gerhard, thank you for pushing this forward. You wrote:



trap-type high-energy collision-induced dissociation



Is that correct? OR should it just be:



trap-type collision-induced dissociation



?



I still a little confused what we will tag the various instruments with.
What will be the recommended for acquisition in these instrument modes?
This?



LTQ                        MS:1002472        name: trap-type
collision-induced dissociation

HCD Orbitrap     MS:1000422        name: beam-type collision-induced
dissociation

QTOF                     MS:1000422        name: beam-type
collision-induced dissociation

4800 TOF/TOF    MS:1002481        name: higher energy beam-type
collision-induced dissociation



As are some others, I'm a bit dismayed that Thermo HCD and QTOF are lumped
into one.



Can we just rename 2481 to higher energy beam-type collision-induced
dissociation

I feel the “er” will just serve to confuse with HCD more, and seems
unnecessary.



I didn’t follow all the discussion. Was my proposal for this:



LTQ                        MS:1002472        name: trap-type
collision-induced dissociation

HCD Orbitrap     MS:100????        name: higher energy beam-type
collision-induced dissociation

QTOF                     MS:1000422        name: beam-type
collision-induced dissociation

4800 TOF/TOF    MS:1002481        name: keV energy beam-type
collision-induced dissociation



voted down?



Thanks,

Eric







-----Original Message-----
From: Gerhard Mayer [mailto:may...@ru...]
Sent: Friday, May 23, 2014 1:46 AM
To: psi...@li...;
psi...@li...
Cc: psi...@li...
Subject: Re: [Psidev-ms-dev] [Psidev-ms-vocab] Release candidate 3.64.0_rc4
of psi-ms.obo



Dear proteomics community,



attached you find the release candidate 3.65.0_rc1 of the psi-ms.obo file.



It contains a new "statistical threshold" term as parent of the

different thresholding mechanisms.



According to the CID terms we now have the following hierarchy:

collision-induced association (synonyms: CID, CAD, collision –activated

association)

beam-type collision-induced dissociation (synonym: HCD)

higher-energy beam-type collision-induced dissociation

trap-type high-energy collision-induced dissociation



that would map to Matt's proposal and Wilfred's buckets as follows:



Am 23.05.2014 06:49, schrieb Wilfred Tang:

> I think the activation type should be described in broad buckets. I

> would guess (for example) that the various QTOF dissociations (ABSciex

> QTOF, Agilent QTOF, Waters QTOF, etc.) would be more similar to one

> another than ABSciex QTOF vs ABSciex TOF/TOF for example. For the sake

> of argument, I'll put down some broad buckets:

> - ion trap collisional dissociation

--> trap-type collision-induced dissociation (MS:1002472)

> - QTOF collisional dissociation

> - HCD collisional dissociation

--> beam-type collision-induced dissociation (MS:1000422)

> - TOF/TOF collisional dissociation

--> higher-energy beam-type collision-induced dissociation (MS:1002481)

> Maybe QTOF collisional dissociation and HCD collisional dissociation

> can be collapsed into one bucket. Does anyone know how similar their

> fragmentations are?

>

> I don't think one should need to read the instrument name to figure

> out the activation type. Every new instrument introduction would break

> things.

>

> Wilfred



Changed CV terms in version 3.65.0_rc1 of psi-ms.obo:

=====================================================

************ Changed synonym to "collisionally activated dissociation"

************ instead of "collision activated dissociation"

************ in order to match the IUPAC recommendations

[Term]

id: MS:1000133

name: collision-induced dissociation

def: "The dissociation of an ion after collisional excitation. The term

collisional-activated dissociation is not recommended." [PSI:MS]

synonym: "CID" EXACT []

synonym: "CAD" EXACT []

synonym: "collisionally activated dissociation" EXACT []

is_a: MS:1000044 ! dissociation method



************ Changed definition to

************ "... The term parent ion is deprecated."

************ in order to match the IUPAC recommendations

[Term]

id: MS:1000340

name: precursor ion

def: "An ion that reacts to form particular product ions. The reaction

can be unimolecular dissociation, ion/molecule reaction, isomerization,

or change in charge state. The term parent ion is not deprecated." [PSI:MS]

synonym: "parent ion" RELATED []

is_a: MS:1000506 ! ion role



************ Renamed to beam-type collision-induced dissociation

[Term]

id: MS:1000422

name: beam-type collision-induced dissociation

def: "A collision-induced dissociation process that occurs in a

beam-type collision cell." [PSI:MS]

synonym: "HCD" EXACT []

is_a: MS:1000133 ! collision-induced dissociation



************ The following two terms are flagged as "UNDER DISCUSSION"

[Term]

id: MS:1002439

name: final PSM list UNDER DISCUSSION

def: "A flag on a list of PSMs (SpectrumIdentificationList) to indicate

that this is the final set of identifications to be interpreted by

consuming software. Amongst the set of SpectrumIdentificationList(s)

that are flagged with the term, each spectrum must not be referenced

from more than one SpectrumIdentificationResult." [PSI:PI]

is_a: MS:1002438 ! spectrum identification list result details



[Term]

id: MS:1002440

name: intermediate PSM list UNDER DISCUSSION

def: "A flag on a list of PSMs (SpectrumIdentificationList) to indicate

that this is not the final set of identifications to be interpreted by

consuming software. This term should be used when results are provided

from multiple search engines for the results from each search engine

before they are combined to give consensus identifications. Amongst the

set of SpectrumIdentificationList(s) that are flagged with the term,

each spectrum may be referenced from more than one

SpectrumIdentificationResult." [PSI:PI]

is_a: MS:1002438 ! spectrum identification list result details







New CV terms in version 3.65.0_rc1 of psi-ms.obo:

=================================================

[Term]

id: MS:1002481

name: higher energy beam-type collision-induced dissociation

def: "A collision-induced dissociation process wherein the projectile

ion has the translational energy higher than approximately 1000 eV."

[PSI:MS]

is_a: MS:1000422 ! beam-type collision-induced dissociation



[Term]

id: MS:1002482

name: statistical threshold

def: "Estimated statistical threshold." [PSI:MS]

is_a: MS:1001060 ! quality estimation method details



[Term]

id: MS:1002483

name: PSM-level statistical threshold

def: "Estimated statistical threshold at PSM-level." [PSI:MS]

is_a: MS:1002482 ! statistical threshold



[Term]

id: MS:1002484

name: peptide-level statistical threshold

def: "Estimated statistical threshold at peptide-level." [PSI:MS]

is_a: MS:1002482 ! statistical threshold



[Term]

id: MS:1002485

name: protein or protein group-level statistical threshold

def: "Estimated statistical threshold at protein-level." [PSI:MS]

is_a: MS:1002482 ! statistical threshold



Best Regards,

Gerhard



-- 

---

Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer

Bioinformatics / Biostatistics

Medizinisches-Proteom-Center (MPC)

Ruhr-Universität Bochum

Zentrum für klinische Forschung I (ZKF I), E.049a

Universitätsstraße 150

D-44801 Bochum



Phone: +49(0)234/32-21006

Fax:        +49(0)234/32-14554

Email:    ger...@ru...

Web:     http://www.medizinisches-proteom-center.de

Re: [Psidev-ms-dev] [Psidev-ms-vocab] Release candidate 3.64.0_rc4 of psi-ms.obo

[Gerhard M. <may...@ru...>]

Dear proteomics community,

attached you find the release candidate 3.65.0_rc1 of the psi-ms.obo file.

It contains a new "statistical threshold" term as parent of the 
different thresholding mechanisms.

According to the CID terms we now have the following hierarchy:
collision-induced association (synonyms: CID, CAD, collision –activated 
association)
beam-type collision-induced dissociation (synonym: HCD)
higher-energy beam-type collision-induced dissociation
trap-type high-energy collision-induced dissociation

that would map to Matt's proposal and Wilfred's buckets as follows:

Am 23.05.2014 06:49, schrieb Wilfred Tang:
> I think the activation type should be described in broad buckets. I 
> would guess (for example) that the various QTOF dissociations (ABSciex 
> QTOF, Agilent QTOF, Waters QTOF, etc.) would be more similar to one 
> another than ABSciex QTOF vs ABSciex TOF/TOF for example. For the sake 
> of argument, I'll put down some broad buckets:
> - ion trap collisional dissociation
--> trap-type collision-induced dissociation (MS:1002472)
> - QTOF collisional dissociation
> - HCD collisional dissociation
--> beam-type collision-induced dissociation (MS:1000422)
> - TOF/TOF collisional dissociation
--> higher-energy beam-type collision-induced dissociation (MS:1002481)
> Maybe QTOF collisional dissociation and HCD collisional dissociation 
> can be collapsed into one bucket. Does anyone know how similar their 
> fragmentations are?
>
> I don't think one should need to read the instrument name to figure 
> out the activation type. Every new instrument introduction would break 
> things.
>
> Wilfred

Changed CV terms in version 3.65.0_rc1 of psi-ms.obo:
=====================================================
************ Changed synonym to "collisionally activated dissociation"
************ instead of "collision activated dissociation"
************ in order to match the IUPAC recommendations
[Term]
id: MS:1000133
name: collision-induced dissociation
def: "The dissociation of an ion after collisional excitation. The term 
collisional-activated dissociation is not recommended." [PSI:MS]
synonym: "CID" EXACT []
synonym: "CAD" EXACT []
synonym: "collisionally activated dissociation" EXACT []
is_a: MS:1000044 ! dissociation method

