psidev-pi-dev — General Development List for Proteomics Informatics

Re: [Psidev-pi-dev] [Psi-announce] PSI DocProc minor update 1.1.2

[Juan A. V. <ju...@eb...>]

Hi Martin,

Everything fine. Thanks a lot for this.

Cheers,

Juan Antionio



> On 26 Apr 2021, at 15:05, Martin Eisenacher <mar...@ru...> wrote:
> 
> Dear colleagues,
> dear persons interested in the PSI developments,
> 
> a minor update of the PSI DocProc definition has been agreed to by the
> steering committee.
> 
> It mentions "online document editing" systems for public review / removed
> the mentioning of the 
> insecure "comment" function on psidev.info website, changes to shortened
> public and 
> invited review phase from 60 to 45 days; changes the license model from
> "Copyright" to "CC-BY-NC 4.0".
> 
> It has to go through a 14-day public review, after which its status could be
> changed to FINAL.
> I attach version 1.1.2 PREFINAL_DIFF with changes marked in comparison to
> 1.1.1, so please add or 
> comment until May 10th!
> 
>  Thank you
>       Martin
> --
> PD DR. MARTIN EISENACHER
> Department Leader
> DEPARTMENT Medical Bioinformatics
> Medizinisches Proteom-Center
> Medical Faculty
> &
> Medical Proteome Analysis
> Center for Proteindiagnostics (PRODI)
> 
> Building PRODI E2.269 | Gesundheitscampus 4 | D-44801 Bochum
> Fon +49 (0)234 32-18104 | Fax +49 (0)234 32-14496
> E-mail mar...@ru...
> www.medizinisches-proteom-center.de
> 
> <20210426_PSI_Document_Process_ver_1.1.2_PREFINAL_DIFF.docx>_______________________________________________
> Psi-announce mailing list
> Psi...@eb...
> https://listserver.ebi.ac.uk/mailman/listinfo/psi-announce

Re: [Psidev-pi-dev] [Psidev-ms-dev] PSI DocProc minor update 1.1.2

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

This looks good to me, thanks!

-----Original Message-----
From: Martin Eisenacher via Psidev-ms-dev
<psi...@li...>
Sent: Monday, April 26, 2021 7:06 AM
To: psi...@li...;
psi...@li...;
psi...@li...; psi...@eb...
Cc: Martin Eisenacher <mar...@ru...>
Subject: [Psidev-ms-dev] PSI DocProc minor update 1.1.2

Dear colleagues,
dear persons interested in the PSI developments,

a minor update of the PSI DocProc definition has been agreed to by the
steering committee.

It mentions "online document editing" systems for public review / removed
the mentioning of the insecure "comment" function on psidev.info website,
changes to shortened public and invited review phase from 60 to 45 days;
changes the license model from "Copyright" to "CC-BY-NC 4.0".

It has to go through a 14-day public review, after which its status could
be changed to FINAL.
I attach version 1.1.2 PREFINAL_DIFF with changes marked in comparison to
1.1.1, so please add or comment until May 10th!

  Thank you
       Martin
--
PD DR. MARTIN EISENACHER
Department Leader
DEPARTMENT Medical Bioinformatics
Medizinisches Proteom-Center
Medical Faculty
&
Medical Proteome Analysis
Center for Proteindiagnostics (PRODI)

Building PRODI E2.269 | Gesundheitscampus 4 | D-44801 Bochum Fon +49
(0)234 32-18104 | Fax +49 (0)234 32-14496 E-mail mar...@ru...
www.medizinisches-proteom-center.de

[Psidev-pi-dev] PSI DocProc minor update 1.1.2

[Martin E. <mar...@ru...>]

Dear colleagues,
dear persons interested in the PSI developments,

a minor update of the PSI DocProc definition has been agreed to by the
steering committee.

It mentions "online document editing" systems for public review / removed
the mentioning of the 
insecure "comment" function on psidev.info website, changes to shortened
public and 
invited review phase from 60 to 45 days; changes the license model from
"Copyright" to "CC-BY-NC 4.0".

It has to go through a 14-day public review, after which its status could be
changed to FINAL.
I attach version 1.1.2 PREFINAL_DIFF with changes marked in comparison to
1.1.1, so please add or 
comment until May 10th!

  Thank you
       Martin
--
PD DR. MARTIN EISENACHER
Department Leader
DEPARTMENT Medical Bioinformatics
Medizinisches Proteom-Center
Medical Faculty
&
Medical Proteome Analysis
Center for Proteindiagnostics (PRODI)

Building PRODI E2.269 | Gesundheitscampus 4 | D-44801 Bochum
Fon +49 (0)234 32-18104 | Fax +49 (0)234 32-14496
E-mail mar...@ru...
www.medizinisches-proteom-center.de

[Psidev-pi-dev] HUPO PSI recommendation document (Universal Spectrum Identifier), 60-days public review

[Martin E. <mar...@ru...>]

Dear colleague,

dear member of the Mass Spectrometry community,

 

please forward this message to potentially interested colleagues!

 

The HUPO Proteomics Standards Initiative (PSI) develops standards 

for documentation and storage of Proteomics data (see 

 <http://www.psidev.info> http://www.psidev.info for an overview of
activities).

 

A recommendation document specifying
the Universal Spectrum Identifier (USI)

has been submitted to the PSI document process.

 

Because it is not a file format, there is neither a Schema definition
nor XML / tab example files, but some practical examples of USIs from 

ProteomeXchange member DBs and others (included in the document).

 

Specification document:
https://github.com/HUPO-PSI/usi/blob/master/Specification/USI_SpecDoc_1.0.dr
aft07_2020-09-29.docx?raw=true

Use case examples: http://www.psidev.info/usi

(USIs used in repository URLs).

Development background:  <https://github.com/HUPO-PSI/usi>
https://github.com/HUPO-PSI/usi

 

After having passed a 30-day review of the PSI steering group 

with minor changes, the proposed document version 1.0.0 DRAFT 7

now goes through 60-days public comments and external 

review phase (end: 18th December 2020).

 

Purpose of the standard (excerpt from the spec. doc.):
"This document presents a specification for a multi-part identifier 

of the form mzspec:<collection>:<msRun>:<indexType>:<indexNumber>:<optional
interpretation> 

for mass spectra so that they may be easily and universally referenced for 

subsequent access. The Universal Spectrum Identifier (USI) describes a 

virtual path to locate a spectrum plus a possible interpretation of that 

spectrum. The USI is being implemented at most ProteomeXchange partner 

repositories and can be freely used by any other software. While initially

implemented for the field of proteomics, its design is amenable to other 

fields that use mass spectrometers for analyte detection."

 

PLEASE SEND COMMENTS directly to mar...@ru...

for example regarding the following criteria:

 

- That it is well formed - that is, it is presented in accordance with the
templates and is clearly written.

- That it is sufficiently detailed and clearly contains and comprehensively
describes the necessary and sufficient explanation of the format.

 

This message is to encourage you to contribute to the standards

development activity by commenting on the material that is attached 

as well as available online. We invite both positive and negative comments.

If negative comments are being made, these could be on the relevance, 

clarity, correctness, appropriateness, etc, of the proposal as 

a whole or of specific parts of the proposal.

 

If you do not feel well placed to comment on this document, but 

know someone who may be, please consider forwarding this request. 

There is no requirement that people commenting should have had any 

prior contact with the PSI.

 

    Many thanks for your valuable time and participation

      Martin Eisenacher (PSI Editor)

 

 

--

PD DR. MARTIN EISENACHER

Department Leader

DEPARTMENT Medical Bioinformatics

Medizinisches Proteom-Center

Medical Faculty

&

Medical Proteome Analysis

Center for Proteindiagnostics (PRODI)

 

Building PRODI E2.269 | Gesundheitscampus 4 | D-44801 Bochum

Fon +49 (0)234 32-18104 | Fax +49 (0)234 32-14496

E-mail  <mailto:mar...@ru...> mar...@ru...

 <http://www.medizinisches-proteom-center.de/>
www.medizinisches-proteom-center.de

 



 

 

[Psidev-pi-dev] XLMOD problem in OLS?

[Eric D. <eri...@is...>]

Hi everyone, I was trying to access the XLMOD controlled vocabulary through
OLS but I’m having trouble.



https://www.ebi.ac.uk/ols/ontologies/xlmod

OLS knows about it. But it is unbrowsable. And trying to download it yields
some weird OWL file that doesn’t seem to include the actual terms.



It looks like the OBO file is here:

https://raw.githubusercontent.com/HUPO-PSI/mzIdentML/master/cv/XLMOD.obo



Is someone able to improve the OLS situation?



Thanks,

Eric

Re: [Psidev-pi-dev] [Psidev-ms-dev] New term needed for timsTOF Flex instrument

[Eric D. <eri...@is...>]

I don’t know much about this instrument itself, but seems reasonable to me.



My only suggested change is to remove the apostrophe. It is incorrectly
used and unnecessary. But I also notice that all Bruker instruments have
this (so Juan was just following the pattern, okay). But I vote that we fix
this everywhere in the CV. i.e. s/Daltonics’/Daltonics/g



Thermo doesn’t have apostrophes, Waters doesn’t have apostrophes. I assume
the intent was to imply a possessive, but I propose we strip that for all
Bruker models. It’s only in the definition anyway, so should not affect
software.



Thanks,

Eric





*From:* Juan Antonio Vizcaino <ju...@eb...>
*Sent:* Thursday, March 5, 2020 3:46 AM
*To:* psi...@li...
*Cc:* psi...@li...; Mass spectrometry standard
development <psi...@li...>; Deepti Jaiswal Kundu <
ja...@eb...>
*Subject:* [Psidev-ms-dev] New term needed for timsTOF Flex instrument



Dear all,



We have a submitter that has generated data coming from an timsTOF fleX
instrument.



This term is not yet in the PSI MS CV. The one that is there is for the
timsTOF Pro (MS:1003005). So I am proposing to add it to the CV.



[Term]
id: MS:1xxxxx
name: timsTOF fleX
def: "Bruker Daltonics' timsTOF fleX." [PSI:MS]
is_a: MS:1000122 ! Bruker Daltonics instrument model





Thanks in advance,



Juan

[Psidev-pi-dev] New term needed for timsTOF Flex instrument

[Juan A. V. <ju...@eb...>]

Dear all,

We have a submitter that has generated data coming from an timsTOF fleX instrument. 

This term is not yet in the PSI MS CV. The one that is there is for the timsTOF Pro (MS:1003005). So I am proposing to add it to the CV.

