psidev-ms-dev — Mass spectroscopy standard development

[Psidev-ms-dev] New version 4.1.19 of psi-ms.obo

[mayerg97 <ger...@ru...>]

Dear proteomics/metabolomics community,

the new version 4.1.19 of the psi-ms.obo file can be downloaded from
https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo


Changed CV terms in version 4.1.19 of psi-ms.obo:
=================================================
************ Changed name from 'unlabeled sample' --> 'label free sample'
[Term]
id: MS:1002038
name: label free sample
def: "A sample that has not been labelled or modified. This is often 
referred to as \"light\" to distinguish from \"heavy\"." [PSI:PI]
synonym: "light sample" EXACT []
is_a: MS:1000548 ! sample attribute


************ Changed name from 'quantification reagent' --> 'sample label'
[Term]
id: MS:1002602
name: sample label
def: "Reagent used in labeled quantification methods." [PSI:PI]
is_a: MS:1002111 ! assay label attribute
is_a: MS:1000548 ! sample attribute


************ Removed the relationship
************ is_a: MS:1000524 ! data file content
************ from the following terms, to avoid redundant subclassing:
id: MS:1000235 (total ion current chromatogram)
id: MS:1000322 (charge inversion mass spectrum)
id: MS:1000325 (constant neutral gain spectrum)
id: MS:1000326 (constant neutral loss spectrum)
id: MS:1000341 (precursor ion spectrum)
id: MS:1000343 (product ion spectrum)
id: MS:1000579 (MS1 spectrum)
id: MS:1000580 (MSn spectrum)
id: MS:1000581 (CRM spectrum)
id: MS:1000582 (SIM spectrum)
id: MS:1000583 (SRM spectrum)
id: MS:1000627 (selected ion current chromatogram)
id: MS:1000628 (basepeak chromatogram)
id: MS:1000789 (enhanced multiply charged spectrum)
id: MS:1000790 (time-delayed fragmentation spectrum)
id: MS:1000812 (absorption chromatogram)
id: MS:1000813 (emission chromatogram)
id: MS:1001472 (selected ion monitoring chromatogram)
id: MS:1001473 (selected reaction monitoring chromatogram)
id: MS:1001474 (consecutive reaction monitoring chromatogram)

Best Regards,
Gerhard

-- 

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

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

*PhD student*

*Medizinisches Proteom-Center*

*DEPARTMENT Medical Bioinformatics*

*Building *ZKF E.055 | Universitätsstraße 150 | D-44801 Bochum

*Fon *+49 (0)234 32-29272 | *Fax *+49 (0)234 32-14554

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

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

[Psidev-ms-dev] Release candidate 4.1.19_rc1 of psi-ms.obo

[mayerg97 <ger...@ru...>]

Dear proteomics/metabolomics community,

following are the changed terms for the release candidate
4.1.19_rc1 of the psi-ms.obo file.


Changed CV terms in version 4.1.19_rc1 of psi-ms.obo:
=====================================================
************ Changed name from 'unlabeled sample' --> 'label free sample'
[Term]
id: MS:1002038
name: label free sample
def: "A sample that has not been labelled or modified. This is often 
referred to as \"light\" to distinguish from \"heavy\"." [PSI:PI]
synonym: "light sample" EXACT []
is_a: MS:1000548 ! sample attribute


************ Changed name from 'quantification reagent' --> 'sample label'
[Term]
id: MS:1002602
name: sample label
def: "Reagent used in labeled quantification methods." [PSI:PI]
is_a: MS:1002111 ! assay label attribute
is_a: MS:1000548 ! sample attribute


************ Removed the relationship
************ is_a: MS:1000524 ! data file content
************ from the following terms, to avoid redundant subclassing:
id: MS:1000235 (total ion current chromatogram)
id: MS:1000322 (charge inversion mass spectrum)
id: MS:1000325 (constant neutral gain spectrum)
id: MS:1000326 (constant neutral loss spectrum)
id: MS:1000341 (precursor ion spectrum)
id: MS:1000343 (product ion spectrum)
id: MS:1000579 (MS1 spectrum)
id: MS:1000580 (MSn spectrum)
id: MS:1000581 (CRM spectrum)
id: MS:1000582 (SIM spectrum)
id: MS:1000583 (SRM spectrum)
id: MS:1000627 (selected ion current chromatogram)
id: MS:1000628 (basepeak chromatogram)
id: MS:1000789 (enhanced multiply charged spectrum)
id: MS:1000790 (time-delayed fragmentation spectrum)
id: MS:1000812 (absorption chromatogram)
id: MS:1000813 (emission chromatogram)
id: MS:1001472 (selected ion monitoring chromatogram)
id: MS:1001473 (selected reaction monitoring chromatogram)
id: MS:1001474 (consecutive reaction monitoring chromatogram)