************ Changed definition to
************ "... The term parent ion is deprecated."
************ in order to match the IUPAC recommendations
[Term]
id: MS:1000340
name: precursor ion
def: "An ion that reacts to form particular product ions. The reaction 
can be unimolecular dissociation, ion/molecule reaction, isomerization, 
or change in charge state. The term parent ion is not deprecated." [PSI:MS]
synonym: "parent ion" RELATED []
is_a: MS:1000506 ! ion role

************ Renamed to beam-type collision-induced dissociation
[Term]
id: MS:1000422
name: beam-type collision-induced dissociation
def: "A collision-induced dissociation process that occurs in a 
beam-type collision cell." [PSI:MS]
synonym: "HCD" EXACT []
is_a: MS:1000133 ! collision-induced dissociation

************ The following two terms are flagged as "UNDER DISCUSSION"
[Term]
id: MS:1002439
name: final PSM list UNDER DISCUSSION
def: "A flag on a list of PSMs (SpectrumIdentificationList) to indicate 
that this is the final set of identifications to be interpreted by 
consuming software. Amongst the set of SpectrumIdentificationList(s) 
that are flagged with the term, each spectrum must not be referenced 
from more than one SpectrumIdentificationResult." [PSI:PI]
is_a: MS:1002438 ! spectrum identification list result details

[Term]
id: MS:1002440
name: intermediate PSM list UNDER DISCUSSION
def: "A flag on a list of PSMs (SpectrumIdentificationList) to indicate 
that this is not the final set of identifications to be interpreted by 
consuming software. This term should be used when results are provided 
from multiple search engines for the results from each search engine 
before they are combined to give consensus identifications. Amongst the 
set of SpectrumIdentificationList(s) that are flagged with the term, 
each spectrum may be referenced from more than one 
SpectrumIdentificationResult." [PSI:PI]
is_a: MS:1002438 ! spectrum identification list result details



New CV terms in version 3.65.0_rc1 of psi-ms.obo:
=================================================
[Term]
id: MS:1002481
name: higher energy beam-type collision-induced dissociation
def: "A collision-induced dissociation process wherein the projectile 
ion has the translational energy higher than approximately 1000 eV." 
[PSI:MS]
is_a: MS:1000422 ! beam-type collision-induced dissociation

[Term]
id: MS:1002482
name: statistical threshold
def: "Estimated statistical threshold." [PSI:MS]
is_a: MS:1001060 ! quality estimation method details

[Term]
id: MS:1002483
name: PSM-level statistical threshold
def: "Estimated statistical threshold at PSM-level." [PSI:MS]
is_a: MS:1002482 ! statistical threshold

[Term]
id: MS:1002484
name: peptide-level statistical threshold
def: "Estimated statistical threshold at peptide-level." [PSI:MS]
is_a: MS:1002482 ! statistical threshold

[Term]
id: MS:1002485
name: protein or protein group-level statistical threshold
def: "Estimated statistical threshold at protein-level." [PSI:MS]
is_a: MS:1002482 ! statistical threshold

Best Regards,
Gerhard

-- 
---
Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
Bioinformatics / Biostatistics
Medizinisches-Proteom-Center (MPC)
Ruhr-Universität Bochum
Zentrum für klinische Forschung I (ZKF I), E.049a
Universitätsstraße 150
D-44801 Bochum
  
Phone:	+49(0)234/32-21006
Fax:	+49(0)234/32-14554
Email:	ger...@ru...
Web:	http://www.medizinisches-proteom-center.de

Re: [Psidev-ms-dev] [Psidev-ms-vocab] New version 3.64.0 of psi-ms.obo

[Wilfred T. <wt...@pr...>]

I thought the idea was to have "beam-type CID" for HCD/QTOF/QQQ and a
separate "higher-energy beam-type CID" term which would cover TOF/TOF and
probably sector instruments too?

Wilfred

On Tue, May 20, 2014 at 11:39 PM, Gerhard Mayer <may...@ru...> wrote:

> Dear proteomics community,
>
> attached you find the new version 3.64.0 of the psi-ms.obo file.
>
> It contains new terms for mzTab, for specifying the neutral losses, for
> collision-induced dissociation, for ion mobility MS, for PeptideShaker
> and for ProteoAnnotator.
>
> The neutral losses are now defined as terms independently from the ions in
> order to decouple the two concepts ion and neutral loss from each other.
>
> The old neutral loss terms have now the suffix " DEPRECATED" in their name,
> but are not obsoleted.
> The new parent term "ion series considered in search" (MS:1002473) now
> contains all the ions and neutral loss terms.
>
> Furthermore some terms from the purgatory branch are now obsolete.
> In addition I corrected some spelling errors in definitions.
>
>
> Changed CV terms in version 3.64.0 of psi-ms.obo:
> =================================================
> ************ The following terms from the purgatory branch are now
> obsoleted:
> MS:1000329 linked scan
> MS:1000268 mass spectrometry
> MS:1000013 resolution type
> MS:1000020 scanning method
> MS:1000459 spectrum instrument description
>
> ************ The following neutral loss terms have now a suffix "
> DEPRECATED"
> ************ They are child of "ions series considered in search"
> (MS:1001066)
> MS:1001148 a ion-H2O DEPRECATED
> MS:1001146 a ion-NH3 DEPRECATED
> MS:1001150 b ion-H2O DEPRECATED
> MS:1002450 b ion-H3PO4 DEPRECATED
> MS:1001149 b ion-NH3 DEPRECATED
> MS:1001152 y ion-H2O DEPRECATED
> MS:1002451 y ion-H3PO4 DEPRECATED
> MS:1001151 y ion-NH3 DEPRECATED
>
> ************ Changed the definition to reflect that it's the branch
> ************ with the DEPRECATED terms
> [Term]
> id: MS:1001066
> name: ions series considered in search
> def: "The description of the DEPRECATED ion fragment series (including
> charges and neutral losses) that are considered by the search engine."
> [PSI:PI]
> is_a: MS:1001249 ! search input details
>
> ************ Renamed the following term from
> ************ "high-energy collision-induced dissociation" to
> ************ "higher-energy beam-type collision-induced dissociation"
> ************ and made it a child of collision-induced dissociation
> (MS:1000133)
> [Term]
> id: MS:1000422
> name: higher-energy beam-type collision-induced dissociation
> def: "A collision-induced dissociation process that occurs in a beam-type
> collision cell." [PSI:MS]
> synonym: "HCD" EXACT []
> is_a: MS:1000133 ! collision-induced dissociation
>
> ************ Obsoleted the term 'product ion drift time'
> [Term]
> id: MS:1001967
> name: product ion drift time
> def: "OBSOLETE The ion drift time of an MS2 product ion." [PSI:MS]
> xref: value-type:xsd\:float "The allowed value-type for this CV term."
> is_a: MS:1002222 ! SRM transition attribute
> relationship: has_units UO:0000028 ! millisecond
> comment: This term was made obsolete because it was replaced by ion
> mobility drift time (MS:1002476).
> is_obsolete: true
>
> ************ Added doi as synonym and corrected the regular expression for
> DOI
> [Term]
> id: MS:1001922
> name: Digital Object Identifier (DOI)
> def: "DOI unique identifier of a publication." [PSI:PI, http://dx.doi.org]
> synonym: "doi" EXACT []
> is_a: MS:1000878 ! external reference identifier
> relationship: has_regexp MS:1002480 ! (10[.][0-9]{4,}(?:[.][0-9]+)*/
> (?:(?!["&\'<>])\S)+)
>
> ************ Corrected the is_a relation for the following term
> [Term]
> id: MS:1002231
> name: ([A-Fa-f0-9]{8}-([A-Fa-f0-9]{4}-){3}[A-Fa-f0-9]{12})
> is_a: MS:1002480 ! regular expression
>
>
>
> New CV terms in version 3.64.0 of psi-ms.obo:
> =============================================
> [Term]
> id: MS:1002452
> name: Maui
> def: "The Maltcms Graphical User Interface." [PSI:PI,
> http://maltcms.sf.net]
> is_a: MS:1001456 ! analysis software
> is_a: MS:1001457 ! data processing software
>
> [Term]
> id: MS:1002453
> name: No fixed modifications searched
> def: "No fixed modifications are included as a parameter for the search,
> and therefore they are not reported." [PSI:PI]
> is_a: MS:1002094 ! common search engine input parameter
>
> [Term]
> id: MS:1002454
> name: No variable modifications searched
> def: "No variable modifications are included as a parameter for the
> search, and therefore they are not reported." [PSI:PI]
> is_a: MS:1002094 ! common search engine input parameter
>
> [Term]
> id: MS:1002455
> name: H2O neutral loss
> def: "Neutral loss of water." [PSI:PI]
> is_a: MS:1000336 ! neutral loss
>
> [Term]
> id: MS:1002456
> name: NH3 neutral loss
> def: "Neutral loss of ammonia." [PSI:PI]
> is_a: MS:1000336 ! neutral loss
>
> [Term]
> id: MS:1002457
> name: H3PO4 neutral loss
> def: "Neutral loss of phosphoric acid." [PSI:PI]
> is_a: MS:1000336 ! neutral loss
>
> [Term]
> id: MS:1002458
> name: PeptideShaker
> def: "PeptideShaker is a software for the interpretation of proteomics
> identification results." [PSI:PI, http://peptide-shaker.googlecode.com]
> is_a: MS:1001456 ! analysis software
>
> [Term]
> id: MS:1002459
> name: MS Amanda csv format
> def: "MS Amanda csv output format." [PSI:PI]
> is_a: MS:1001040 ! intermediate analysis format
>
> [Term]
> id: MS:1002460
> name: protein group-level global FNR
> def: "Estimation of the global false negative rate of protein groups."
> [PSI:PI]
> is_a: MS:1002346 ! protein group-level result details
> relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive
>
> [Term]
> id: MS:1002461
> name: protein group-level confidence
> def: "Estimation of the global confidence of protein groups." [PSI:PI]
> is_a: MS:1002346 ! protein group-level result details
>
> [Term]
> id: MS:1002462
> name: distinct peptide-level global FNR
> def: "Estimation of the global false negative rate for distinct peptides
> once redundant identifications of the same peptide have been removed (id
> est multiple PSMs have been collapsed to one entry)." [PSI:PI]
> is_a: MS:1001105 ! peptide result details
> relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive
>
> [Term]
> id: MS:1002463
> name: distinct peptide-level global confidence
> def: "Estimation of the global confidence for distinct peptides once
> redundant identifications of the same peptide have been removed (id est
> multiple PSMs have been collapsed to one entry)." [PSI:PI]
> is_a: MS:1001105 ! peptide result details
>
> [Term]
> id: MS:1002464
> name: PSM-level global FNR
> def: "Estimation of the global false negative rate of peptide spectrum
> matches." [PSI:PI]
> is_a: MS:1002345 ! PSM-level result details
> relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive
>
> [Term]
> id: MS:1002465
> name: PSM-level global confidence
> def: "Estimation of the global confidence of peptide spectrum matches."
> [PSI:PI]
> is_a: MS:1002345 ! PSM-level result details
>
> [Term]
> id: MS:1002466
> name: PeptideShaker PSM score
> def: "The probability based PeptideShaker PSM score." [PSI:PI]
> is_a: MS:1001153 ! search engine specific score
> is_a: MS:1001143 ! search engine specific score for PSMs
> relationship: has_order MS:1002108 ! higher score better
>
> [Term]
> id: MS:1002467
> name: PeptideShaker PSM confidence
> def: "The probability based PeptideShaker PSM confidence." [PSI:PI]
> is_a: MS:1001153 ! search engine specific score
> is_a: MS:1001143 ! search engine specific score for PSMs
> relationship: has_order MS:1002108 ! higher score better
>
> [Term]
> id: MS:1002468
> name: PeptideShaker peptide score
> def: "The probability based PeptideShaker peptide score." [PSI:PI]
> is_a: MS:1001153 ! search engine specific score
> relationship: has_order MS:1002108 ! higher score better
>
> [Term]
> id: MS:1002469
> name: PeptideShaker peptide confidence
> def: "The probability based PeptideShaker peptide confidence." [PSI:PI]
> is_a: MS:1001153 ! search engine specific score
> relationship: has_order MS:1002108 ! higher score better
>
> [Term]
> id: MS:1002470
> name: PeptideShaker protein group score
> def: "The probability based PeptideShaker protein group score." [PSI:PI]
> is_a: MS:1001153 ! search engine specific score
> relationship: has_order MS:1002108 ! higher score better
>
> [Term]
> id: MS:1002471
> name: PeptideShaker protein group confidence
> def: "The probability based PeptideShaker protein group confidence."
> [PSI:PI]
> is_a: MS:1001153 ! search engine specific score
> relationship: has_order MS:1002108 ! higher score better
>
> [Term]
> id: MS:1002472
> name: trap-type collision-induced dissociation
> def: "A collision-induced dissociation process that occurs in a trap-type
> collision cell." [PSI:PI]
> is_a: MS:1000133 ! collision-induced dissociation
>
> [Term]
> id: MS:1002473
> name: ion series considered in search
> def: "The description of the ion fragment series (including charges and
> neutral losses) that are considered by the search engine." [PSI:PI]
> is_a: MS:1001249 ! search input details
>
> [Term]
> id: MS:1002474
> name: ProteoAnnotator:non-canonical gene model score
> def: "The sum of peptide-level scores for peptides mapped only to
> non-canonical gene models within the group." [PSI:PI]
> xref: value-type:xsd\:double "The allowed value-type for this CV term."
> is_a: MS:1001147 ! protein ambiguity group result details
> relationship: has_order MS:1002108 ! higher score better
>
> [Term]
> id: MS:1002475
> name: ProteoAnnotator:count alternative peptides
> def: "The count of the number of peptide sequences mapped to non-canonical
> gene models only within the group." [PSI:PI]
> xref: value-type:xsd\:integer "The allowed value-type for this CV term."
> is_a: MS:1001147 ! protein ambiguity group result details
>
> [Term]
> id: MS:1002476
> name: ion mobility drift time
> def: "Drift time of an ion or spectrum of ions as measured in an ion
> mobility mass spectrometer. This time might refer to the central value of a
> bin into which all ions within a narrow range of drift time have been
> aggregated." [PSI:MS]
> xref: value-type:xsd\:float "The allowed value-type for this CV term."
> is_a: MS:1000455 ! ion selection attribute
> relationship: has_units UO:0000028 ! millisecond
>
> [Term]
> id: MS:1002477
> name: mean drift time array
> def: "Array of drift times, averaged from a matrix of binned m/z and drift
> time values, corresponding to spectrum of individual peaks encoded with an
> m/z array." [PSI:MS]
> xref: value-type:xsd\:float "The allowed value-type for this CV term."
> is_a: MS:1000513 ! binary data array
> relationship: has_units UO:0000028 ! millisecond
> relationship: has_units UO:0000010 ! second
>
> [Term]
> id: MS:1002478
> name: mean charge array
> def: "Array of mean charge values where the mean charge is calculated as a
> weighted mean of the charges of individual peaks that are aggregated into a
> processed spectrum." [PSI:MS]
> xref: binary-data-type:MS\:1000521 "32-bit float"
> is_a: MS:1000513 ! binary data array
>
> [Term]
> id: MS:1002479
> name: regular expression
> def: "Regular expression." [PSI:PI]
> relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass
> Spectrometry Vocabularies
>
> [Term]
> id: MS:1002480
> name: (10[.][0-9]{4,}(?:[.][0-9]+)*/(?:(?!["&\'<>])\S)+)
> def: "Regular expression for a digital object identifier (DOI)." [PSI:PI,
> http://dx.doi.org/]
> is_a: MS:1002479 ! regular expression
>
> Best Regards,
> Gerhard
>
> --
> ---
> Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
> Bioinformatics / Biostatistics
> Medizinisches-Proteom-Center (MPC)
> Ruhr-Universität Bochum
> Zentrum für klinische Forschung I (ZKF I), E.049a
> Universitätsstraße 150
> D-44801 Bochum
>  Phone: +49(0)234/32-21006
> Fax:    +49(0)234/32-14554
> Email:  ger...@ru...
> Web:    http://www.medizinisches-proteom-center.de
>
>
>
> ------------------------------------------------------------------------------
> "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
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> _______________________________________________
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> https://lists.sourceforge.net/lists/listinfo/psidev-ms-vocab
>
>

[Psidev-ms-dev] New version 3.64.0 of psi-ms.obo

[Gerhard M. <may...@ru...>]

Dear proteomics community,

attached you find the new version 3.64.0 of the psi-ms.obo file.

It contains new terms for mzTab, for specifying the neutral losses, for
collision-induced dissociation, for ion mobility MS, for PeptideShaker
and for ProteoAnnotator.

The neutral losses are now defined as terms independently from the ions in
order to decouple the two concepts ion and neutral loss from each other.

The old neutral loss terms have now the suffix " DEPRECATED" in their name,
but are not obsoleted.
The new parent term "ion series considered in search" (MS:1002473) now
contains all the ions and neutral loss terms.

Furthermore some terms from the purgatory branch are now obsolete.
In addition I corrected some spelling errors in definitions.


Changed CV terms in version 3.64.0 of psi-ms.obo:
=================================================
************ The following terms from the purgatory branch are now 
obsoleted:
MS:1000329 linked scan
MS:1000268 mass spectrometry
MS:1000013 resolution type
MS:1000020 scanning method
MS:1000459 spectrum instrument description

************ The following neutral loss terms have now a suffix " 
DEPRECATED"
************ They are child of "ions series considered in search" 
(MS:1001066)
MS:1001148 a ion-H2O DEPRECATED
MS:1001146 a ion-NH3 DEPRECATED
MS:1001150 b ion-H2O DEPRECATED
MS:1002450 b ion-H3PO4 DEPRECATED
MS:1001149 b ion-NH3 DEPRECATED
MS:1001152 y ion-H2O DEPRECATED
MS:1002451 y ion-H3PO4 DEPRECATED
MS:1001151 y ion-NH3 DEPRECATED

************ Changed the definition to reflect that it's the branch
************ with the DEPRECATED terms
[Term]
id: MS:1001066
name: ions series considered in search
def: "The description of the DEPRECATED ion fragment series (including 
charges and neutral losses) that are considered by the search engine." 
[PSI:PI]
is_a: MS:1001249 ! search input details

************ Renamed the following term from
************ "high-energy collision-induced dissociation" to
************ "higher-energy beam-type collision-induced dissociation"
************ and made it a child of collision-induced dissociation 
(MS:1000133)
[Term]
id: MS:1000422
name: higher-energy beam-type collision-induced dissociation
def: "A collision-induced dissociation process that occurs in a 
beam-type collision cell." [PSI:MS]
synonym: "HCD" EXACT []
is_a: MS:1000133 ! collision-induced dissociation

************ Obsoleted the term 'product ion drift time'
[Term]
id: MS:1001967
name: product ion drift time
def: "OBSOLETE The ion drift time of an MS2 product ion." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002222 ! SRM transition attribute
relationship: has_units UO:0000028 ! millisecond
comment: This term was made obsolete because it was replaced by ion 
mobility drift time (MS:1002476).
is_obsolete: true