[Term]
id: MS:1xxxxx
name: timsTOF fleX
def: "Bruker Daltonics' timsTOF fleX." [PSI:MS]
is_a: MS:1000122 ! Bruker Daltonics instrument model


Thanks in advance,

Juan

[Psidev-pi-dev] New version 4.1.35 of psi-ms.obo

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

Dear proteomics/metabolomics community,

following are the new and changed terms for the
version 4.1.35 of the psi-ms.obo file,
which can be downloaded from
https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo


New CV terms in version 4.1.35 of psi-ms.obo:
=============================================
[Term]
id: MS:1003083
name: raw data file
def: "Data file that contains original data as generated by an 
instrument, although not necessarily in the original data format (i.e. 
an original raw file converted to a different format is still a raw data 
file)." [PSI:MS]
is_a: MS:1000577 ! source data file

[Term]
id: MS:1003084
name: processed data file
def: "File that contains data that has been substantially processed or 
transformed from what was originally acquired by an instrument." [PSI:MS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1000577 ! source data file

[Term]
id: MS:1003085
name: previous MSn-1 scan precursor intensity
def: "Intensity of the precursor ion in the previous MSn-1 scan (prior 
in time to the referencing MSn scan). For an MS2 scan, this means the 
MS1 precursor intensity. It is unspecified on whether this is an apex 
(across m/z) intensity, integrated (across m/z) intensity, a centroided 
peak intensity of unknown origin, or even summed across several 
isotopes." [PSI:MS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001141 ! intensity of precursor ion
is_a: MS:1000499 ! spectrum attribute

[Term]
id: MS:1003086
name: precursor apex intensity
def: "Intensity of the precursor ion current as measured by its apex 
point over time and m/z. It is unspecified whether this is the intensity 
of the selected isotope or the most intense isotope." [PSI:MS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001141 ! intensity of precursor ion
is_a: MS:1000499 ! spectrum attribute

[Term]
id: MS:1003087
name: supported by repository but incomplete data and/or metadata
def: "Dataset for which the identifications and/or spectra/traces are in 
formats that can be parsed by the hosting data repository such that 
internal references between identifications and spectra/traces are 
preserved and browsable at the repository. However, some metadata is not 
properly described due to lack of CV terms or some auxiliary data, such 
as data used to create a spectral library or a sequence search database 
crucial to the analysis, is not available." [PSI:PI]
is_a: MS:1002844 ! Experiment additional parameter

[Term]
id: MS:1003088
name: truncation and zlib compression
def: "Compression using truncation and zlib." 
[https://github.com/biospi/pwiz]
xref: value-type:xsd\:int "The number of mantissa bits truncated."
is_a: MS:1000572 ! binary data compression type

[Term]
id: MS:1003089
name: truncation, delta prediction and zlib compression
def: "Compression using truncation, delta prediction and zlib." 
[https://github.com/biospi/pwiz]
xref: value-type:xsd\:int "The number of mantissa bits truncated."
is_a: MS:1000572 ! binary data compression type

[Term]
id: MS:1003090
name: truncation, linear prediction and zlib compression
def: "Compression using truncation, linear prediction and zlib." 
[https://github.com/biospi/pwiz]
xref: value-type:xsd\:int "The number of mantissa bits truncated."
is_a: MS:1000572 ! binary data compression type


Changed CV terms in version 4.1.35 of psi-ms.obo:
=================================================
************ Added is_a relation
[Term]
id: MS:1000224
name: molecular mass
def: "Mass of a molecule measured in unified atomic mass units (u or 
Da)." [https://en.wikipedia.org/wiki/Molecular_mass]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000861 ! molecular entity property
relationship: has_units UO:0000002 ! mass unit

************ renamed and added relationship: part_of MS:1002806 ! ion
[Term]
id: MS:1000507
name: ion property
def: "Nonphysical characteristic attributed to an ion." [PSI:MS]
relationship: part_of MS:1002806 ! ion

************ Added is_a relation
[Term]
id: MS:1002959
name: isomer
def: "One of several species (or molecular entities) that have the same 
atomic composition (molecular formula) but different line formulae or 
different stereochemical formulae." 
[https://goldbook.iupac.org/html/I/I03289.html]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1000859 ! molecule

************ renamed and added is_a relation
[Term]
id: MS:1000577
name: source data file
def: "Data file from which an entity is sourced." [PSI:MS]
synonym: "source file" EXACT []
relationship: part_of MS:1001458 ! spectrum generation information
is_a: MS:1000499 ! spectrum attribute

************ changed the definition
[Term]
id: MS:1002856
name: Supported dataset by repository
def: "Dataset for which the identifications and/or spectra/traces are in 
formats that can be parsed by the hosting data repository such that 
internal references between identifications and spectra/traces are 
preserved and browsable at the repository. This is usually called a 
complete submission." [PSI:PI]
is_a: MS:1002844 ! Experiment additional parameter

[Term]
id: MS:1002857
name: Unsupported dataset by repository
def: "Dataset for which the identifications and/or spectra/traces are in 
formats that cannot be parsed by the hosting data repository and thus 
internal references between identifications and spectra/traces are not 
browsable at the repository. This is usually called a partial 
submission." [PSI:PI]
is_a: MS:1002844 ! Experiment additional parameter

Best Regards,
Gerhard

-- 

*----------------------------------------------------------------------*

*Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER*

*Research associate*

*Ruhr-Universität Bochum, Medizinisches Proteom-Center*

*DEPARTMENT Medical Bioinformatics*

*Building ProDi E2.234 | Gesundheitscampus 4 | D-44801 Bochum*

*Fon: *+49 (0)234 32-18110 | *Fax: *+49 (0)234 32-14496

*E-Mail: *ger...@ru... <mailto:ger...@ru...>

*Web: *www.ruhr-uni-bochum.de/mpc <http://www.ruhr-uni-bochum.de/mpc>

[Psidev-pi-dev] New version 4.1.33 of psi-ms.obo

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

Dear proteomics/metabolomics community,

following are the new terms for the version 4.1.33 of the psi-ms.obo file,
which can be downloaded from
https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo

It contains new terms for spectral libraries and a term for the MS-DIAL 
software.

We also reorganized part of the CV, renamed some terms,
reactivated some obsolete terms and made some definitions more clear.


New CV terms in version 4.1.33 of psi-ms.obo:
=============================================
[Term]
id: MS:1003033
name: molecular entity attribute
def: "Non-inherent characteristic attributed to a molecular entity." 
[PSI:PI]
relationship: part_of MS:1000881 ! molecular entity

[Term]
id: MS:1003034
name: atom
def: "Smallest constituent unit of ordinary matter that constitutes a 
chemical element." [https://en.wikipedia.org/wiki/Atom]
is_a: MS:1000881 ! molecular entity

[Term]
id: MS:1003035
name: small molecule
def: "Low molecular weight (< 900 daltons) organic compound that may 
regulate a biological process." 
[https://en.wikipedia.org/wiki/Small_molecule]
is_a: MS:1000859 ! molecule

[Term]
id: MS:1003036
name: metabolite
def: "Small molecule that is the intermediate end product of 
metabolism." [https://en.wikipedia.org/wiki/Metabolite]
is_a: MS:1003035 ! small molecule

[Term]
id: MS:1003037
name: ribonucleotide
def: "Nucleotide containing ribose as its pentose component." 
[https://en.wikipedia.org/wiki/Ribonucleotide]
is_a: MS:1003035 ! small molecule

[Term]
id: MS:1003038
name: deoxyribonucleotide
def: "Monomer, or single unit, of DNA, or deoxyribonucleic acid." 
[https://en.wikipedia.org/wiki/Deoxyribonucleotide]
is_a: MS:1003035 ! small molecule

[Term]
id: MS:1003039
name: amino acid
def: "Organic molecule that contains amine (-NH2) and carboxyl (-COOH) 
functional groups, along with a side chain (R group) that is specific to 
each amino acid." [https://en.wikipedia.org/wiki/Amino_acid]
is_a: MS:1003035 ! small molecule

[Term]
id: MS:1003040
name: monosaccharide
def: "Simplest form of sugar and the most basic units of carbohydrate 
that cannot be further hydrolyzed to a simpler molecule." 
[https://en.wikipedia.org/wiki/Monosaccharide]
is_a: MS:1003035 ! small molecule

[Term]
id: MS:1003041
name: nucleic acid
def: "Molecule composed of a chain of nucleotides." 
[https://en.wikipedia.org/wiki/Nucleic_acid]
is_a: MS:1000859 ! molecule

[Term]
id: MS:1003042
name: polysaccharide
def: "Polymeric carbohydrate molecules composed of long chains of 
monosaccharide units bound together by glycosidic linkages." 
[https://en.wikipedia.org/wiki/Polysaccharide]
is_a: MS:1000859 ! molecule

[Term]
id: MS:1003043
name: number of residues
def: "Number of amino acid residues in a peptide, commonly referred to 
as the peptide length." [PSI:PI]
is_a: MS:1000887 ! peptide attribute

[Term]
id: MS:1003044
name: number of missed cleavages
def: "Number of amino acid residue bonds that should have been cleaved 
by the cleavage agent used, but were not." [PSI:PI]
is_a: MS:1000887 ! peptide attribute

[Term]
id: MS:1003045
name: peptide-to-protein mapping
def: "Process of mapping a peptide sequence to a protein sequence." [PSI:PI]
is_a: MS:1000887 ! peptide attribute

[Term]
id: MS:1003046
name: peptide-to-protein mapping attribute
def: "Nonphysical characteristic attributed to the result of 
peptide-to-protein mapping." [PSI:PI]
is_a: MS:1003045 ! peptide-to-protein mapping

[Term]
id: MS:1003047
name: protein sequence offset
def: "Offset in number of residues from the n terminus of the protein at 
which the peptide begins. Use 1 when the first residue of the peptide 
sequence is the first residue of the protein sequence." [PSI:PI]
is_a: MS:1003046 ! peptide-to-protein mapping attribute

[Term]
id: MS:1003048
name: number of enzymatic termini
def: "Total number of termini that match standard rules for the cleavage 
agent, 2 when both termini match cleavage agent rules, 1 when only one 
terminus does, and 0 if neither terminus matches cleavage agent rules." 
[PSI:PI]
is_a: MS:1003046 ! peptide-to-protein mapping attribute

[Term]
id: MS:1003049
name: peptidoform
def: "Peptide that contains zero or more mass modifications on the 
termini or side chains of its amino acid residues, and may be 
differentiated from other peptidoforms with the same peptide sequence 
but different mass modification configurations." [PSI:PI]
is_a: MS:1000860 ! peptide

[Term]
id: MS:1003050
name: peptidoform attribute
def: "Non-inherent characteristic attributed to a peptidoform." [PSI:PI]
relationship: part_of MS:1003049 ! peptidoform

[Term]
id: MS:1003051
name: peptidoform ion
def: "Peptidoform that has formed an adduct with an ion, thereby 
rendering it potentially detectable with a mass spectrometer. Commonly 
called a 'precursor' or 'precursor ion' or 'parent ion'." [PSI:PI]
is_a: MS:1003049 ! peptidoform
synonym: "precursor" RELATED []
synonym: "precursor ion" RELATED []
synonym: "parent ion" RELATED []

[Term]
id: MS:1003052
name: peptidoform ion property
def: "Inherent or measurable characteristic of a peptidoform ion." [PSI:PI]
relationship: part_of MS:1003051 ! peptidoform ion

[Term]
id: MS:1003053
name: theoretical monoisotopic m/z
def: "Mass-to-charge ratio of a peptidoform ion composed of the most 
common isotope of each atom computed from the putative knowledge of its 
molecular constituents." [PSI:PI]
is_a: MS:1003052 ! peptidoform ion property

[Term]
id: MS:1003054
name: theoretical average m/z
def: "Mass-to-charge ratio of a peptidoform ion computed from the 
putative knowledge of its molecular constituents, averaged over the 
distribution of naturally occurring isotopes." [PSI:PI]
is_a: MS:1003052 ! peptidoform ion property

[Term]
id: MS:1003055
name: adduct
def: "Product of a direct addition of two or more distinct molecules, 
resulting in a single reaction product containing all atoms of all 
components. The resultant is considered a distinct molecular species." 
[https://en.wikipedia.org/wiki/Adduct]
is_a: MS:1000859 ! molecule

[Term]
id: MS:1003056
name: adduct ion property
def: "Physical measurable characteristic of an adduct ion." [PSI:PI]
relationship: part_of MS:1000353 ! adduct ion

[Term]
id: MS:1003057
name: scan number
def: "Ordinal number of the scan indicating its order of acquisition 
within a mass spectrometry acquisition run." [PSI:PI]
is_a: MS:1000503 ! scan attribute

[Term]
id: MS:1003058
name: spectrum property
def: "Inherent or measurable characteristic of a spectrum." [PSI:PI]
relationship: part_of MS:1000442 ! spectrum

[Term]
id: MS:1003059
name: number of peaks
def: "Number of peaks or features in a spectrum. For a peak-picked 
spectrum, this will correspond to the number of data points. For a 
non-peak-picked spectrum, this corresponds to the number of features 
discernable in the spectrum, which will be fewer than the number of data 
points." [PSI:PI]
is_a: MS:1003058 ! spectrum property

[Term]
id: MS:1003060
name: number of data points
def: "Number of data points in a spectrum. For a peak-picked spectrum, 
this will correspond to the number of peaks. For a non-peak-picked 
spectrum, this corresponds to the number of values in the data array, 
which are not all peaks." [PSI:PI]
is_a: MS:1003058 ! spectrum property

[Term]
id: MS:1003061
name: spectrum name
def: "Label attached to a spectrum uniquely naming it within a 
collection of spectra, often in a spectral library. It is often a string 
combination of peptide sequence, charge, mass modifications, collision 
energy, but will obviously be different for small molecules or 
unidentified spectra. It must be unique within a collection." [PSI:PI]
is_a: MS:1000499 ! spectrum attribute

[Term]
id: MS:1003062
name: spectrum index
def: "Integer index value associated with a spectrum within a collection 
of spectra, often in a spectral library. By custom, index counters 
should begin with 0." [PSI:PI]
is_a: MS:1000499 ! spectrum attribute