************ Added doi as synonym and corrected the regular expression 
for DOI
[Term]
id: MS:1001922
name: Digital Object Identifier (DOI)
def: "DOI unique identifier of a publication." [PSI:PI, http://dx.doi.org]
synonym: "doi" EXACT []
is_a: MS:1000878 ! external reference identifier
relationship: has_regexp MS:1002480 ! 
(10[.][0-9]{4,}(?:[.][0-9]+)*/(?:(?!["&\'<>])\S)+)

************ Corrected the is_a relation for the following term
[Term]
id: MS:1002231
name: ([A-Fa-f0-9]{8}-([A-Fa-f0-9]{4}-){3}[A-Fa-f0-9]{12})
is_a: MS:1002480 ! regular expression



New CV terms in version 3.64.0 of psi-ms.obo:
=============================================
[Term]
id: MS:1002452
name: Maui
def: "The Maltcms Graphical User Interface." [PSI:PI, http://maltcms.sf.net]
is_a: MS:1001456 ! analysis software
is_a: MS:1001457 ! data processing software

[Term]
id: MS:1002453
name: No fixed modifications searched
def: "No fixed modifications are included as a parameter for the search, 
and therefore they are not reported." [PSI:PI]
is_a: MS:1002094 ! common search engine input parameter

[Term]
id: MS:1002454
name: No variable modifications searched
def: "No variable modifications are included as a parameter for the 
search, and therefore they are not reported." [PSI:PI]
is_a: MS:1002094 ! common search engine input parameter

[Term]
id: MS:1002455
name: H2O neutral loss
def: "Neutral loss of water." [PSI:PI]
is_a: MS:1000336 ! neutral loss

[Term]
id: MS:1002456
name: NH3 neutral loss
def: "Neutral loss of ammonia." [PSI:PI]
is_a: MS:1000336 ! neutral loss

[Term]
id: MS:1002457
name: H3PO4 neutral loss
def: "Neutral loss of phosphoric acid." [PSI:PI]
is_a: MS:1000336 ! neutral loss

[Term]
id: MS:1002458
name: PeptideShaker
def: "PeptideShaker is a software for the interpretation of proteomics 
identification results." [PSI:PI, http://peptide-shaker.googlecode.com]
is_a: MS:1001456 ! analysis software

[Term]
id: MS:1002459
name: MS Amanda csv format
def: "MS Amanda csv output format." [PSI:PI]
is_a: MS:1001040 ! intermediate analysis format

[Term]
id: MS:1002460
name: protein group-level global FNR
def: "Estimation of the global false negative rate of protein groups." 
[PSI:PI]
is_a: MS:1002346 ! protein group-level result details
relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive

[Term]
id: MS:1002461
name: protein group-level confidence
def: "Estimation of the global confidence of protein groups." [PSI:PI]
is_a: MS:1002346 ! protein group-level result details

[Term]
id: MS:1002462
name: distinct peptide-level global FNR
def: "Estimation of the global false negative rate for distinct peptides 
once redundant identifications of the same peptide have been removed (id 
est multiple PSMs have been collapsed to one entry)." [PSI:PI]
is_a: MS:1001105 ! peptide result details
relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive

[Term]
id: MS:1002463
name: distinct peptide-level global confidence
def: "Estimation of the global confidence for distinct peptides once 
redundant identifications of the same peptide have been removed (id est 
multiple PSMs have been collapsed to one entry)." [PSI:PI]
is_a: MS:1001105 ! peptide result details

[Term]
id: MS:1002464
name: PSM-level global FNR
def: "Estimation of the global false negative rate of peptide spectrum 
matches." [PSI:PI]
is_a: MS:1002345 ! PSM-level result details
relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive

[Term]
id: MS:1002465
name: PSM-level global confidence
def: "Estimation of the global confidence of peptide spectrum matches." 
[PSI:PI]
is_a: MS:1002345 ! PSM-level result details

[Term]
id: MS:1002466
name: PeptideShaker PSM score
def: "The probability based PeptideShaker PSM score." [PSI:PI]
is_a: MS:1001153 ! search engine specific score
is_a: MS:1001143 ! search engine specific score for PSMs
relationship: has_order MS:1002108 ! higher score better

[Term]
id: MS:1002467
name: PeptideShaker PSM confidence
def: "The probability based PeptideShaker PSM confidence." [PSI:PI]
is_a: MS:1001153 ! search engine specific score
is_a: MS:1001143 ! search engine specific score for PSMs
relationship: has_order MS:1002108 ! higher score better

[Term]
id: MS:1002468
name: PeptideShaker peptide score
def: "The probability based PeptideShaker peptide score." [PSI:PI]
is_a: MS:1001153 ! search engine specific score
relationship: has_order MS:1002108 ! higher score better

[Term]
id: MS:1002469
name: PeptideShaker peptide confidence
def: "The probability based PeptideShaker peptide confidence." [PSI:PI]
is_a: MS:1001153 ! search engine specific score
relationship: has_order MS:1002108 ! higher score better

[Term]
id: MS:1002470
name: PeptideShaker protein group score
def: "The probability based PeptideShaker protein group score." [PSI:PI]
is_a: MS:1001153 ! search engine specific score
relationship: has_order MS:1002108 ! higher score better

[Term]
id: MS:1002471
name: PeptideShaker protein group confidence
def: "The probability based PeptideShaker protein group confidence." 
[PSI:PI]
is_a: MS:1001153 ! search engine specific score
relationship: has_order MS:1002108 ! higher score better

[Term]
id: MS:1002472
name: trap-type collision-induced dissociation
def: "A collision-induced dissociation process that occurs in a 
trap-type collision cell." [PSI:PI]
is_a: MS:1000133 ! collision-induced dissociation

[Term]
id: MS:1002473
name: ion series considered in search
def: "The description of the ion fragment series (including charges and 
neutral losses) that are considered by the search engine." [PSI:PI]
is_a: MS:1001249 ! search input details

[Term]
id: MS:1002474
name: ProteoAnnotator:non-canonical gene model score
def: "The sum of peptide-level scores for peptides mapped only to 
non-canonical gene models within the group." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001147 ! protein ambiguity group result details
relationship: has_order MS:1002108 ! higher score better

[Term]
id: MS:1002475
name: ProteoAnnotator:count alternative peptides
def: "The count of the number of peptide sequences mapped to 
non-canonical gene models only within the group." [PSI:PI]
xref: value-type:xsd\:integer "The allowed value-type for this CV term."
is_a: MS:1001147 ! protein ambiguity group result details

[Term]
id: MS:1002476
name: ion mobility drift time
def: "Drift time of an ion or spectrum of ions as measured in an ion 
mobility mass spectrometer. This time might refer to the central value 
of a bin into which all ions within a narrow range of drift time have 
been aggregated." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000455 ! ion selection attribute
relationship: has_units UO:0000028 ! millisecond

[Term]
id: MS:1002477
name: mean drift time array
def: "Array of drift times, averaged from a matrix of binned m/z and 
drift time values, corresponding to spectrum of individual peaks encoded 
with an m/z array." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000513 ! binary data array
relationship: has_units UO:0000028 ! millisecond
relationship: has_units UO:0000010 ! second

[Term]
id: MS:1002478
name: mean charge array
def: "Array of mean charge values where the mean charge is calculated as 
a weighted mean of the charges of individual peaks that are aggregated 
into a processed spectrum." [PSI:MS]
xref: binary-data-type:MS\:1000521 "32-bit float"
is_a: MS:1000513 ! binary data array

[Term]
id: MS:1002479
name: regular expression
def: "Regular expression." [PSI:PI]
relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass 
Spectrometry Vocabularies

[Term]
id: MS:1002480
name: (10[.][0-9]{4,}(?:[.][0-9]+)*/(?:(?!["&\'<>])\S)+)
def: "Regular expression for a digital object identifier (DOI)." 
[PSI:PI, http://dx.doi.org/]
is_a: MS:1002479 ! regular expression

Best Regards,
Gerhard

-- 
---
Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
Bioinformatics / Biostatistics
Medizinisches-Proteom-Center (MPC)
Ruhr-Universität Bochum
Zentrum für klinische Forschung I (ZKF I), E.049a
Universitätsstraße 150
D-44801 Bochum
  
Phone:	+49(0)234/32-21006
Fax:	+49(0)234/32-14554
Email:	ger...@ru...
Web:	http://www.medizinisches-proteom-center.de

Re: [Psidev-ms-dev] Proposal for implementing ion mobility MS in mzML

[Eric D. <ede...@sy...>]

Hi Matt, this is excellent. I look forward to this functionality. Gerhard
has beaten me to proposing new terms for these. So I have extracted the
relevant subset of terms he proposed in his full CV RC email 8 hours ago
and pasted them into this thread. I have made a few minor adjustments to
the terms as shown in red. Does this seem good for everyone?



Thanks,

Eric



[Term]

id: MS:1002476

name: ion mobility drift time

def: "Drift time of an ion or spectrum of ions as measured in an ion

mobility mass spectrometer. This time might refer to the central value

of a bin into which all ions within a narrow range of drift time have

been aggregated." [PSI:MS]

xref: value-type:xsd\:float "The allowed value-type for this CV term."

is_a: MS:1000455 ! ion selection attribute

relationship: has_units UO:0000028 ! millisecond



[Term]

id: MS:1002477

name: mean drift time array

def: "Array of drift times, averaged from a matrix of binned m/z and

drift time values, corresponding to spectrum of individual peaks encoded

with an m/z array." [PSI:MS]

xref: value-type:xsd\:float "The allowed value-type for this CV term."

is_a: MS:1000513 ! binary data array

relationship: has_units UO:0000028 ! millisecond

relationship: has_units UO:0000010 ! second

relationship: has_units UO:0000031 ! minute



[Term]

id: MS:1002478

name: mean charge array

def: "Array of mean charge values where the mean charge is calculated as

a weighted mean of the charges of individual peaks that are aggregated

into a processed spectrum." [PSI:MS]

xref: binary-data-type:MS\:1000519 "32-bit integer"

xref: binary-data-type:MS\:1000521 "32-bit float"

is_a: MS:1000513 ! binary data array



[Term]

id: MS:1002479

name: charge-reduced m/z array

def: "A data array of m/z values which have been transformed to z=1."
[PSI:MS]

xref: binary-data-type:MS\:1000521 "32-bit float"

xref: binary-data-type:MS\:1000523 "64-bit float"

is_a: MS:1000514 ! m/z array

relationship: has_units MS:1000040 ! m/z





************ Obsoleted the term 'product ion drift time'

[Term]

id: MS:1001967

name: product ion drift time

def: "OBSOLETE The ion drift time of an MS2 product ion." [PSI:MS]

xref: value-type:xsd\:float "The allowed value-type for this CV term."

is_a: MS:1002222 ! SRM transition attribute

relationship: has_units UO:0000028 ! millisecond

comment: This term was made obsolete because it was replaced by ion
mobility drift time (MS:1002476).

is_obsolete: true





*From:* Chambers, Matthew [mailto:mat...@gm...]
*Sent:* Wednesday, May 14, 2014 9:43 AM
*To:* psi...@li...
*Subject:* Re: [Psidev-ms-dev] Proposal for implementing ion mobility MS in
mzML



Hi all,

I'm about to commit ion mobility support to ProteoWizard trunk using
userParams for drift time, so I think I've now waited long enough to
comment on this proposal. ;) We're currently only supporting mode 1
discussed below, but mode 2 shouldn't be hard to add.

On 4/20/2013 5:32 AM, Eric Deutsch wrote:

Hi everyone, here follows a proposal for implementing ion mobility MS in
mzML, which does not currently explicitly support IM-MS. This is based on a
discussion with Waters representatives at the HUPO PSI workshop in
Liverpool last week.



First for FAIMS, each spectrum should be tagged with the cvParam “FAIMS
compensation voltage” MS:1001581: The DC potential applied to the
asymmetric waveform in FAIMS that compensates for the difference between
high and low field mobility of an ion. This appears to be complete and
stable.



TODO: Verify that msconvert indeed supports this

TODO: Verify that the mapping file explicitly provides for this optional
cvParam

As far as I know, it does. But I rarely see FAIMS data; I don't think I
even have a test RAW file for it.


Now for the traditional IM-MS, there appear to be two modes:

1) Full profile data (i.e. no post-processing or peak picking)

2) Processed, peak-picked data



For mode 1) The data will be encoded in a series of full profile scans, one
for each profile spectrum and each profile spectrum will be tagged with its
drift time. The only current suitable term in the CV is “product ion drift
time” MS:1001967: The ion drift time of an MS2 product ion. After some
discussion, it was concluded that there is no reason to distinguish between
a product or precursor or other ion when providing its drift time. So I
propose we obsolete this term and add the term “ion mobility drift time”,
which would store the drift time as a float with units milliseconds. Each
spectrum would be tagged with its drift time in this way.



TODO: Obsolete “product ion drift time” MS:1001967 as unneeded and replaced
with more generic term

TODO: Create new term “ion mobility drift time” with definition “Drift time
of an ion or spectrum of ions as measured in an ion mobility mass
spectrometer. This time might refer to the central value of a bin into
which all ions within a narrow range of drift time have been aggregated.”

This is the CV term I need now, so let's get this done sooner rather than
later (i.e. without waiting to address the rest of the issues discussed
below). Gerhard, please obsolete "product ion drift time" and add this "ion
mobility drift time" term and give us a release candidate.



Therefore, if an instrument collected either MS1 or MS2 ions using the ion
mobility device, it would produce a series of profile-mode spectra, each
labeled with this new CV term containing the central drift time of ions
aggregated into that spectrum.



For mode 2) where some software has taken this series of profile spectra
with different drift times and produced a simplified peak-picked spectrum
with peaks centroided across m/z and drift time, the data will be encoded
into a single spectrum with an extra data array for mean drift time.



Currently supported data arrays are:

- m/z array

- intensity array

- charge array

- wavelength array        (this is for E-M radiation spectra)

- signal to noise array

- time array                    (envisioned for some time-domain spectrum,
not otherwise suitable for <Chromatogram>)

- et al.



TODO: Add term “mean drift time array”: Array of drift times, averaged from
a matrix of binned m/z and drift time values, corresponding to spectrum of
individual peaks encoded with an m/z array.

The average drift time array makes sense to me.


So, something else that Waters does upon processing the raw data into a
processed single spectrum is reducing the charge to 1. i.e. if the product
ion spectrum contains z=2 and z=3 peaks, this would be de-isotoped and
transformed to z=1 equivalent. This is customarily not done in mzML until
now. Although it should be noted in passing that msconvert CAN and DOES do
this for some instruments at least when converting from a raw format to
MGF, but not to mzML. How should this be encoded? Option 1 is to continue
to use the “m/z array” cvParam, but add another parameter on the
binarydataarray that indicates that the “m/z array” has been charge reduced
to z=1. Option 2 is to introduce a separate term “charge-reduced m/z array”
where we define it to mean that all m/z values have been transformed to
z=1. What do you think? I think I’m leaning to Option 2. This would mean
that existing software would not know how to access this new array. But it
is probably the case that existing software should not be accessing the
charge reduced data without explicit code changes to handle this case. Or
maybe it is friendlier to just reuse the original “m/z array” with a
modifier. Existing software would not know about the modified, but it could
access the reduced m/z values and presumably do something pretty reasonable
with them anyway. Most search engines should not be too dismayed as
receiving all z=1 peaks. And some are known to prefer it.



TODO: Decide how to implement this and add the appropriate new CV term.

I don't think this is too important. In fact, it should already be covered
(as "charge state deconvolution" in the data processing details, which
software should check. It is even less of an issue than peak picking and
deisotoping. If search engines don't check whether data is profile or
centroid they can easily do an extremely poor analysis. It's so important
we gave each spectrum its own top-level CV term for profile or centroid. I
don't think charge state deconvolution warrants the same treatment.



And one final, similar item during the above processing the Waters software
calculates an average charge. So suppose that if during acquisition both a
charge 2+ precursor at 300 m/z and 3+ precursor ion at 200 m/z were present
in equal amounts (with the same drift time), then there would be a final,
combined charge reduced peak at 600 m/z and an average charge of 2.5. We
could consider using the current “charge array” term with a modifier that
it is an average, but the current datatype is integer, so we would have to
change that to a float. Otherwise, we would need to add a new term “mean
charge array” with a definition like “Array of mean charge values where the
mean charge is calculated as a weighted mean of the charges of individual
peaks that are aggregated into a processed spectrum.” Or similar.



TODO: Decide whether we reuse “charge array” with a modifier CV term and
change its datatype to integer, or introduced a new term for “mean charge”.

I don't have a very strong opinion whether we should create a new kind of
array for this or simply modify the current term's datatype and augment its
definition to say that the values may represent an average. Changing data
type could certainly break current software which expects a charge array of
integers, so it's probably better to make a new term.

-Matt

[Psidev-ms-dev] Release candidate 3.64.0_rc4 of psi-ms.obo

[Gerhard M. <may...@ru...>]

Dear proteomics community,

attached you find the release candidate 3.64.0_rc4 of the psi-ms.obo file.

It contains new terms for mzTab, for specifying the neutral losses, for
collision-induced dissociation, for ion mobility MS, for PeptideShaker
and for ProteoAnnotator.

The neutral losses are now defined as terms independently from the ions in
order to decouple the two concepts ion and neutral loss from each other.

The old neutral loss terms have now the suffix " DEPRECATED" in their name,
but are not obsoleted.
The new parent term "ion series considered in search" (MS:1002473) now
contains all the ions and neutral loss terms.

Furthermore some terms from the purgatory branch are now obsolete.
In addition I corrected some spelling errors in definitions.