[Term]
id: MS:1003063
name: universal spectrum identifier
def: "PSI universal spectrum identifier (USI) multipart key that 
uniquely identifies a spectrum available in a ProteomeXchange datasets 
or spectral library." [PSI:PI]
is_a: MS:1000499 ! spectrum attribute

[Term]
id: MS:1003064
name: spectrum aggregation attribute
def: "Non-inherent characteristic attributed to spectrum aggregation." 
[PSI:PI]
is_a: MS:1000499 ! spectrum attribute

[Term]
id: MS:1003065
name: spectrum aggregation type
def: "Categorization of a spectrum based on its type of aggregation 
(e.g., individual spectrum, consensus spectrum, best replicate spectrum, 
etc.)." [PSI:PI]
is_a: MS:1003064 ! spectrum aggregation attribute

[Term]
id: MS:1003066
name: singleton spectrum
def: "Spectrum that is not the result of some aggregation process." [PSI:PI]
is_a: MS:1003065 ! spectrum aggregation type

[Term]
id: MS:1003067
name: consensus spectrum
def: "Spectrum that is the result of merging several replicate spectra 
to form a spectrum that is more representative of its class and ideally 
less noisy that any of its source replicates." [PSI:PI]
is_a: MS:1003065 ! spectrum aggregation type

[Term]
id: MS:1003068
name: best replicate spectrum
def: "Spectrum that is considered the most representative from a pool of 
replicate spectra." [PSI:PI]
is_a: MS:1003065 ! spectrum aggregation type

[Term]
id: MS:1003069
name: number of replicate spectra available
def: "Number of replicate spectra available for use during the 
aggregation process." [PSI:PI]
is_a: MS:1003064 ! spectrum aggregation attribute

[Term]
id: MS:1003070
name: number of replicate spectra used
def: "Number of replicate spectra used during the aggregation process. 
This is generally applicable when there are many replicates available, 
but some are discarded as being low S/N, blended, or otherwise 
unsuitable, and the remaining set is then used for merging via a 
consensus algorithm." [PSI:PI]
is_a: MS:1003064 ! spectrum aggregation attribute

[Term]
id: MS:1003071
name: spectrum origin attribute
def: "Non-inherent characteristic attributed to spectrum aggregation." 
[PSI:PI]
is_a: MS:1000499 ! spectrum attribute

[Term]
id: MS:1003072
name: spectrum origin type
def: "Categorization of a spectrum based on its origin (e.g., observed 
spectrum, predicted spectrum, demultiplexed spectrum, etc.)." [PSI:PI]
is_a: MS:1003071 ! spectrum origin attribute

[Term]
id: MS:1003073
name: observed spectrum
def: "Spectrum that originates from an analysis attempt of a single 
analyte species on an instrument." [PSI:PI]
is_a: MS:1003072 ! spectrum origin type

[Term]
id: MS:1003074
name: predicted spectrum
def: "Spectrum that originates from a compututational algorithm that 
attempts to predict spectra." [PSI:PI]
is_a: MS:1003072 ! spectrum origin type

[Term]
id: MS:1003075
name: demultiplexed spectrum
def: "Spectrum that originates from an attempted extraction of a single 
ion spieces from a multiplexed spectrum that contains multiple ion 
species." [PSI:PI]
is_a: MS:1003072 ! spectrum origin type

[Term]
id: MS:1003076
name: uninterpreted spectrum
def: "Spectrum provided in the form of plain numerical values without 
any information pertaining to the interpretation of features." [PSI:PI]
is_a: MS:1000442 ! spectrum

[Term]
id: MS:1003077
name: interpreted spectrum
def: "Spectrum provided in a form where specific features of the 
spectrum are interpreted to provide putative explanations for some 
feature." [PSI:PI]
is_a: MS:1000442 ! spectrum

[Term]
id: MS:1003078
name: interpreted spectrum attribute
def: "Non-inherent characteristic attributed to an interpreted 
spectrum." [PSI:PI]
relationship: part_of MS:1003077 ! interpreted spectrum

[Term]
id: MS:1003079
name: total unassigned intensity fraction
def: "Fraction of intensity summed from all unassigned peaks divided by 
the intensity summed from all peaks in the spectrum." [PSI:PI]
is_a: MS:1003078 ! interpreted spectrum attribute

[Term]
id: MS:1003080
name: top 20 peak unassigned intensity fraction
def: "Fraction of intensity summed from unassigned peaks among the top 
20 divided by the intensity summed from all top 20 peaks in the 
spectrum." [PSI:PI]
is_a: MS:1003078 ! interpreted spectrum attribute

[Term]
id: MS:1003081
name: unidentified modification monoisotopic mass delta
def: "Monoisotopic mass delta in Daltons of an amino acid residue 
modification whose atomic composition or molecular identity has not been 
determined. This term should not be used for modifications of known 
molecular identity such as those available in Unimod, RESID or PSI-MOD. 
This term MUST NOT be used inside the <Modification> element in 
mzIdentML." [PSI:PI]
is_a: MS:1001471 ! peptide modification details
xref: value-type:xsd\:double "The allowed value-type for this CV term."
relationship: has_units UO:0000221 ! dalton

[Term]
id: MS:1003082
name: MS-DIAL
def: "Data processing software for untargeted metabolomics and 
lipidomics that supports multiple instruments and MS vendors." 
[PMID:25938372]
is_a: MS:1002878 ! small molecule software
is_a: MS:1001457 ! data processing software

Best Regards,
Gerhard

-- 

*----------------------------------------------------------------------*

*Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER*

*Research associate*

*Ruhr-Universität Bochum, Medizinisches Proteom-Center*

*DEPARTMENT Medical Bioinformatics*

*Building ProDi E2.234 | Gesundheitscampus 4 | D-44801 Bochum*

*Fon: *+49 (0)234 32-18110 | *Fax: *+49 (0)234 32-14496

*E-Mail: *ger...@ru... <mailto:ger...@ru...>

*Web: *www.ruhr-uni-bochum.de/mpc <http://www.ruhr-uni-bochum.de/mpc>

Re: [Psidev-pi-dev] [Psidev-ms-dev] Release candidate 4.1.33_rc1 of psi-ms.obo

[Eric D. <eri...@is...>]

Many thanks for putting this together, Gerhard. Here are some suggested
refinements or corrections:



[Term]

id: MS:1003065

name: spectrum aggregation type

def: "Categorization of a spectrum based on its type of aggregation (e.g.,
individual spectrum, consensus spectrum, best replicate spectrum, etc.)."
[PSI:PI]

is_a: MS:1003064 ! spectrum aggregation attribute



[Term]

id: MS:1003072

name: spectrum origin type

def: "Categorization of a spectrum based on its origin (e.g., observed
spectrum, predicted spectrum, demultiplexed spectrum, etc.)." [PSI-PI]

is_a: MS:1003071 ! spectrum origin attribute



[Term]

id: MS:1003033

name: molecular entity attribute

def: "Non-inherent characteristic attributed to a molecular entity."
[PSI:PI]

relationship: part_of MS:1000881 ! molecular entity



[Term]

id: MS:1003050

name: peptidoform attribute

def: "Non-inherent characteristic attributed to a peptidoform." [PSI:PI]

relationship: part_of MS:1003049 ! peptidoform





[Term]

id: MS:1003052

name: peptidoform ion property

def: "Inherent or measurable characteristic of a peptidoform ion." [PSI:PI]

relationship: part_of MS:1003051 ! peptidoform ion



[Term]

id: MS:1003058

name: spectrum property

def: " Inherent or measurable characteristic of a spectrum." [PSI:PI]

relationship: part_of MS:1000442 ! spectrum



[Term]

id: MS:1003064

name: spectrum aggregation attribute

def: "Non-inherent characteristic attributed to spectrum aggregation."
[PSI:PI]

is_a: MS:1000499 ! spectrum attribute



[Term]

id: MS:1003071

name: spectrum origin attribute

def: "Non-inherent characteristic attributed to spectrum aggregation."
[PSI:PI]

is_a: MS:1000499 ! spectrum attribute



[Term]

id: MS:1003078

name: interpreted spectrum attribute

def: "Non-inherent characteristic attributed to an interpreted spectrum."
[PSI:PI]

relationship: part_of MS:1003077 ! interpreted spectrum



[Term]

id: MS:1003082

name: MS-DIAL

def: "Data processing software for untargeted metabolomics and lipidomics
that supports multiple instruments and MS vendors." [PMID:25938372]

is_a: MS:1002878 ! small molecule software

is_a: MS:1001457 ! data processing software







*From:* Gerhard Mayer via Psidev-ms-dev <psi...@li...>

*Sent:* Thursday, January 16, 2020 12:10 AM
*To:* psi...@li...;
psi...@li...; psi...@li...
*Cc:* Gerhard Mayer <may...@ru...>
*Subject:* [Psidev-ms-dev] Release candidate 4.1.33_rc1 of psi-ms.obo



Dear proteomics/metabolomics community,

following are the new terms for the release version 4.1.33_rc1 of
the psi-ms.obo file.

It contains new terms for spectral libraries
and a term for the MS-DIAL software.

We also reorganized part of the CV, renamed some terms,
reactivated some obsolete terms and made some definitions more clear.
Please unpack and diff the two files to see the detailed changes.


New CV terms in version 4.1.33_rc1 of psi-ms.obo:
=================================================
[Term]
id: MS:1003033
name: molecular entity attribute
def: "A nonphysical characteristic attributed to a molecular entity."
[PSI:PI]
relationship: part_of MS:1000881 ! molecular entity

[Term]
id: MS:1003034
name: atom
def: "Smallest constituent unit of ordinary matter that constitutes a
chemical element." [https://en.wikipedia.org/wiki/Atom]
is_a: MS:1000881 ! molecular entity

[Term]
id: MS:1003035
name: small molecule
def: "Low molecular weight (< 900 daltons) organic compound that may
regulate a biological process." [
https://en.wikipedia.org/wiki/Small_molecule]
is_a: MS:1000859 ! molecule

[Term]
id: MS:1003036
name: metabolite
def: "Small molecule that is the intermediate end product of metabolism." [
https://en.wikipedia.org/wiki/Metabolite]
is_a: MS:1003035 ! small molecule

[Term]
id: MS:1003037
name: ribonucleotide
def: "Nucleotide containing ribose as its pentose component." [
https://en.wikipedia.org/wiki/Ribonucleotide]
is_a: MS:1003035 ! small molecule

[Term]
id: MS:1003038
name: deoxyribonucleotide
def: "Monomer, or single unit, of DNA, or deoxyribonucleic acid." [
https://en.wikipedia.org/wiki/Deoxyribonucleotide]
is_a: MS:1003035 ! small molecule

[Term]
id: MS:1003039
name: amino acid
def: "Organic molecule that contains amine (-NH2) and carboxyl (-COOH)
functional groups, along with a side chain (R group) that is specific to
each amino acid." [https://en.wikipedia.org/wiki/Amino_acid]
is_a: MS:1003035 ! small molecule

[Term]
id: MS:1003040
name: monosaccharide
def: "Simplest form of sugar and the most basic units of carbohydrate that
cannot be further hydrolyzed to a simpler molecule." [
https://en.wikipedia.org/wiki/Monosaccharide]
is_a: MS:1003035 ! small molecule

[Term]
id: MS:1003041
name: nucleic acid
def: "Molecule composed of a chain of nucleotides." [
https://en.wikipedia.org/wiki/Nucleic_acid]
is_a: MS:1000859 ! molecule

[Term]
id: MS:1003042
name: polysaccharide
def: "Polymeric carbohydrate molecules composed of long chains of
monosaccharide units bound together by glycosidic linkages." [
https://en.wikipedia.org/wiki/Polysaccharide]
is_a: MS:1000859 ! molecule

[Term]
id: MS:1003043
name: number of residues
def: "Number of amino acid residues in a peptide, commonly referred to as
the peptide length." [PSI:PI]
is_a: MS:1000887 ! peptide attribute

[Term]
id: MS:1003044
name: number of missed cleavages
def: "Number of amino acid residue bonds that should have been cleaved by
the cleavage agent used, but were not." [PSI:PI]
is_a: MS:1000887 ! peptide attribute