Changed CV terms in version 3.64.0_rc4 of psi-ms.obo:
=====================================================
************ The following terms from the purgatory branch are now 
obsoleted:
MS:1000329 linked scan
MS:1000268 mass spectrometry
MS:1000013 resolution type
MS:1000020 scanning method
MS:1000459 spectrum instrument description

************ The following neutral loss terms have now a suffix " 
DEPRECATED"
************ They are child of "ions series considered in search" 
(MS:1001066)
MS:1001148 a ion-H2O DEPRECATED
MS:1001146 a ion-NH3 DEPRECATED
MS:1001150 b ion-H2O DEPRECATED
MS:1002450 b ion-H3PO4 DEPRECATED
MS:1001149 b ion-NH3 DEPRECATED
MS:1001152 y ion-H2O DEPRECATED
MS:1002451 y ion-H3PO4 DEPRECATED
MS:1001151 y ion-NH3 DEPRECATED

************ Changed the definition to reflect that it's the branch
************ with the DEPRECATED terms
[Term]
id: MS:1001066
name: ions series considered in search
def: "The description of the DEPRECATED ion fragment series (including 
charges and neutral losses) that are considered by the search engine." 
[PSI:PI]
is_a: MS:1001249 ! search input details

************ Renamed the following term from
************ "high-energy collision-induced dissociation" to
************ "beam-type high-energy collision-induced dissociation"
************ and made it a child of collision-induced dissociation 
(MS:1000133)
[Term]
id: MS:1000422
name: beam-type high-energy collision-induced dissociation
def: "A collision-induced dissociation process wherein the projectile 
ion has the translational energy higher than approximately 1000 eV." 
[PSI:MS]
synonym: "HCD" EXACT []
is_a: MS:1000133 ! collision-induced dissociation

************ Obsoleted the term 'product ion drift time'
[Term]
id: MS:1001967
name: product ion drift time
def: "OBSOLETE The ion drift time of an MS2 product ion." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002222 ! SRM transition attribute
relationship: has_units UO:0000028 ! millisecond
comment: This term was made obsolete because it was replaced by ion 
mobility drift time (MS:1002476).
is_obsolete: true



New CV terms in version 3.64.0_rc4 of psi-ms.obo:
=================================================
[Term]
id: MS:1002452
name: Maui
def: "The Maltcms Graphical User Interface." [PSI:PI, http://maltcms.sf.net]
is_a: MS:1001456 ! analysis software
is_a: MS:1001457 ! data processing software

[Term]
id: MS:1002453
name: No fixed modifications searched
def: "No fixed modifications are included as a parameter for the search, 
and therefore they are not reported." [PSI:PI]
is_a: MS:1002094 ! common search engine input parameter

[Term]
id: MS:1002454
name: No variable modifications searched
def: "No variable modifications are included as a parameter for the 
search, and therefore they are not reported." [PSI:PI]
is_a: MS:1002094 ! common search engine input parameter

[Term]
id: MS:1002455
name: H2O neutral loss
def: "Neutral loss of water." [PSI:PI]
is_a: MS:1000336 ! neutral loss

[Term]
id: MS:1002456
name: NH3 neutral loss
def: "Neutral loss of ammonia." [PSI:PI]
is_a: MS:1000336 ! neutral loss

[Term]
id: MS:1002457
name: H3PO4 neutral loss
def: "Neutral loss of phosphoric acid." [PSI:PI]
is_a: MS:1000336 ! neutral loss

[Term]
id: MS:1002458
name: PeptideShaker
def: "PeptideShaker is a software for the interpretation of proteomics 
identification results." [PSI:PI, http://peptide-shaker.googlecode.com]
is_a: MS:1001456 ! analysis software

[Term]
id: MS:1002459
name: MS Amanda csv format
def: "MS Amanda csv output format." [PSI:PI]
is_a: MS:1001040 ! intermediate analysis format

[Term]
id: MS:1002460
name: protein group-level global FNR
def: "Estimation of the global false negative rate of protein groups." 
[PSI:PI]
is_a: MS:1002346 ! protein group-level result details
relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive

[Term]
id: MS:1002461
name: protein group-level confidence
def: "Estimation of the global confidence of protein groups." [PSI:PI]
is_a: MS:1002346 ! protein group-level result details

[Term]
id: MS:1002462
name: distinct peptide-level global FNR
def: "Estimation of the global false negative rate for distinct peptides 
once redundant identifications of the same peptide have been removed (id 
est multiple PSMs have been collapsed to one entry)." [PSI:PI]
is_a: MS:1001105 ! peptide result details
relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive

[Term]
id: MS:1002463
name: distinct peptide-level global confidence
def: "Estimation of the global confidence for distinct peptides once 
redundant identifications of the same peptide have been removed (id est 
multiple PSMs have been collapsed to one entry)." [PSI:PI]
is_a: MS:1001105 ! peptide result details

[Term]
id: MS:1002464
name: PSM-level global FNR
def: "Estimation of the global false negative rate of peptide spectrum 
matches." [PSI:PI]
is_a: MS:1002345 ! PSM-level result details
relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive

[Term]
id: MS:1002465
name: PSM-level global confidence
def: "Estimation of the global confidence of peptide spectrum matches." 
[PSI:PI]
is_a: MS:1002345 ! PSM-level result details

[Term]
id: MS:1002466
name: PeptideShaker PSM score
def: "The probability based PeptideShaker PSM score." [PSI:PI]
is_a: MS:1001153 ! search engine specific score
is_a: MS:1001143 ! search engine specific score for PSMs
relationship: has_order MS:1002108 ! higher score better

[Term]
id: MS:1002467
name: PeptideShaker PSM confidence
def: "The probability based PeptideShaker PSM confidence." [PSI:PI]
is_a: MS:1001153 ! search engine specific score
is_a: MS:1001143 ! search engine specific score for PSMs
relationship: has_order MS:1002108 ! higher score better

[Term]
id: MS:1002468
name: PeptideShaker peptide score
def: "The probability based PeptideShaker peptide score." [PSI:PI]
is_a: MS:1001153 ! search engine specific score
relationship: has_order MS:1002108 ! higher score better

[Term]
id: MS:1002469
name: PeptideShaker peptide confidence
def: "The probability based PeptideShaker peptide confidence." [PSI:PI]
is_a: MS:1001153 ! search engine specific score
relationship: has_order MS:1002108 ! higher score better

[Term]
id: MS:1002470
name: PeptideShaker protein group score
def: "The probability based PeptideShaker protein group score." [PSI:PI]
is_a: MS:1001153 ! search engine specific score
relationship: has_order MS:1002108 ! higher score better

[Term]
id: MS:1002471
name: PeptideShaker protein group confidence
def: "The probability based PeptideShaker protein group confidence." 
[PSI:PI]
is_a: MS:1001153 ! search engine specific score
relationship: has_order MS:1002108 ! higher score better

[Term]
id: MS:1002472
name: trap-type high-energy collision-induced dissociation
def: "A trap-type collision-induced dissociation process wherein the 
projectile ion has the translational energy higher than approximately 
1000 eV." [PSI:PI]
is_a: MS:1000133 ! collision-induced dissociation

[Term]
id: MS:1002473
name: ion series considered in search
def: "The description of the ion fragment series (including charges and 
neutral losses) that are considered by the search engine." [PSI:PI]
is_a: MS:1001249 ! search input details

[Term]
id: MS:1002474
name: ProteoAnnotator:non-canonical gene model score
def: "The sum of peptide-level scores for peptides mapped only to 
non-canonical gene models within the group." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001147 ! protein ambiguity group result details
relationship: has_order MS:1002108 ! higher score better

[Term]
id: MS:1002475
name: ProteoAnnotator:count alternative peptides
def: "The count of the number of peptide sequences mapped to 
non-canonical gene models only within the group." [PSI:PI]
xref: value-type:xsd\:integer "The allowed value-type for this CV term."
is_a: MS:1001147 ! protein ambiguity group result details

[Term]
id: MS:1002476
name: ion mobility drift time
def: "Drift time of an ion or spectrum of ions as measured in an ion 
mobility mass spectrometer. This time might refer to the central value 
of a bin into which all ions within a narrow range of drift time have 
been aggregated." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000455 ! ion selection attribute
relationship: has_units UO:0000028 ! millisecond

[Term]
id: MS:1002477
name: mean drift time array
def: "Array of drift times, averaged from a matrix of binned m/z and 
drift time values, corresponding to spectrum of individual peaks encoded 
with an m/z array." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000513 ! binary data array
relationship: has_units UO:0000028 ! millisecond
relationship: has_units UO:0000010 ! second
relationship: has_units UO:0000031 ! minute

[Term]
id: MS:1002478
name: mean charge array
def: "Array of mean charge values where the mean charge is calculated as 
a weighted mean of the charges of individual peaks that are aggregated 
into a processed spectrum." [PSI:MS]
xref: binary-data-type:MS\:1000519 "32-bit integer"
is_a: MS:1000513 ! binary data array

[Term]
id: MS:1002479
name: charge-reduced m/z array
def: "A data array of all m/z values transformed to z=1." [PSI:MS]
xref: binary-data-type:MS\:1000521 "32-bit float"
xref: binary-data-type:MS\:1000523 "64-bit float"
is_a: MS:1000514 ! m/z array
relationship: has_units MS:1000040 ! m/z

Best Regards,
Gerhard

-- 
---
Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
Bioinformatics / Biostatistics
Medizinisches-Proteom-Center (MPC)
Ruhr-Universität Bochum
Zentrum für klinische Forschung I (ZKF I), E.049a
Universitätsstraße 150
D-44801 Bochum
  
Phone:	+49(0)234/32-21006
Fax:	+49(0)234/32-14554
Email:	ger...@ru...
Web:	http://www.medizinisches-proteom-center.de

Re: [Psidev-ms-dev] Proposal for implementing ion mobility MS in mzML

[Chambers, M. <mat...@gm...>]

It might indeed make sense to add a new nativeID format for the IMS 
data. I'm currently calculating the nativeID as a scan number using the 
formula:
(frameIndex * driftBinsPerFrame) + driftBinIndex

But this requires knowing the drift bins per frame in order to get back 
to a frame and bin index. I'm not too concerned about it for the sake of 
grouping related spectra together because the LC elution time (indeed 
stored as scan start time) will be the same for all bins in a frame. 
It's more like a data provenance issue to me.