[Term]
id: MS:1003045
name: peptide-to-protein mapping
def: "Process of mapping a peptide sequence to a protein sequence." [PSI:PI]
is_a: MS:1000887 ! peptide attribute

[Term]
id: MS:1003046
name: peptide-to-protein mapping attribute
def: "Nonphysical characteristic attributed to the result of
peptide-to-protein mapping." [PSI:PI]
is_a: MS:1003045 ! peptide-to-protein mapping

[Term]
id: MS:1003047
name: protein sequence offset
def: "Offset in number of residues from the n terminus of the protein at
which the peptide begins. Use 1 when the first residue of the peptide
sequence is the first residue of the protein sequence." [PSI:PI]
is_a: MS:1003046 ! peptide-to-protein mapping attribute

[Term]
id: MS:1003048
name: number of enzymatic termini
def: "Total number of termini that match standard rules for the cleavage
agent, 2 when both termini match cleavage agent rules, 1 when only one
terminus does, and 0 if neither terminus matches cleavage agent rules."
[PSI:PI]
is_a: MS:1003046 ! peptide-to-protein mapping attribute

[Term]
id: MS:1003049
name: peptidoform
def: "Peptide that contains zero or more mass modifications on the termini
or side chains of its amino acid residues, and may be differentiated from
other peptidoforms with the same peptide sequence but different mass
modification configurations." [PSI:PI]
is_a: MS:1000860 ! peptide

[Term]
id: MS:1003050
name: peptidoform attribute
def: "Nonphysical characteristic attributed to a peptidoform." [PSI:PI]
relationship: part_of MS:1003049 ! peptidoform

[Term]
id: MS:1003051
name: peptidoform ion
def: "Peptidoform that has formed an adduct with an ion, thereby rendering
it potentially detectable with a mass spectrometer. Commonly called a
'precursor' or 'precursor ion' or 'parent ion'." [PSI:PI]
is_a: MS:1003049 ! peptidoform
synonym: "precursor" RELATED []
synonym: "precursor ion" RELATED []
synonym: "parent ion" RELATED []

[Term]
id: MS:1003052
name: peptidoform ion property
def: "A physical characteristic of a peptidoform ion." [PSI:PI]
relationship: part_of MS:1003051 ! peptidoform ion

[Term]
id: MS:1003053
name: theoretical monoisotopic m/z
def: "Mass-to-charge ratio of a peptidoform ion composed of the most common
isotope of each atom computed from the putative knowledge of its molecular
constituents." [PSI:PI]
is_a: MS:1003052 ! peptidoform ion property

[Term]
id: MS:1003054
name: theoretical average m/z
def: "Mass-to-charge ratio of a peptidoform ion computed from the putative
knowledge of its molecular constituents, averaged over the distribution of
naturally occurring isotopes." [PSI:PI]
is_a: MS:1003052 ! peptidoform ion property

[Term]
id: MS:1003055
name: adduct
def: "Product of a direct addition of two or more distinct molecules,
resulting in a single reaction product containing all atoms of all
components. The resultant is considered a distinct molecular species." [
https://en.wikipedia.org/wiki/Adduct]
is_a: MS:1000859 ! molecule

[Term]
id: MS:1003056
name: adduct ion property
def: "Physical measurable characteristic of an adduct ion." [PSI:PI]
relationship: part_of MS:1000353 ! adduct ion

[Term]
id: MS:1003057
name: scan number
def: "Ordinal number of the scan indicating its order of acquisition within
a mass spectrometry acquisition run." [PSI:PI]
is_a: MS:1000503 ! scan attribute

[Term]
id: MS:1003058
name: spectrum property
def: "Physical measurable characteristic of a spectrum." [PSI:PI]
relationship: part_of MS:1000442 ! spectrum

[Term]
id: MS:1003059
name: number of peaks
def: "Number of peaks or features in a spectrum. For a peak-picked
spectrum, this will correspond to the number of data points. For a
non-peak-picked spectrum, this corresponds to the number of features
discernable in the spectrum, which will be fewer than the number of data
points." [PSI:PI]
is_a: MS:1003058 ! spectrum property

[Term]
id: MS:1003060
name: number of data points
def: "Number of data points in a spectrum. For a peak-picked spectrum, this
will correspond to the number of peaks. For a non-peak-picked spectrum,
this corresponds to the number of values in the data array, which are not
all peaks." [PSI:PI]
is_a: MS:1003058 ! spectrum property

[Term]
id: MS:1003061
name: spectrum name
def: "Label attached to a spectrum uniquely naming it within a collection
of spectra, often in a spectral library. It is often a string combination
of peptide sequence, charge, mass modifications, collision energy, but will
obviously be different for small molecules or unidentified spectra. It must
be unique within a collection." [PSI:PI]
is_a: MS:1000499 ! spectrum attribute

[Term]
id: MS:1003062
name: spectrum index
def: "Integer index value associated with a spectrum within a collection of
spectra, often in a spectral library. By custom, index counters should
begin with 0." [PSI:PI]
is_a: MS:1000499 ! spectrum attribute

[Term]
id: MS:1003063
name: universal spectrum identifier
def: "PSI universal spectrum identifier (USI) multipart key that uniquely
identifies a spectrum available in a ProteomeXchange datasets or spectral
library." [PSI:PI]
is_a: MS:1000499 ! spectrum attribute

[Term]
id: MS:1003064
name: spectrum aggregation attribute
def: "Nonphysical characteristic attributed to spectrum aggregation."
[PSI:PI]
is_a: MS:1000499 ! spectrum attribute

[Term]
id: MS:1003065
name: spectrum aggregation type
def: "Categorization of a spectrum based on the type of aggregation it is
based on (e.g., an individual spectrum, a consensus spectrum, best
replicate spectrum, etc.)." [PSI:PI]
is_a: MS:1003064 ! spectrum aggregation attribute

[Term]
id: MS:1003066
name: singleton spectrum
def: "Spectrum that is not the result of some aggregation process." [PSI:PI]
is_a: MS:1003065 ! spectrum aggregation type

[Term]
id: MS:1003067
name: consensus spectrum
def: "Spectrum that is the result of merging several replicate spectra to
form a spectrum that is more representative of its class and ideally less
noisy that any of its source replicates." [PSI:PI]
is_a: MS:1003065 ! spectrum aggregation type

[Term]
id: MS:1003068
name: best replicate spectrum
def: "Spectrum that is considered the most representative from a pool of
replicate spectra." [PSI:PI]
is_a: MS:1003065 ! spectrum aggregation type

[Term]
id: MS:1003069
name: number of replicate spectra available
def: "Number of replicate spectra available for use during the aggregation
process." [PSI:PI]
is_a: MS:1003064 ! spectrum aggregation attribute

[Term]
id: MS:1003070
name: number of replicate spectra used
def: "Number of replicate spectra used during the aggregation process. This
is generally applicable when there are many replicates available, but some
are discarded as being low S/N, blended, or otherwise unsuitable, and the
remaining set is then used for merging via a consensus algorithm." [PSI:PI]
is_a: MS:1003064 ! spectrum aggregation attribute

[Term]
id: MS:1003071
name: spectrum origin attribute
def: "Nonphysical characteristic attributed to spectrum aggregation."
[PSI:PI]
is_a: MS:1000499 ! spectrum attribute

[Term]
id: MS:1003072
name: spectrum origin type
def: "Categorization of a spectrum based on its type of aggregation (e.g.,
an individual spectrum, a consensus spectrum, best replicate spectrum,
etc.)." [PSI:PI]
is_a: MS:1003071 ! spectrum origin attribute

[Term]
id: MS:1003073
name: observed spectrum
def: "Spectrum that originates from an analysis attempt of a single analyte
species on an instrument." [PSI:PI]
is_a: MS:1003072 ! spectrum origin type

[Term]
id: MS:1003074
name: predicted spectrum
def: "Spectrum that originates from a compututational algorithm that
attempts to predict spectra." [PSI:PI]
is_a: MS:1003072 ! spectrum origin type

[Term]
id: MS:1003075
name: demultiplexed spectrum
def: "Spectrum that originates from an attempted extraction of a single ion
spieces from a multiplexed spectrum that contains multiple ion species."
[PSI:PI]
is_a: MS:1003072 ! spectrum origin type

[Term]
id: MS:1003076
name: uninterpreted spectrum
def: "Spectrum provided in the form of plain numerical values without any
information pertaining to the interpretation of features." [PSI:PI]
is_a: MS:1000442 ! spectrum

[Term]
id: MS:1003077
name: interpreted spectrum
def: "Spectrum provided in a form where specific features of the spectrum
are interpreted to provide putative explanations for some feature." [PSI:PI]
is_a: MS:1000442 ! spectrum

[Term]
id: MS:1003078
name: interpreted spectrum attribute
def: "Nonphysical characteristic attributed to an interpreted spectrum."
[PSI:PI]
relationship: part_of MS:1003077 ! interpreted spectrum

[Term]
id: MS:1003079
name: total unassigned intensity fraction
def: "Fraction of intensity summed from all unassigned peaks divided by the
intensity summed from all peaks in the spectrum." [PSI:PI]
is_a: MS:1003078 ! interpreted spectrum attribute

[Term]
id: MS:1003080
name: top 20 peak unassigned intensity fraction
def: "Fraction of intensity summed from unassigned peaks among the top 20
divided by the intensity summed from all top 20 peaks in the spectrum."
[PSI:PI]
is_a: MS:1003078 ! interpreted spectrum attribute

[Term]
id: MS:1003081
name: unidentified modification monoisotopic mass delta
def: "Monoisotopic mass delta in Daltons of an amino acid residue
modification whose atomic composition or molecular identity has not been
determined. This term should not be used for modifications of known
molecular identity such as those available in Unimod, RESID or PSI-MOD.
This term MUST NOT be used inside the <Modification> element in mzIdentML."
[PSI:PI]
is_a: MS:1001471 ! peptide modification details
xref: value-type:xsd\:double "The allowed value-type for this CV term."
relationship: has_units UO:0000221 ! dalton

[Term]
id: MS:1003082
name: MS-DIAL
def: "MS-DIAL is a universal program for untargeted metabolomics and
lipidomics that supports multiple instruments and MS vendors."
[PMID:25938372]
is_a: MS:1002878 ! small molecule software
is_a: MS:1001457 ! data processing software

Best Regards,
Gerhard

-- 

*----------------------------------------------------------------------*

*Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER*

*Research associate*

*Ruhr-Universität Bochum, Medizinisches Proteom-Center*

*DEPARTMENT Medical Bioinformatics*

*Building ProDi E2.234 | Gesundheitscampus 4 | D-44801 Bochum*

*Fon: *+49 (0)234 32-18110 | *Fax: *+49 (0)234 32-14496

*E-Mail: *ger...@ru...

*Web: *www.ruhr-uni-bochum.de/mpc

[Psidev-pi-dev] Release candidate 4.1.33_rc1 of psi-ms.obo

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

Dear proteomics/metabolomics community,

following are the new terms for the release version 4.1.33_rc1 of
the psi-ms.obo file.

It contains new terms for spectral libraries
and a term for the MS-DIAL software.

We also reorganized part of the CV, renamed some terms,
reactivated some obsolete terms and made some definitions more clear.
Please unpack and diff the two files to see the detailed changes.


New CV terms in version 4.1.33_rc1 of psi-ms.obo:
=================================================
[Term]
id: MS:1003033
name: molecular entity attribute
def: "A nonphysical characteristic attributed to a molecular entity." 
[PSI:PI]
relationship: part_of MS:1000881 ! molecular entity

[Term]
id: MS:1003034
name: atom
def: "Smallest constituent unit of ordinary matter that constitutes a 
chemical element." [https://en.wikipedia.org/wiki/Atom]
is_a: MS:1000881 ! molecular entity

[Term]
id: MS:1003035
name: small molecule
def: "Low molecular weight (< 900 daltons) organic compound that may 
regulate a biological process." 
[https://en.wikipedia.org/wiki/Small_molecule]
is_a: MS:1000859 ! molecule

[Term]
id: MS:1003036
name: metabolite
def: "Small molecule that is the intermediate end product of 
metabolism." [https://en.wikipedia.org/wiki/Metabolite]
is_a: MS:1003035 ! small molecule

[Term]
id: MS:1003037
name: ribonucleotide
def: "Nucleotide containing ribose as its pentose component." 
[https://en.wikipedia.org/wiki/Ribonucleotide]
is_a: MS:1003035 ! small molecule

[Term]
id: MS:1003038
name: deoxyribonucleotide
def: "Monomer, or single unit, of DNA, or deoxyribonucleic acid." 
[https://en.wikipedia.org/wiki/Deoxyribonucleotide]
is_a: MS:1003035 ! small molecule

[Term]
id: MS:1003039
name: amino acid
def: "Organic molecule that contains amine (-NH2) and carboxyl (-COOH) 
functional groups, along with a side chain (R group) that is specific to 
each amino acid." [https://en.wikipedia.org/wiki/Amino_acid]
is_a: MS:1003035 ! small molecule

[Term]
id: MS:1003040
name: monosaccharide
def: "Simplest form of sugar and the most basic units of carbohydrate 
that cannot be further hydrolyzed to a simpler molecule." 
[https://en.wikipedia.org/wiki/Monosaccharide]
is_a: MS:1003035 ! small molecule

[Term]
id: MS:1003041
name: nucleic acid
def: "Molecule composed of a chain of nucleotides." 
[https://en.wikipedia.org/wiki/Nucleic_acid]
is_a: MS:1000859 ! molecule

[Term]
id: MS:1003042
name: polysaccharide
def: "Polymeric carbohydrate molecules composed of long chains of 
monosaccharide units bound together by glycosidic linkages." 
[https://en.wikipedia.org/wiki/Polysaccharide]
is_a: MS:1000859 ! molecule

[Term]
id: MS:1003043
name: number of residues
def: "Number of amino acid residues in a peptide, commonly referred to 
as the peptide length." [PSI:PI]
is_a: MS:1000887 ! peptide attribute

[Term]
id: MS:1003044
name: number of missed cleavages
def: "Number of amino acid residue bonds that should have been cleaved 
by the cleavage agent used, but were not." [PSI:PI]
is_a: MS:1000887 ! peptide attribute

[Term]
id: MS:1003045
name: peptide-to-protein mapping
def: "Process of mapping a peptide sequence to a protein sequence." [PSI:PI]
is_a: MS:1000887 ! peptide attribute

[Term]
id: MS:1003046
name: peptide-to-protein mapping attribute
def: "Nonphysical characteristic attributed to the result of 
peptide-to-protein mapping." [PSI:PI]
is_a: MS:1003045 ! peptide-to-protein mapping

[Term]
id: MS:1003047
name: protein sequence offset
def: "Offset in number of residues from the n terminus of the protein at 
which the peptide begins. Use 1 when the first residue of the peptide 
sequence is the first residue of the protein sequence." [PSI:PI]
is_a: MS:1003046 ! peptide-to-protein mapping attribute

[Term]
id: MS:1003048
name: number of enzymatic termini
def: "Total number of termini that match standard rules for the cleavage 
agent, 2 when both termini match cleavage agent rules, 1 when only one 
terminus does, and 0 if neither terminus matches cleavage agent rules." 
[PSI:PI]
is_a: MS:1003046 ! peptide-to-protein mapping attribute

[Term]
id: MS:1003049
name: peptidoform
def: "Peptide that contains zero or more mass modifications on the 
termini or side chains of its amino acid residues, and may be 
differentiated from other peptidoforms with the same peptide sequence 
but different mass modification configurations." [PSI:PI]
is_a: MS:1000860 ! peptide

[Term]
id: MS:1003050
name: peptidoform attribute
def: "Nonphysical characteristic attributed to a peptidoform." [PSI:PI]
relationship: part_of MS:1003049 ! peptidoform

[Term]
id: MS:1003051
name: peptidoform ion
def: "Peptidoform that has formed an adduct with an ion, thereby 
rendering it potentially detectable with a mass spectrometer. Commonly 
called a 'precursor' or 'precursor ion' or 'parent ion'." [PSI:PI]
is_a: MS:1003049 ! peptidoform
synonym: "precursor" RELATED []
synonym: "precursor ion" RELATED []
synonym: "parent ion" RELATED []

[Term]
id: MS:1003052
name: peptidoform ion property
def: "A physical characteristic of a peptidoform ion." [PSI:PI]
relationship: part_of MS:1003051 ! peptidoform ion

[Term]
id: MS:1003053
name: theoretical monoisotopic m/z
def: "Mass-to-charge ratio of a peptidoform ion composed of the most 
common isotope of each atom computed from the putative knowledge of its 
molecular constituents." [PSI:PI]
is_a: MS:1003052 ! peptidoform ion property

[Term]
id: MS:1003054
name: theoretical average m/z
def: "Mass-to-charge ratio of a peptidoform ion computed from the 
putative knowledge of its molecular constituents, averaged over the 
distribution of naturally occurring isotopes." [PSI:PI]
is_a: MS:1003052 ! peptidoform ion property

[Term]
id: MS:1003055
name: adduct
def: "Product of a direct addition of two or more distinct molecules, 
resulting in a single reaction product containing all atoms of all 
components. The resultant is considered a distinct molecular species." 
[https://en.wikipedia.org/wiki/Adduct]
is_a: MS:1000859 ! molecule

[Term]
id: MS:1003056
name: adduct ion property
def: "Physical measurable characteristic of an adduct ion." [PSI:PI]
relationship: part_of MS:1000353 ! adduct ion

[Term]
id: MS:1003057
name: scan number
def: "Ordinal number of the scan indicating its order of acquisition 
within a mass spectrometry acquisition run." [PSI:PI]
is_a: MS:1000503 ! scan attribute

[Term]
id: MS:1003058
name: spectrum property
def: "Physical measurable characteristic of a spectrum." [PSI:PI]
relationship: part_of MS:1000442 ! spectrum

[Term]
id: MS:1003059
name: number of peaks
def: "Number of peaks or features in a spectrum. For a peak-picked 
spectrum, this will correspond to the number of data points. For a 
non-peak-picked spectrum, this corresponds to the number of features 
discernable in the spectrum, which will be fewer than the number of data 
points." [PSI:PI]
is_a: MS:1003058 ! spectrum property

[Term]
id: MS:1003060
name: number of data points
def: "Number of data points in a spectrum. For a peak-picked spectrum, 
this will correspond to the number of peaks. For a non-peak-picked 
spectrum, this corresponds to the number of values in the data array, 
which are not all peaks." [PSI:PI]
is_a: MS:1003058 ! spectrum property

[Term]
id: MS:1003061
name: spectrum name
def: "Label attached to a spectrum uniquely naming it within a 
collection of spectra, often in a spectral library. It is often a string 
combination of peptide sequence, charge, mass modifications, collision 
energy, but will obviously be different for small molecules or 
unidentified spectra. It must be unique within a collection." [PSI:PI]
is_a: MS:1000499 ! spectrum attribute

[Term]
id: MS:1003062
name: spectrum index
def: "Integer index value associated with a spectrum within a collection 
of spectra, often in a spectral library. By custom, index counters 
should begin with 0." [PSI:PI]
is_a: MS:1000499 ! spectrum attribute

[Term]
id: MS:1003063
name: universal spectrum identifier
def: "PSI universal spectrum identifier (USI) multipart key that 
uniquely identifies a spectrum available in a ProteomeXchange datasets 
or spectral library." [PSI:PI]
is_a: MS:1000499 ! spectrum attribute

[Term]
id: MS:1003064
name: spectrum aggregation attribute
def: "Nonphysical characteristic attributed to spectrum aggregation." 
[PSI:PI]
is_a: MS:1000499 ! spectrum attribute

[Term]
id: MS:1003065
name: spectrum aggregation type
def: "Categorization of a spectrum based on the type of aggregation it 
is based on (e.g., an individual spectrum, a consensus spectrum, best 
replicate spectrum, etc.)." [PSI:PI]
is_a: MS:1003064 ! spectrum aggregation attribute

[Term]
id: MS:1003066
name: singleton spectrum
def: "Spectrum that is not the result of some aggregation process." [PSI:PI]
is_a: MS:1003065 ! spectrum aggregation type

[Term]
id: MS:1003067
name: consensus spectrum
def: "Spectrum that is the result of merging several replicate spectra 
to form a spectrum that is more representative of its class and ideally 
less noisy that any of its source replicates." [PSI:PI]
is_a: MS:1003065 ! spectrum aggregation type

[Term]
id: MS:1003068
name: best replicate spectrum
def: "Spectrum that is considered the most representative from a pool of 
replicate spectra." [PSI:PI]
is_a: MS:1003065 ! spectrum aggregation type

[Term]
id: MS:1003069
name: number of replicate spectra available
def: "Number of replicate spectra available for use during the 
aggregation process." [PSI:PI]
is_a: MS:1003064 ! spectrum aggregation attribute

[Term]
id: MS:1003070
name: number of replicate spectra used
def: "Number of replicate spectra used during the aggregation process. 
This is generally applicable when there are many replicates available, 
but some are discarded as being low S/N, blended, or otherwise 
unsuitable, and the remaining set is then used for merging via a 
consensus algorithm." [PSI:PI]
is_a: MS:1003064 ! spectrum aggregation attribute

[Term]
id: MS:1003071
name: spectrum origin attribute
def: "Nonphysical characteristic attributed to spectrum aggregation." 
[PSI:PI]
is_a: MS:1000499 ! spectrum attribute

[Term]
id: MS:1003072
name: spectrum origin type
def: "Categorization of a spectrum based on its type of aggregation 
(e.g., an individual spectrum, a consensus spectrum, best replicate 
spectrum, etc.)." [PSI:PI]
is_a: MS:1003071 ! spectrum origin attribute

[Term]
id: MS:1003073
name: observed spectrum
def: "Spectrum that originates from an analysis attempt of a single 
analyte species on an instrument." [PSI:PI]
is_a: MS:1003072 ! spectrum origin type

[Term]
id: MS:1003074
name: predicted spectrum
def: "Spectrum that originates from a compututational algorithm that 
attempts to predict spectra." [PSI:PI]
is_a: MS:1003072 ! spectrum origin type

[Term]
id: MS:1003075
name: demultiplexed spectrum
def: "Spectrum that originates from an attempted extraction of a single 
ion spieces from a multiplexed spectrum that contains multiple ion 
species." [PSI:PI]
is_a: MS:1003072 ! spectrum origin type

[Term]
id: MS:1003076
name: uninterpreted spectrum
def: "Spectrum provided in the form of plain numerical values without 
any information pertaining to the interpretation of features." [PSI:PI]
is_a: MS:1000442 ! spectrum

[Term]
id: MS:1003077
name: interpreted spectrum
def: "Spectrum provided in a form where specific features of the 
spectrum are interpreted to provide putative explanations for some 
feature." [PSI:PI]
is_a: MS:1000442 ! spectrum

[Term]
id: MS:1003078
name: interpreted spectrum attribute
def: "Nonphysical characteristic attributed to an interpreted spectrum." 
[PSI:PI]
relationship: part_of MS:1003077 ! interpreted spectrum

[Term]
id: MS:1003079
name: total unassigned intensity fraction
def: "Fraction of intensity summed from all unassigned peaks divided by 
the intensity summed from all peaks in the spectrum." [PSI:PI]
is_a: MS:1003078 ! interpreted spectrum attribute

[Term]
id: MS:1003080
name: top 20 peak unassigned intensity fraction
def: "Fraction of intensity summed from unassigned peaks among the top 
20 divided by the intensity summed from all top 20 peaks in the 
spectrum." [PSI:PI]
is_a: MS:1003078 ! interpreted spectrum attribute

[Term]
id: MS:1003081
name: unidentified modification monoisotopic mass delta
def: "Monoisotopic mass delta in Daltons of an amino acid residue 
modification whose atomic composition or molecular identity has not been 
determined. This term should not be used for modifications of known 
molecular identity such as those available in Unimod, RESID or PSI-MOD. 
This term MUST NOT be used inside the <Modification> element in 
mzIdentML." [PSI:PI]
is_a: MS:1001471 ! peptide modification details
xref: value-type:xsd\:double "The allowed value-type for this CV term."
relationship: has_units UO:0000221 ! dalton

[Term]
id: MS:1003082
name: MS-DIAL
def: "MS-DIAL is a universal program for untargeted metabolomics and 
lipidomics that supports multiple instruments and MS vendors." 
[PMID:25938372]
is_a: MS:1002878 ! small molecule software
is_a: MS:1001457 ! data processing software