-Matt


On 12/6/2013 12:55 PM, Monroe, Matthew E wrote:
>
> The one caveat that I will add is that we acquire ion mobility MS data 
> using an LC front end, so it would be great if the format updates 
> support that.  We call all of the spectra acquired from a given LC 
> elution time a single "frame".  All of the mass spectra in that frame 
> have the same LC elution time, but have their own (incrementing) ion 
> mobility drift times, similar to the mode 1 (Full profile data) 
> use-case discussed below.  We should be able to store this data in 
> mzML format provided we can attach an LC elution time tag to each 
> profile-mode mass spectrum (likely 
> accession*=*"MS:1000016"name*=*"scan start time"), plus also an ion 
> mobility drift time.  Ideally we would also like to tag each mass 
> spectrum with a frame number (integer), which will make it obvious 
> that a set of mass spectra all come from the same frame. Without this 
> frame number tag, the only way to group the related spectra together 
> would be using the LC elution time.
>
> Here's how each spectrum entry might look if we encode frame and scan 
> in the "id" attribute:
>
> *<spectrum*index*=*"0"id*=*"frame=1 scan=0"
>
> *<spectrum*index*=*"1"id*=*"frame=1 scan=1"
>
> *<spectrum*index*=*"2"id*=*"frame=1 scan=2"
>
> *<spectrum*index*=*"3"id*=*"frame=1 scan=3"
>
> ...
>
> *<spectrum*index*=*"358"id*=*"frame=1 scan=358"
>
> *<spectrum*index*=*"359"id*=*"frame=1 scan=359"
>
> *<spectrum*index*=*"360"id*=*"frame=2 scan=0"
>
> *<spectrum*index*=*"361"id*=*"frame=2 scan=1"
>
> *<spectrum*index*=*"362"id*=*"frame=2 scan=2"
>
> ...
>
> The alternative is to encode the frame and scan info in explicit 
> cvParam entries.
>
> Matt Monroe
>
> *From:*Eric Deutsch [mailto:ede...@sy...]
> *Sent:* Friday, December 06, 2013 6:11 AM
> *To:* Mass spectrometry standard development; Han...@wa...; 
> David L. Tabb; Matt Chambers; Brendan MacLean
> *Cc:* Eric Deutsch
> *Subject:* Re: [Psidev-ms-dev] Proposal for implementing ion mobility 
> MS in mzML
>
> Hi everyone, in chatting with Brendan here in Dagstuhl, I learned that 
> Matt is teetering on the brink of implementing proper support for ion 
> mobility MS in ProteoWizard. I would like to refresh this thread with 
> a proposal on how to implement IM-MS in mzML. This proposal was 
> unencumbered by any actual implementation attempts, and we expected 
> there would have to be refinements when someone actually performed the 
> implementation. Since it seems that this is nigh, please examine this, 
> and I hope it can be a useful guide. Perhaps Matt can study this and 
> comment on whether this is useful, or if he will do things 
> differently, or if this is not relevant. Please let me know if a 
> telecall chat is warranted.
>
> Thank you!
>
> Eric
>
> *From:*Eric Deutsch [mailto:ede...@sy... 
> <mailto:ede...@sy...>]
> *Sent:* Saturday, April 20, 2013 3:32 AM
> *To:* Mass spectrometry standard development; Han...@wa... 
> <mailto:Han...@wa...>; David L. Tabb
> *Cc:* Eric Deutsch
> *Subject:* Proposal for implementing ion mobility MS in mzML
>
> Hi everyone, here follows a proposal for implementing ion mobility MS 
> in mzML, which does not currently explicitly support IM-MS. This is 
> based on a discussion with Waters representatives at the HUPO PSI 
> workshop in Liverpool last week.
>
> First for FAIMS, each spectrum should be tagged with the cvParam 
> "FAIMS compensation voltage" MS:1001581: The DC potential applied to 
> the asymmetric waveform in FAIMS that compensates for the difference 
> between high and low field mobility of an ion. This appears to be 
> complete and stable.
>
> TODO: Verify that msconvert indeed supports this
>
> TODO: Verify that the mapping file explicitly provides for this 
> optional cvParam
>
> Now for the traditional IM-MS, there appear to be two modes:
>
> 1) Full profile data (i.e. no post-processing or peak picking)
>
> 2) Processed, peak-picked data
>
> For mode 1) The data will be encoded in a series of full profile 
> scans, one for each profile spectrum and each profile spectrum will be 
> tagged with its drift time. The only current suitable term in the CV 
> is "product ion drift time" MS:1001967: The ion drift time of an MS2 
> product ion. After some discussion, it was concluded that there is no 
> reason to distinguish between a product or precursor or other ion when 
> providing its drift time. So I propose we obsolete this term and add 
> the term "ion mobility drift time", which would store the drift time 
> as a float with units milliseconds. Each spectrum would be tagged with 
> its drift time in this way.
>
> TODO: Obsolete "product ion drift time" MS:1001967 as unneeded and 
> replaced with more generic term
>
> TODO: Create new term "ion mobility drift time" with definition "Drift 
> time of an ion or spectrum of ions as measured in an ion mobility mass 
> spectrometer. This time might refer to the central value of a bin into 
> which all ions within a narrow range of drift time have been aggregated."
>

Re: [Psidev-ms-dev] Proposal for implementing ion mobility MS in mzML

[Chambers, M. <mat...@gm...>]

Hi all,

I'm about to commit ion mobility support to ProteoWizard trunk using 
userParams for drift time, so I think I've now waited long enough to 
comment on this proposal. ;) We're currently only supporting mode 1 
discussed below, but mode 2 shouldn't be hard to add.

On 4/20/2013 5:32 AM, Eric Deutsch wrote:
>
> Hi everyone, here follows a proposal for implementing ion mobility MS 
> in mzML, which does not currently explicitly support IM-MS. This is 
> based on a discussion with Waters representatives at the HUPO PSI 
> workshop in Liverpool last week.
>
> First for FAIMS, each spectrum should be tagged with the cvParam 
> "FAIMS compensation voltage" MS:1001581: The DC potential applied to 
> the asymmetric waveform in FAIMS that compensates for the difference 
> between high and low field mobility of an ion. This appears to be 
> complete and stable.
>
> TODO: Verify that msconvert indeed supports this
>
> TODO: Verify that the mapping file explicitly provides for this 
> optional cvParam
>
As far as I know, it does. But I rarely see FAIMS data; I don't think I 
even have a test RAW file for it.


> Now for the traditional IM-MS, there appear to be two modes:
>
> 1) Full profile data (i.e. no post-processing or peak picking)
>
> 2) Processed, peak-picked data
>
> For mode 1) The data will be encoded in a series of full profile 
> scans, one for each profile spectrum and each profile spectrum will be 
> tagged with its drift time. The only current suitable term in the CV 
> is "product ion drift time" MS:1001967: The ion drift time of an MS2 
> product ion. After some discussion, it was concluded that there is no 
> reason to distinguish between a product or precursor or other ion when 
> providing its drift time. So I propose we obsolete this term and add 
> the term "ion mobility drift time", which would store the drift time 
> as a float with units milliseconds. Each spectrum would be tagged with 
> its drift time in this way.
>
> TODO: Obsolete "product ion drift time" MS:1001967 as unneeded and 
> replaced with more generic term
>
> TODO: Create new term "ion mobility drift time" with definition "Drift 
> time of an ion or spectrum of ions as measured in an ion mobility mass 
> spectrometer. This time might refer to the central value of a bin into 
> which all ions within a narrow range of drift time have been aggregated."
>
This is the CV term I need now, so let's get this done sooner rather 
than later (i.e. without waiting to address the rest of the issues 
discussed below). Gerhard, please obsolete "product ion drift time" and 
add this "ion mobility drift time" term and give us a release candidate.

> Therefore, if an instrument collected either MS1 or MS2 ions using the 
> ion mobility device, it would produce a series of profile-mode 
> spectra, each labeled with this new CV term containing the central 
> drift time of ions aggregated into that spectrum.
>
> For mode 2) where some software has taken this series of profile 
> spectra with different drift times and produced a simplified 
> peak-picked spectrum with peaks centroided across m/z and drift time, 
> the data will be encoded into a single spectrum with an extra data 
> array for mean drift time.
>
> Currently supported data arrays are:
>
> - m/z array
>
> - intensity array
>
> - charge array
>
> - wavelength array        (this is for E-M radiation spectra)
>
> - signal to noise array
>
> - time array                    (envisioned for some time-domain 
> spectrum, not otherwise suitable for <Chromatogram>)
>
> - et al.
>
> TODO: Add term "mean drift time array": Array of drift times, averaged 
> from a matrix of binned m/z and drift time values, corresponding to 
> spectrum of individual peaks encoded with an m/z array.
>
The average drift time array makes sense to me.


> So, something else that Waters does upon processing the raw data into 
> a processed single spectrum is reducing the charge to 1. i.e. if the 
> product ion spectrum contains z=2 and z=3 peaks, this would be 
> de-isotoped and transformed to z=1 equivalent. This is customarily not 
> done in mzML until now. Although it should be noted in passing that 
> msconvert CAN and DOES do this for some instruments at least when 
> converting from a raw format to MGF, but not to mzML. How should this 
> be encoded? Option 1 is to continue to use the "m/z array" cvParam, 
> but add another parameter on the binarydataarray that indicates that 
> the "m/z array" has been charge reduced to z=1. Option 2 is to 
> introduce a separate term "charge-reduced m/z array" where we define 
> it to mean that all m/z values have been transformed to z=1. What do 
> you think? I think I'm leaning to Option 2. This would mean that 
> existing software would not know how to access this new array. But it 
> is probably the case that existing software should not be accessing 
> the charge reduced data without explicit code changes to handle this 
> case. Or maybe it is friendlier to just reuse the original "m/z array" 
> with a modifier. Existing software would not know about the modified, 
> but it could access the reduced m/z values and presumably do something 
> pretty reasonable with them anyway. Most search engines should not be 
> too dismayed as receiving all z=1 peaks. And some are known to prefer it.
>
> TODO: Decide how to implement this and add the appropriate new CV term.
>
I don't think this is too important. In fact, it should already be 
covered (as "charge state deconvolution" in the data processing details, 
which software should check. It is even less of an issue than peak 
picking and deisotoping. If search engines don't check whether data is 
profile or centroid they can easily do an extremely poor analysis. It's 
so important we gave each spectrum its own top-level CV term for profile 
or centroid. I don't think charge state deconvolution warrants the same 
treatment.