Best Regards,
Gerhard

-- 

*----------------------------------------------------------------------*

*Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER*

*Research associate*

*Ruhr-Universität Bochum, Medizinisches Proteom-Center*

*DEPARTMENT Medical Bioinformatics*

*Building ProDi E2.234 | Gesundheitscampus 4 | D-44801 Bochum*

*Fon: *+49 (0)234 32-18110 | *Fax: *+49 (0)234 32-14496

*E-Mail: *ger...@ru... <mailto:ger...@ru...>

*Web: *www.ruhr-uni-bochum.de/mpc <http://www.ruhr-uni-bochum.de/mpc>

[Psidev-pi-dev] PSI202 Registration open

[Jones, A. <And...@li...>]

Dear all,
We are pleased to announce that the 2020 Annual workshop for the Proteomics Standards Initiative (PSI) will take place in San Diego USA, Mon 23rd to Thurs 26th March 2020, and registration is now open: http://www.psidev.info/hupo-psi-meeting-2020
There is no cost to attend the workshop, with lunches, coffee/tea and a workshop dinner included. You will have to cover your own costs for travel and hotels.
The workshop will focus on developing data standards related to mass spectrometry for spectral libraries, the Universal Spectrum Identifier, quality control and capturing study metadata, and on the molecular interactions side on mapping standards to Cytoscape.
We will be welcoming the new PSI work group - Intrinsically Disordered Proteins (IDP). We are also planning a new session related to standards for glycoproteomics, to scope out the community need in this area.
The PSI is always keen to recruit new members, so please join if you think you may be interested in data sharing and standards for proteomics. Please also get in touch, if you are interested to join PSI activities in general but cannot travel to San Diego.
Best wishes
Andy Jones (PSI Chair)

Re: [Psidev-pi-dev] [CompMS] Re: [Psi-announce] PSI2020 - Save the Date

[Zaia, J. <jz...@bu...>]

I have been in touch with Nathan Edwards (Georgetown University, copied).  He expressed interest in attending the session to discuss supporting glycoproteomics data.

Best regards,

Joe

From: Eric Deutsch <eri...@is...>
Sent: Tuesday, November 26, 2019 7:40 PM
To: Robert Chalkley <cha...@cg...>; Zaia, Joseph <jz...@bu...>; Jones, Andy <And...@li...>; psi...@eb...; ps...@eb...; Mass spectrometry standard development <psi...@li...>; psi...@li...; Co...@go...
Subject: Re: [Psidev-pi-dev] [CompMS] Re: [Psi-announce] PSI2020 - Save the Date

Hi Robert, great, thanks for contributing! We will try to schedule a specific session for this and announce it so that everyone knows when it is in advance.

Thanks,
Eric


From: co...@go...<mailto:co...@go...> <co...@go...<mailto:co...@go...>> On Behalf Of Robert Chalkley
Sent: Monday, November 25, 2019 9:01 AM
To: Zaia, Joseph <jz...@bu...<mailto:jz...@bu...>>; Jones, Andy <And...@li...<mailto:And...@li...>>; psi...@eb...<mailto:psi...@eb...>; ps...@eb...<mailto:ps...@eb...>; Mass spectrometry standard development <psi...@li...<mailto:psi...@li...>>; psi...@li...<mailto:psi...@li...>; Co...@go...<mailto:Co...@go...>
Subject: [CompMS] Re: [Psi-announce] [Psidev-pi-dev] PSI2020 - Save the Date


I would also be keen to be involved in discussions about supporting glycopeptide data.

Robert
On 11/22/2019 11:21 AM, Zaia, Joseph wrote:
Dear All,

I would like to initiate discussion for expanding the use cases for proteomics to include complex protein glycosylation.  Glycosylation is as a rule heterogeneous, with 30 or so glycoforms per glycosite.  In addition, the glycan dissociates during tandem MS experiments.  The software and data standards need to be expanded to include the glycosylation size, heterogeneity, and tandem MS dissociation.  At present, quantitative software (Skyline and others) do not recognize glycosylation.  Without this recognition the quantitative tools developed for peptides cannot be adapted without tedious effort on the part of the user.  Therefore, there is need to expand the manner by which peptides are represented informatically.  It is important that glycopeptides be included in the use cases for mzIdentML and mzQuant.  It is also important that spectral library generating software be expanded to allow glycosylated peptides to facilitate use of data independent experiments for glycoproteins.

Would it be possible for me to communicate these ideas at the PSI Workshop in San Diego?

Thank you.

Joe Zaia
From: Jones, Andy <And...@li...><mailto:And...@li...>
Sent: Thursday, November 21, 2019 11:29 AM
To: psi...@eb...<mailto:psi...@eb...>; ps...@eb...<mailto:ps...@eb...>; Mass spectrometry standard development <psi...@li...><mailto:psi...@li...>; psi...@li...<mailto:psi...@li...>; Co...@go...<mailto:Co...@go...>
Subject: [Psidev-pi-dev] PSI2020 - Save the Date

Hi all,

We are pleased to announce that the 2020 Annual workshop for the Proteomics Standards Initiative (PSI) will take place in San Diego USA, Mon 23rd to Thurs 26th March 2020. The workshop will focus on developing data standards related to mass spectrometry for spectral libraries, the universal spectrum identifier, quality control and capturing study metadata, and in the molecular interactions side on mapping standards to Cytoscape. We will also be welcoming the new PSI work group – Intrinsically Disordered Proteins (IDP).

Please save the date if you might be interested to attend, we are always pleased to welcome new groups into the PSI. The registration page will be made available in the coming weeks.

Best wishes
Andy Jones on behalf of the PSI steering committee



_______________________________________________

Psi-announce mailing list

Psi...@eb...<mailto:Psi...@eb...>

https://listserver.ebi.ac.uk/mailman/listinfo/psi-announce

--

Robert Chalkley PhD

Adjunct Professor

Genentech Hall, N474A

Tel: 415 476 5189

Fax: 415 502 1655



Mass Spectrometry Facility

University of California San Francisco

600 16th Street,

Genentech Hall, suite N472A

San Francisco, CA 94143-2240






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Re: [Psidev-pi-dev] [CompMS] Re: [Psi-announce] PSI2020 - Save the Date

[Eric D. <eri...@is...>]

Hi Robert, great, thanks for contributing! We will try to schedule a
specific session for this and announce it so that everyone knows when it is
in advance.



Thanks,

Eric





*From:* co...@go... <co...@go...> *On Behalf Of *Robert
Chalkley
*Sent:* Monday, November 25, 2019 9:01 AM
*To:* Zaia, Joseph <jz...@bu...>; Jones, Andy <And...@li...>;
psi...@eb...; ps...@eb...; Mass spectrometry standard
development <psi...@li...>;
psi...@li...; Co...@go...
*Subject:* [CompMS] Re: [Psi-announce] [Psidev-pi-dev] PSI2020 - Save the
Date



I would also be keen to be involved in discussions about supporting
glycopeptide data.

Robert

On 11/22/2019 11:21 AM, Zaia, Joseph wrote:

Dear All,



I would like to initiate discussion for expanding the use cases for
proteomics to include complex protein glycosylation.  Glycosylation is as a
rule heterogeneous, with 30 or so glycoforms per glycosite.  In addition,
the glycan dissociates during tandem MS experiments.  The software and data
standards need to be expanded to include the glycosylation size,
heterogeneity, and tandem MS dissociation.  At present, quantitative
software (Skyline and others) do not recognize glycosylation.  Without this
recognition the quantitative tools developed for peptides cannot be adapted
without tedious effort on the part of the user.  Therefore, there is need
to expand the manner by which peptides are represented informatically.  It
is important that glycopeptides be included in the use cases for mzIdentML
and mzQuant.  It is also important that spectral library generating
software be expanded to allow glycosylated peptides to facilitate use of
data independent experiments for glycoproteins.



Would it be possible for me to communicate these ideas at the PSI Workshop
in San Diego?



Thank you.



Joe Zaia

*From:* Jones, Andy <And...@li...>
<And...@li...>
*Sent:* Thursday, November 21, 2019 11:29 AM
*To:* psi...@eb...; ps...@eb...; Mass spectrometry standard
development <psi...@li...>
<psi...@li...>; psi...@li...;
Co...@go...
*Subject:* [Psidev-pi-dev] PSI2020 - Save the Date



Hi all,



We are pleased to announce that the 2020 Annual workshop for the Proteomics
Standards Initiative (PSI) will take place in San Diego USA, Mon 23rd to
Thurs 26th March 2020. The workshop will focus on developing data standards
related to mass spectrometry for spectral libraries, the universal spectrum
identifier, quality control and capturing study metadata, and in the
molecular interactions side on mapping standards to Cytoscape. We will also
be welcoming the new PSI work group – Intrinsically Disordered Proteins
(IDP).



Please save the date if you might be interested to attend, we are always
pleased to welcome new groups into the PSI. The registration page will be
made available in the coming weeks.



Best wishes

Andy Jones on behalf of the PSI steering committee





_______________________________________________

Psi-announce mailing list

Psi...@eb...

https://listserver.ebi.ac.uk/mailman/listinfo/psi-announce

-- 

Robert Chalkley PhD

Adjunct Professor

Genentech Hall, N474A

Tel: 415 476 5189

Fax: 415 502 1655



Mass Spectrometry Facility

University of California San Francisco

600 16th Street,

Genentech Hall, suite N472A

San Francisco, CA 94143-2240







-- 
You received this message because you are subscribed to the Google Groups
"CompMS" group.
To unsubscribe from this group and stop receiving emails from it, send an
email to com...@go....
To view this discussion on the web visit
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<https://groups.google.com/d/msgid/compms/53fa5771-c50a-6f0d-5d17-de723112a016%40cgl.ucsf.edu?utm_medium=email&utm_source=footer>
.

Re: [Psidev-pi-dev] [Psi-announce] PSI2020 - Save the Date

[Robert C. <cha...@cg...>]

I would also be keen to be involved in discussions about supporting 
glycopeptide data.

Robert

On 11/22/2019 11:21 AM, Zaia, Joseph wrote:
>
> Dear All,
>
> I would like to initiate discussion for expanding the use cases for 
> proteomics to include complex protein glycosylation. Glycosylation is 
> as a rule heterogeneous, with 30 or so glycoforms per glycosite.  In 
> addition, the glycan dissociates during tandem MS experiments.  The 
> software and data standards need to be expanded to include the 
> glycosylation size, heterogeneity, and tandem MS dissociation.  At 
> present, quantitative software (Skyline and others) do not recognize 
> glycosylation.  Without this recognition the quantitative tools 
> developed for peptides cannot be adapted without tedious effort on the 
> part of the user.  Therefore, there is need to expand the manner by 
> which peptides are represented informatically.  It is important that 
> glycopeptides be included in the use cases for mzIdentML and mzQuant.  
> It is also important that spectral library generating software be 
> expanded to allow glycosylated peptides to facilitate use of data 
> independent experiments for glycoproteins.
>
> Would it be possible for me to communicate these ideas at the PSI 
> Workshop in San Diego?
>
> Thank you.
>
> Joe Zaia
>
> *From:* Jones, Andy <And...@li...>
> *Sent:* Thursday, November 21, 2019 11:29 AM
> *To:* psi...@eb...; ps...@eb...; Mass spectrometry 
> standard development <psi...@li...>; 
> psi...@li...; Co...@go...
> *Subject:* [Psidev-pi-dev] PSI2020 - Save the Date
>
> Hi all,
>
> We are pleased to announce that the 2020 Annual workshop for the 
> Proteomics Standards Initiative (PSI) will take place in San Diego 
> USA, Mon 23^rd to Thurs 26^th March 2020. The workshop will focus on 
> developing data standards related to mass spectrometry for spectral 
> libraries, the universal spectrum identifier, quality control and 
> capturing study metadata, and in the molecular interactions side on 
> mapping standards to Cytoscape. We will also be welcoming the new PSI 
> work group – Intrinsically Disordered Proteins (IDP).
>
> Please save the date if you might be interested to attend, we are 
> always pleased to welcome new groups into the PSI. The registration 
> page will be made available in the coming weeks.
>
> Best wishes
>
> Andy Jones on behalf of the PSI steering committee
>
>
> _______________________________________________
> Psi-announce mailing list
> Psi...@eb...
> https://listserver.ebi.ac.uk/mailman/listinfo/psi-announce

-- 
Robert Chalkley PhD
Adjunct Professor
Genentech Hall, N474A
Tel: 415 476 5189
Fax: 415 502 1655

Mass Spectrometry Facility
University of California San Francisco
600 16th Street,
Genentech Hall, suite N472A
San Francisco, CA 94143-2240

Re: [Psidev-pi-dev] [CompMS] PSI2020 - Save the Date

[Zaia, J. <jz...@bu...>]

Thanks, Juan. I look forward to attending the spring HUPO-PSI meeting.

Joe

From: Juan Antonio Vizcaino <ju...@eb...>
Sent: Monday, November 25, 2019 8:04 AM
To: Zaia, Joseph <jz...@bu...>
Cc: Andy Jones <And...@li...>; psi...@eb...; ps...@eb...; Mass spectrometry standard development <psi...@li...>; psi...@li...; Co...@go...
Subject: Re: [CompMS] [Psidev-pi-dev] PSI2020 - Save the Date

Dear Joe,

Thanks for your e-mail.

You are very welcome to present in San Diego. We are still discussing the agenda, but we will make sure you get a slot.

Best regards,

Juan




On 22 Nov 2019, at 19:21, Zaia, Joseph <jz...@bu...<mailto:jz...@bu...>> wrote:

Dear All,

I would like to initiate discussion for expanding the use cases for proteomics to include complex protein glycosylation.  Glycosylation is as a rule heterogeneous, with 30 or so glycoforms per glycosite.  In addition, the glycan dissociates during tandem MS experiments.  The software and data standards need to be expanded to include the glycosylation size, heterogeneity, and tandem MS dissociation.  At present, quantitative software (Skyline and others) do not recognize glycosylation.  Without this recognition the quantitative tools developed for peptides cannot be adapted without tedious effort on the part of the user.  Therefore, there is need to expand the manner by which peptides are represented informatically.  It is important that glycopeptides be included in the use cases for mzIdentML and mzQuant.  It is also important that spectral library generating software be expanded to allow glycosylated peptides to facilitate use of data independent experiments for glycoproteins.

Would it be possible for me to communicate these ideas at the PSI Workshop in San Diego?

Thank you.

Joe Zaia
From: Jones, Andy <And...@li...<mailto:And...@li...>>
Sent: Thursday, November 21, 2019 11:29 AM
To: psi...@eb...<mailto:psi...@eb...>; ps...@eb...<mailto:ps...@eb...>; Mass spectrometry standard development <psi...@li...<mailto:psi...@li...>>; psi...@li...<mailto:psi...@li...>; Co...@go...<mailto:Co...@go...>
Subject: [Psidev-pi-dev] PSI2020 - Save the Date

Hi all,

We are pleased to announce that the 2020 Annual workshop for the Proteomics Standards Initiative (PSI) will take place in San Diego USA, Mon 23rd to Thurs 26th March 2020. The workshop will focus on developing data standards related to mass spectrometry for spectral libraries, the universal spectrum identifier, quality control and capturing study metadata, and in the molecular interactions side on mapping standards to Cytoscape. We will also be welcoming the new PSI work group – Intrinsically Disordered Proteins (IDP).

Please save the date if you might be interested to attend, we are always pleased to welcome new groups into the PSI. The registration page will be made available in the coming weeks.

Best wishes
Andy Jones on behalf of the PSI steering committee


--
You received this message because you are subscribed to the Google Groups "CompMS" group.
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Re: [Psidev-pi-dev] [CompMS] PSI2020 - Save the Date

[Juan A. V. <ju...@eb...>]

Dear Joe,

Thanks for your e-mail.

You are very welcome to present in San Diego. We are still discussing the agenda, but we will make sure you get a slot.

Best regards,

Juan



> On 22 Nov 2019, at 19:21, Zaia, Joseph <jz...@bu...> wrote:
> 
> Dear All,
>  
> I would like to initiate discussion for expanding the use cases for proteomics to include complex protein glycosylation.  Glycosylation is as a rule heterogeneous, with 30 or so glycoforms per glycosite.  In addition, the glycan dissociates during tandem MS experiments.  The software and data standards need to be expanded to include the glycosylation size, heterogeneity, and tandem MS dissociation.  At present, quantitative software (Skyline and others) do not recognize glycosylation.  Without this recognition the quantitative tools developed for peptides cannot be adapted without tedious effort on the part of the user.  Therefore, there is need to expand the manner by which peptides are represented informatically.  It is important that glycopeptides be included in the use cases for mzIdentML and mzQuant.  It is also important that spectral library generating software be expanded to allow glycosylated peptides to facilitate use of data independent experiments for glycoproteins.
>  
> Would it be possible for me to communicate these ideas at the PSI Workshop in San Diego? 
>  
> Thank you.
>  
> Joe Zaia
> From: Jones, Andy <And...@li... <mailto:And...@li...>> 
> Sent: Thursday, November 21, 2019 11:29 AM
> To: psi...@eb... <mailto:psi...@eb...>; ps...@eb... <mailto:ps...@eb...>; Mass spectrometry standard development <psi...@li... <mailto:psi...@li...>>; psi...@li... <mailto:psi...@li...>; Co...@go... <mailto:Co...@go...>
> Subject: [Psidev-pi-dev] PSI2020 - Save the Date
>  
> Hi all,
>  
> We are pleased to announce that the 2020 Annual workshop for the Proteomics Standards Initiative (PSI) will take place in San Diego USA, Mon 23rd to Thurs 26th March 2020. The workshop will focus on developing data standards related to mass spectrometry for spectral libraries, the universal spectrum identifier, quality control and capturing study metadata, and in the molecular interactions side on mapping standards to Cytoscape. We will also be welcoming the new PSI work group – Intrinsically Disordered Proteins (IDP).
>  
> Please save the date if you might be interested to attend, we are always pleased to welcome new groups into the PSI. The registration page will be made available in the coming weeks.
>  
> Best wishes
> Andy Jones on behalf of the PSI steering committee
>  
> 
> -- 
> You received this message because you are subscribed to the Google Groups "CompMS" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to com...@go... <mailto:com...@go...>.
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Re: [Psidev-pi-dev] PSI2020 - Save the Date

[Zaia, J. <jz...@bu...>]

Dear All,

I would like to initiate discussion for expanding the use cases for proteomics to include complex protein glycosylation.  Glycosylation is as a rule heterogeneous, with 30 or so glycoforms per glycosite.  In addition, the glycan dissociates during tandem MS experiments.  The software and data standards need to be expanded to include the glycosylation size, heterogeneity, and tandem MS dissociation.  At present, quantitative software (Skyline and others) do not recognize glycosylation.  Without this recognition the quantitative tools developed for peptides cannot be adapted without tedious effort on the part of the user.  Therefore, there is need to expand the manner by which peptides are represented informatically.  It is important that glycopeptides be included in the use cases for mzIdentML and mzQuant.  It is also important that spectral library generating software be expanded to allow glycosylated peptides to facilitate use of data independent experiments for glycoproteins.

Would it be possible for me to communicate these ideas at the PSI Workshop in San Diego?

Thank you.

Joe Zaia
From: Jones, Andy <And...@li...>
Sent: Thursday, November 21, 2019 11:29 AM
To: psi...@eb...; ps...@eb...; Mass spectrometry standard development <psi...@li...>; psi...@li...; Co...@go...
Subject: [Psidev-pi-dev] PSI2020 - Save the Date

Hi all,

We are pleased to announce that the 2020 Annual workshop for the Proteomics Standards Initiative (PSI) will take place in San Diego USA, Mon 23rd to Thurs 26th March 2020. The workshop will focus on developing data standards related to mass spectrometry for spectral libraries, the universal spectrum identifier, quality control and capturing study metadata, and in the molecular interactions side on mapping standards to Cytoscape. We will also be welcoming the new PSI work group - Intrinsically Disordered Proteins (IDP).

Please save the date if you might be interested to attend, we are always pleased to welcome new groups into the PSI. The registration page will be made available in the coming weeks.

Best wishes
Andy Jones on behalf of the PSI steering committee

[Psidev-pi-dev] PSI2020 - Save the Date

[Jones, A. <And...@li...>]

Hi all,

We are pleased to announce that the 2020 Annual workshop for the Proteomics Standards Initiative (PSI) will take place in San Diego USA, Mon 23rd to Thurs 26th March 2020. The workshop will focus on developing data standards related to mass spectrometry for spectral libraries, the universal spectrum identifier, quality control and capturing study metadata, and in the molecular interactions side on mapping standards to Cytoscape. We will also be welcoming the new PSI work group - Intrinsically Disordered Proteins (IDP).

Please save the date if you might be interested to attend, we are always pleased to welcome new groups into the PSI. The registration page will be made available in the coming weeks.

Best wishes
Andy Jones on behalf of the PSI steering committee

Re: [Psidev-pi-dev] Proteomics standards for glycosylated proteins

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

Dear Joseph,

at the moment we plan for Mon 23^rd to Thurs 26^th March 2020 at UCSD in 
San Diego.

The official announcement and registration page will be posted soon on 
our HUPO-PSI website
on http://www.psidev.info/events

Cheers,
Gerhard


On 20.11.2019 21:54, Zaia, Joseph wrote:
>
> Dear Gerhard,
>
> Thank you for your reply.  I have subscribed to the PSI-PI mailing list.
>
> In principle, I am interested in attending the HUPO-PSI spring 
> meeting.  But I cannot find information about the date and location.  
> Could you send me a link?
>
> Many thanks.
>
> Joe
>
> *From:*Gerhard Mayer <may...@ru...>
> *Sent:* Wednesday, November 20, 2019 10:52 AM
> *To:* Zaia, Joseph <jz...@bu...>; psi...@li...
> *Cc:* Klein, Joshua, Adam <ja...@bu...>; Hackett, William, Edwin 
> <weh...@bu...>
> *Subject:* Re: Proteomics standards for glycosylated proteins
>
> Dear Joseph,
>
> yes, support for glycoproteomics is still missing in mzIdentML and
> I agree that this would be an important extension for a future version 
> of mzIdentML.
>
> Since the mzIdentML standard (https://github.com/HUPO-PSI/mzIdentML) 
> is a community effort
> of the Proteomics Informatics (PI) group of the HUPO-PSI 
> (http://www.psidev.info),
> I forward your request to the PSI-PI mailing list 
> (psi...@li... 
> <mailto:psi...@li...>).
> You are invited to subscribe to that list at 
> https://sourceforge.net/projects/psidev/lists/psidev-pi-dev 
> <https://sourceforge.net/projects/psidev/lists/psidev-pi-dev>
>
> Maybe you and/or your associates can attend to the next HUPO-PSI 
> spring meeting to discuss glycoproteomics support in more details?
> HUPO-PSI always welcomes new contributors for further development of 
> their standard formats.
>
> Best regards
> Gerhard Mayer
> HUPO-PSI ontology coordinator
>
> On 20.11.2019 16:26, Zaia, Joseph wrote:
>
>     Dear Gerhard,
>
>     I am writing to initiate discussion of proteomics exchange
>     standards for glycosylated proteins.  My research group develops
>     mass spectrometry based methods and bioinformatics for
>     quantification of glycoprotein glycosylation. We suggest that the
>     use cases for mzIdentML standard be expanded to include
>     site-specific protein glycosylation.  We note that the use cases
>     for the mzIdentML1 2.0 release include protein cross-linking and
>     molecular interaction data that can be inferred from
>     cross-linking.  There is a growing need to expand this to include
>     glycosylation.
>
>     Many cell surface and extracellular proteins undergo glycosylation
>     as they pass through the secretory pathway.  The glycosylation
>     reactions do not go to completion, resulting in microheterogeneity
>     at each protein glycosylation site.  Glycans are relatively large
>     chemical modifications that undergo dissociation during tandem MS
>     events.  Therefore, it is necessary to modify mzIdentML and/or
>     other exchange standards to include this reality.
>
>     We are eager to engage you and other HUPO Proteome Standards
>     Initiative members in discussing how to expand the scope or
>     exchange standards to include glycoproteins.  Can you suggest
>     stake holders who should be included in this conversation?
>
>     Many thanks!
>
>     Joe Zaia
>
>     Joseph Zaia (he/his/him)
>
>     Professor, Biochemistry
>
>     Member, Bioinformatics Program
>
>     Associate Director, Center for Biomedical Mass Spectrometry
>
>     Boston University Medical Campus
>
>     670 Albany St., Rm. 509
>
>     Boston, MA 02118
>
>     USA
>
>     Office: 1-617-358-2429
>
> -- 
>
> *----------------------------------------------------------------------*
>
> *Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER*
>
> *Research associate*
>
> *Ruhr-Universität Bochum, Medizinisches Proteom-Center*
>
> *DEPARTMENT Medical Bioinformatics*
>
> *Building ProDi E2.234 | Gesundheitscampus 4 | D-44801 Bochum*
>
> *Fon: *+49 (0)234 32-18110 | *Fax: *+49 (0)234 32-14496
>
> *E-Mail: *ger...@ru... <mailto:ger...@ru...>
>
> *Web: *www.ruhr-uni-bochum.de/mpc <http://www.ruhr-uni-bochum.de/mpc>
>
-- 

*----------------------------------------------------------------------*

*Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER*

*Research associate*

*Ruhr-Universität Bochum, Medizinisches Proteom-Center*

*DEPARTMENT Medical Bioinformatics*

*Building ProDi E2.234 | Gesundheitscampus 4 | D-44801 Bochum*

*Fon: *+49 (0)234 32-18110 | *Fax: *+49 (0)234 32-14496

*E-Mail: *ger...@ru... <mailto:ger...@ru...>

*Web: *www.ruhr-uni-bochum.de/mpc <http://www.ruhr-uni-bochum.de/mpc>

Re: [Psidev-pi-dev] Proteomics standards for glycosylated proteins

[Zaia, J. <jz...@bu...>]

Dear Gerhard,

Thank you for your reply.  I have subscribed to the PSI-PI mailing list.