> And one final, similar item during the above processing the Waters 
> software calculates an average charge. So suppose that if during 
> acquisition both a charge 2+ precursor at 300 m/z and 3+ precursor ion 
> at 200 m/z were present in equal amounts (with the same drift time), 
> then there would be a final, combined charge reduced peak at 600 m/z 
> and an average charge of 2.5. We could consider using the current 
> "charge array" term with a modifier that it is an average, but the 
> current datatype is integer, so we would have to change that to a 
> float. Otherwise, we would need to add a new term "mean charge array" 
> with a definition like "Array of mean charge values where the mean 
> charge is calculated as a weighted mean of the charges of individual 
> peaks that are aggregated into a processed spectrum." Or similar.
>
> TODO: Decide whether we reuse "charge array" with a modifier CV term 
> and change its datatype to integer, or introduced a new term for "mean 
> charge".
>
I don't have a very strong opinion whether we should create a new kind 
of array for this or simply modify the current term's datatype and 
augment its definition to say that the values may represent an average. 
Changing data type could certainly break current software which expects 
a charge array of integers, so it's probably better to make a new term.

-Matt

[Psidev-ms-dev] Release candidate 3.64.0_rc3 of psi-ms.obo

[Gerhard M. <may...@ru...>]

Dear proteomics community,

attached you find the release candidate 3.64.0_rc3 of the psi-ms.obo file.

It contains new terms for mzTab, for specifying the neutral losses, for
collision-induced dissociation and for PeptideShaker.

The neutral losses are now defined as terms independently from the ions in
order to decouple the two concepts ion and neutral loss from each other.

The old neutral loss terms have now the suffix " DEPRECATED" in their name,
but are not obsoleted.
The new parent term "ion series considered in search" (MS:1002473) now
contains all the ions and neutral loss terms.

Furthermore some terms from the purgatory branch are now obsolete.
In addition I corrected some spelling errors in definitions.


Changed CV terms in version 3.64.0_rc3 of psi-ms.obo:
=====================================================
************ The following terms from the purgatory branch are now 
obsoleted:
MS:1000329 linked scan
MS:1000268 mass spectrometry
MS:1000013 resolution type
MS:1000020 scanning method
MS:1000459 spectrum instrument description

************ The following neutral loss terms have now a suffix " 
DEPRECATED"
************ They are child of "ions series considered in search" 
(MS:1001066)
MS:1001148 a ion-H2O DEPRECATED
MS:1001146 a ion-NH3 DEPRECATED
MS:1001150 b ion-H2O DEPRECATED
MS:1002450 b ion-H3PO4 DEPRECATED
MS:1001149 b ion-NH3 DEPRECATED
MS:1001152 y ion-H2O DEPRECATED
MS:1002451 y ion-H3PO4 DEPRECATED
MS:1001151 y ion-NH3 DEPRECATED

************ Changed the definition to reflect that it's the branch
************ with the DEPRECATED terms
[Term]
id: MS:1001066
name: ions series considered in search
def: "The description of the DEPRECATED ion fragment series (including 
charges and neutral losses) that are considered by the search engine." 
[PSI:PI]
is_a: MS:1001249 ! search input details

************ Renamed the following term from
************ "high-energy collision-induced dissociation" to
************ "beam-type high-energy collision-induced dissociation"
************ and made it a child of collision-induced dissociation 
(MS:1000133)
[Term]
id: MS:1000422
name: beam-type high-energy collision-induced dissociation
def: "A collision-induced dissociation process wherein the projectile 
ion has the translational energy higher than approximately 1000 eV." 
[PSI:MS]
synonym: "HCD" EXACT []
is_a: MS:1000133 ! collision-induced dissociation


New CV terms in version 3.64.0_rc3 of psi-ms.obo:
=================================================
[Term]
id: MS:1002452
name: Maui
def: "The Maltcms Graphical User Interface." [PSI:PI, http://maltcms.sf.net]
is_a: MS:1001456 ! analysis software
is_a: MS:1001457 ! data processing software

[Term]
id: MS:1002453
name: No fixed modifications searched
def: "No fixed modifications are included as a parameter for the search, 
and therefore they are not reported." [PSI:PI]
is_a: MS:1002094 ! common search engine input parameter

[Term]
id: MS:1002454
name: No variable modifications searched
def: "No variable modifications are included as a parameter for the 
search, and therefore they are not reported." [PSI:PI]
is_a: MS:1002094 ! common search engine input parameter

[Term]
id: MS:1002455
name: H2O neutral loss
def: "Neutral loss of water." [PSI:PI]
is_a: MS:1000336 ! neutral loss

[Term]
id: MS:1002456
name: NH3 neutral loss
def: "Neutral loss of ammonia." [PSI:PI]
is_a: MS:1000336 ! neutral loss

[Term]
id: MS:1002457
name: H3PO4 neutral loss
def: "Neutral loss of phosphoric acid." [PSI:PI]
is_a: MS:1000336 ! neutral loss

[Term]
id: MS:1002458
name: PeptideShaker
def: "PeptideShaker is a software for the interpretation of proteomics 
identification results." [PSI:PI, http://peptide-shaker.googlecode.com]
is_a: MS:1001456 ! analysis software

[Term]
id: MS:1002459
name: MS Amanda csv format
def: "MS Amanda csv output format." [PSI:PI]
is_a: MS:1001040 ! intermediate analysis format

[Term]
id: MS:1002460
name: protein group-level global FNR
def: "Estimation of the global false negative rate of protein groups." 
[PSI:PI]
is_a: MS:1002346 ! protein group-level result details
relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive

[Term]
id: MS:1002461
name: protein group-level confidence
def: "Estimation of the global confidence of protein groups." [PSI:PI]
is_a: MS:1002346 ! protein group-level result details

[Term]
id: MS:1002462
name: distinct peptide-level global FNR
def: "Estimation of the global false negative rate for distinct peptides 
once redundant identifications of the same peptide have been removed (id 
est multiple PSMs have been collapsed to one entry)." [PSI:PI]
is_a: MS:1001105 ! peptide result details
relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive

[Term]
id: MS:1002463
name: distinct peptide-level global confidence
def: "Estimation of the global confidence for distinct peptides once 
redundant identifications of the same peptide have been removed (id est 
multiple PSMs have been collapsed to one entry)." [PSI:PI]
is_a: MS:1001105 ! peptide result details

[Term]
id: MS:1002464
name: PSM-level global FNR
def: "Estimation of the global false negative rate of peptide spectrum 
matches." [PSI:PI]
is_a: MS:1002345 ! PSM-level result details
relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive

[Term]
id: MS:1002465
name: PSM-level global confidence
def: "Estimation of the global confidence of peptide spectrum matches." 
[PSI:PI]
is_a: MS:1002345 ! PSM-level result details

[Term]
id: MS:1002466
name: PeptideShaker PSM score
def: "The probability based PeptideShaker PSM score." [PSI:PI]
is_a: MS:1001153 ! search engine specific score
is_a: MS:1001143 ! search engine specific score for PSMs
relationship: has_order MS:1002108 ! higher score better

[Term]
id: MS:1002467
name: PeptideShaker PSM confidence
def: "The probability based PeptideShaker PSM confidence." [PSI:PI]
is_a: MS:1001153 ! search engine specific score
is_a: MS:1001143 ! search engine specific score for PSMs
relationship: has_order MS:1002108 ! higher score better

[Term]
id: MS:1002468
name: PeptideShaker peptide score
def: "The probability based PeptideShaker peptide score." [PSI:PI]
is_a: MS:1001153 ! search engine specific score
relationship: has_order MS:1002108 ! higher score better

[Term]
id: MS:1002469
name: PeptideShaker peptide confidence
def: "The probability based PeptideShaker peptide confidence." [PSI:PI]
is_a: MS:1001153 ! search engine specific score
relationship: has_order MS:1002108 ! higher score better

[Term]
id: MS:1002470
name: PeptideShaker protein group score
def: "The probability based PeptideShaker protein group score." [PSI:PI]
is_a: MS:1001153 ! search engine specific score
relationship: has_order MS:1002108 ! higher score better

[Term]
id: MS:1002471
name: PeptideShaker protein group confidence
def: "The probability based PeptideShaker protein group confidence." 
[PSI:PI]
is_a: MS:1001153 ! search engine specific score
relationship: has_order MS:1002108 ! higher score better

[Term]
id: MS:1002472
name: trap-type high-energy collision-induced dissociation
def: "A trap-type collision-induced dissociation process wherein the 
projectile ion has the translational energy higher than approximately 
1000 eV." [PSI:PI]
is_a: MS:1000133 ! collision-induced dissociation

[Term]
id: MS:1002473
name: ion series considered in search
def: "The description of the ion fragment series (including charges and 
neutral losses) that are considered by the search engine." [PSI:PI]
is_a: MS:1001249 ! search input details

Best Regards,
Gerhard

-- 
---
Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
Bioinformatics / Biostatistics
Medizinisches-Proteom-Center (MPC)
Ruhr-Universität Bochum
Zentrum für klinische Forschung I (ZKF I), E.049a
Universitätsstraße 150
D-44801 Bochum
  
Phone:	+49(0)234/32-21006
Fax:	+49(0)234/32-14554
Email:	ger...@ru...
Web:	http://www.medizinisches-proteom-center.de