In principle, I am interested in attending the HUPO-PSI spring meeting.  But I cannot find information about the date and location.  Could you send me a link?

Many thanks.

Joe

From: Gerhard Mayer <may...@ru...>
Sent: Wednesday, November 20, 2019 10:52 AM
To: Zaia, Joseph <jz...@bu...>; psi...@li...
Cc: Klein, Joshua, Adam <ja...@bu...>; Hackett, William, Edwin <weh...@bu...>
Subject: Re: Proteomics standards for glycosylated proteins


Dear Joseph,

yes, support for glycoproteomics is still missing in mzIdentML and
I agree that this would be an important extension for a future version of mzIdentML.

Since the mzIdentML standard (https://github.com/HUPO-PSI/mzIdentML) is a community effort
of the Proteomics Informatics (PI) group of the HUPO-PSI (http://www.psidev.info),
I forward your request to the PSI-PI mailing list (psi...@li...<mailto:psi...@li...>).
You are invited to subscribe to that list at https://sourceforge.net/projects/psidev/lists/psidev-pi-dev

Maybe you and/or your associates can attend to the next HUPO-PSI spring meeting to discuss glycoproteomics support in more details?
HUPO-PSI always welcomes new contributors for further development of their standard formats.

Best regards
Gerhard Mayer
HUPO-PSI ontology coordinator


On 20.11.2019 16:26, Zaia, Joseph wrote:
Dear Gerhard,

I am writing to initiate discussion of proteomics exchange standards for glycosylated proteins.  My research group develops mass spectrometry based methods and bioinformatics for quantification of glycoprotein glycosylation. We suggest that the use cases for mzIdentML standard be expanded to include site-specific protein glycosylation.  We note that the use cases for the mzIdentML1 2.0 release include protein cross-linking and molecular interaction data that can be inferred from cross-linking.  There is a growing need to expand this to include glycosylation.

Many cell surface and extracellular proteins undergo glycosylation as they pass through the secretory pathway.  The glycosylation reactions do not go to completion, resulting in microheterogeneity at each protein glycosylation site.  Glycans are relatively large chemical modifications that undergo dissociation during tandem MS events.  Therefore, it is necessary to modify mzIdentML and/or other exchange standards to include this reality.

We are eager to engage you and other HUPO Proteome Standards Initiative members in discussing how to expand the scope or exchange standards to include glycoproteins.  Can you suggest stake holders who should be included in this conversation?

Many thanks!

Joe Zaia

Joseph Zaia (he/his/him)
Professor, Biochemistry
Member, Bioinformatics Program
Associate Director, Center for Biomedical Mass Spectrometry
Boston University Medical Campus
670 Albany St., Rm. 509
Boston, MA 02118
USA
Office: 1-617-358-2429

--


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

Dipl. Inform. med., Dipl. Wirtsch. Inf. GERHARD MAYER

Research associate

Ruhr-Universität Bochum, Medizinisches Proteom-Center

DEPARTMENT Medical Bioinformatics

Building ProDi E2.234 | Gesundheitscampus 4 | D-44801 Bochum

Fon: +49 (0)234 32-18110 | Fax: +49 (0)234 32-14496

E-Mail: ger...@ru...<mailto:ger...@ru...>

Web: www.ruhr-uni-bochum.de/mpc<http://www.ruhr-uni-bochum.de/mpc>

Re: [Psidev-pi-dev] Proteomics standards for glycosylated proteins

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

Dear Joseph,

yes, support for glycoproteomics is still missing in mzIdentML and
I agree that this would be an important extension for a future version 
of mzIdentML.

Since the mzIdentML standard (https://github.com/HUPO-PSI/mzIdentML) is 
a community effort
of the Proteomics Informatics (PI) group of the HUPO-PSI 
(http://www.psidev.info),
I forward your request to the PSI-PI mailing list 
(psi...@li...).
You are invited to subscribe to that list at 
https://sourceforge.net/projects/psidev/lists/psidev-pi-dev

Maybe you and/or your associates can attend to the next HUPO-PSI spring 
meeting to discuss glycoproteomics support in more details?
HUPO-PSI always welcomes new contributors for further development of 
their standard formats.

Best regards
Gerhard Mayer
HUPO-PSI ontology coordinator


On 20.11.2019 16:26, Zaia, Joseph wrote:
>
> Dear Gerhard,
>
> I am writing to initiate discussion of proteomics exchange standards 
> for glycosylated proteins.  My research group develops mass 
> spectrometry based methods and bioinformatics for quantification of 
> glycoprotein glycosylation. We suggest that the use cases for 
> mzIdentML standard be expanded to include site-specific protein 
> glycosylation.  We note that the use cases for the mzIdentML1 2.0 
> release include protein cross-linking and molecular interaction data 
> that can be inferred from cross-linking. There is a growing need to 
> expand this to include glycosylation.
>
> Many cell surface and extracellular proteins undergo glycosylation as 
> they pass through the secretory pathway.  The glycosylation reactions 
> do not go to completion, resulting in microheterogeneity at each 
> protein glycosylation site.  Glycans are relatively large chemical 
> modifications that undergo dissociation during tandem MS events.  
> Therefore, it is necessary to modify mzIdentML and/or other exchange 
> standards to include this reality.
>
> We are eager to engage you and other HUPO Proteome Standards 
> Initiative members in discussing how to expand the scope or exchange 
> standards to include glycoproteins.  Can you suggest stake holders who 
> should be included in this conversation?
>
> Many thanks!
>
> Joe Zaia
>
> Joseph Zaia (he/his/him)
>
> Professor, Biochemistry
>
> Member, Bioinformatics Program
>
> Associate Director, Center for Biomedical Mass Spectrometry
>
> Boston University Medical Campus
>
> 670 Albany St., Rm. 509
>
> Boston, MA 02118
>
> USA
>
> Office: 1-617-358-2429
>
-- 

*----------------------------------------------------------------------*

*Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER*

*Research associate*

*Ruhr-Universität Bochum, Medizinisches Proteom-Center*

*DEPARTMENT Medical Bioinformatics*

*Building ProDi E2.234 | Gesundheitscampus 4 | D-44801 Bochum*

*Fon: *+49 (0)234 32-18110 | *Fax: *+49 (0)234 32-14496

*E-Mail: *ger...@ru... <mailto:ger...@ru...>

*Web: *www.ruhr-uni-bochum.de/mpc <http://www.ruhr-uni-bochum.de/mpc>

[Psidev-pi-dev] New version 4.1.32 of psi-ms.obo

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

Dear proteomics/metabolomics community,

following are the new terms for the version 4.1.32 of the psi-ms.obo file,

which can be downloaded from
https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo


New CV terms in version 4.1.32 of psi-ms.obo:
=============================================
[Term]
id: MS:1003032
name: compound identification confidence code in MS-DIAL
def: "The confidence code to describe the confidence of annotated 
compounds as defined by the MS-DIAL program." [PMID:25938372, 
http://prime.psc.riken.jp/Metabolomics_Software/MS-DIAL]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002895 ! small molecule identification attribute

Best Regards,
Gerhard

-- 

*----------------------------------------------------------------------*

*Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER*

*Research associate*

*Ruhr-Universität Bochum, Medizinisches Proteom-Center*

*DEPARTMENT Medical Bioinformatics*

*Building ProDi E2.234 | Gesundheitscampus 4 | D-44801 Bochum*

*Fon: *+49 (0)234 32-18110 | *Fax: *+49 (0)234 32-14496

*E-Mail: *ger...@ru... <mailto:ger...@ru...>

*Web: *www.ruhr-uni-bochum.de/mpc <http://www.ruhr-uni-bochum.de/mpc>

[Psidev-pi-dev] Release candidate 4.1.32_rc1 of psi-ms.obo

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

Dear proteomics/metabolomics community,

following are the new terms for the release candidate 4.1.32_rc1 of
the psi-ms.obo file.

New CV terms in version 4.1.32_rc1 of psi-ms.obo:
=================================================
[Term]
id: MS:1003032
name: compound identification confidence code in MS-DIAL
def: "The confidence code to describe the confidence of annotated 
compounds as defined by the MS-DIAL program." [PMID:25938372, 
http://prime.psc.riken.jp/Metabolomics_Software/MS-DIAL]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002895 ! small molecule identification attribute

Best Regards,
Gerhard

-- 

*----------------------------------------------------------------------*

*Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER*

*Research associate*

*Ruhr-Universität Bochum, Medizinisches Proteom-Center*

*DEPARTMENT Medical Bioinformatics*

*Building ProDi E2.234 | Gesundheitscampus 4 | D-44801 Bochum*

*Fon: *+49 (0)234 32-18110 | *Fax: *+49 (0)234 32-14496

*E-Mail: *ger...@ru... <mailto:ger...@ru...>

*Web: *www.ruhr-uni-bochum.de/mpc <http://www.ruhr-uni-bochum.de/mpc>

[Psidev-pi-dev] New version 4.1.31 of psi-ms.obo

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

Dear proteomics/metabolomics community,

following are the new and modified  terms from the version 4.1.31 of the 
psi-ms.obo file.
It can be downloaded from
https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo

New CV terms version 4.1.31_rc1 of psi-ms.obo:
==============================================
[Term]
id: MS:1003031
name: CPTAC accession number
def: "Main identifier of a CPTAC dataset." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1000878 ! external reference identifier

Modified CV terms version 4.1.31_rc1 of psi-ms.obo:
===================================================
[Term]
id: MS:1002810
name: adduct ion mass X m/z
def: "Theoretical m/z of the X component in the adduct M+X or M-X. This 
term was formerly called 'adduct ion mass', but it is not really a mass. 
It corresponds to the column mislabeled as 'Mass' at 
https://fiehnlab.ucdavis.edu/staff/kind/Metabolomics/MS-Adduct-Calculator." 
[DOI:10.1016/S1044-0305(99)00089-6, 
http://fiehnlab.ucdavis.edu/staff/kind/Metabolomics/MS-Adduct-Calculator]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002809 ! adduct ion attribute

Best regards
Gerhard
-- 

*----------------------------------------------------------------------*

*Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER*

*Research associate*

*Ruhr-Universität Bochum, Medizinisches Proteom-Center*

*DEPARTMENT Medical Bioinformatics*

*Building ProDi E2.234 | Gesundheitscampus 4 | D-44801 Bochum*

*Fon: *+49 (0)234 32-18110 | *Fax: *+49 (0)234 32-14496

*E-Mail: *ger...@ru... <mailto:ger...@ru...>

*Web: *www.ruhr-uni-bochum.de/mpc <http://www.ruhr-uni-bochum.de/mpc>