Best Regards,
Gerhard

-- 

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

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

*PhD student*

*Medizinisches Proteom-Center*

*DEPARTMENT Medical Bioinformatics*

*Building *ZKF E.055 | Universitätsstraße 150 | D-44801 Bochum

*Fon *+49 (0)234 32-29272 | *Fax *+49 (0)234 32-14554

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

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

[Psidev-ms-dev] New version 4.1.18 of psi-ms.obo

[mayerg97 <ger...@ru...>]

Dear proteomics/metabolomics community,

the new version 4.1.18 of the psi-ms.obo file can be downloaded from
https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo


Changed CV terms in version 4.1.18 of psi-ms.obo:
=================================================
************ Changed name from maturation peptide --> propeptide
[Term]
id: PEFF:0001034
name: propeptide
def: "Short peptide that is cleaved off a newly synthesized protein and 
generally immediately degraded in the process of protein maturation, and 
is not a signal peptide or transit peptide." [PSI:PEFF]
is_a: PEFF:0001032 ! PEFF molecule processing keyword
xref: value-type:xsd\:string "The allowed value-type for this CV term."
relationship: has_regexp PEFF:1002001 ! regular expression for PEFF 
description line


Best Regards,
Gerhard

-- 

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

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

*PhD student*

*Medizinisches Proteom-Center*

*DEPARTMENT Medical Bioinformatics*

*Building *ZKF E.055 | Universitätsstraße 150 | D-44801 Bochum

*Fon *+49 (0)234 32-29272 | *Fax *+49 (0)234 32-14554

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

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

[Psidev-ms-dev] PSI2019 plans

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

Hi all,

Apologies for the cross-posting. The PSI steering committee will shortly be finalising the venue for the PSI2019 meeting. If you have been to a previous meeting or might be interested in participating in 2019, please can you complete this very short google form to indicate your preferred venue: https://goo.gl/forms/8t4CogZu3xVzRVJQ2, before end Oct i.e. within one week. We would like to take on board community considerations for overseas travel before selecting the final location in early November. We expect to announce the final, selected location by mid November.

Best wishes
Andy Jones

[Psidev-ms-dev] New version 4.1.17 of psi-ms.obo

[mayerg97 <ger...@ru...>]

Dear proteomics/metabolomics community,

the new version 4.1.17 of the psi-ms.obo file can be downloaded from
https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo

It contains major updates to the PEFF CV terms:

[Term]
id: PEFF:0000001
name: PEFF CV term
def: "PSI Extended FASTA Format controlled vocabulary term." [PSI:PEFF]
relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass 
Spectrometry Vocabularies

[Term]
id: PEFF:0000002
name: PEFF file header section term
def: "CV term that may appear in a PEFF file header section." [PSI:PEFF]
is_a: PEFF:0000001 ! PEFF CV term

[Term]
id: PEFF:0000003
name: PEFF file sequence entry term
def: "CV term that may appear in a description line of a PEFF file 
individual sequence entry." [PSI:PEFF]
is_a: PEFF:0000001 ! PEFF CV term

[Term]
id: PEFF:0000008
name: DbName
def: "PEFF keyword for the sequence database name." [PSI:PEFF]
is_a: PEFF:0000002 ! PEFF file header section term
xref: value-type:xsd\:string "The allowed value-type for this CV term."

[Term]
id: PEFF:0000009
name: Prefix
def: "PEFF keyword for the sequence database prefix." [PSI:PEFF]
is_a: PEFF:0000002 ! PEFF file header section term
xref: value-type:xsd\:string "The allowed value-type for this CV term."

[Term]
id: PEFF:0000010
name: DbDescription
def: "PEFF keyword for the sequence database short description." [PSI:PEFF]
is_a: PEFF:0000002 ! PEFF file header section term
xref: value-type:xsd\:string "The allowed value-type for this CV term."

[Term]
id: PEFF:0000011
name: Decoy
def: "PEFF keyword for the specifying whether the sequence database is a 
decoy database." [PSI:PEFF]
is_a: PEFF:0000002 ! PEFF file header section term
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."

[Term]
id: PEFF:0000012
name: DbSource
def: "PEFF keyword for the source of the database file." [PSI:PEFF]
is_a: PEFF:0000002 ! PEFF file header section term
xref: value-type:xsd\:string "The allowed value-type for this CV term."

[Term]
id: PEFF:0000013
name: DbVersion
def: "PEFF keyword for the database version (release date) according to 
database provider." [PSI:PEFF]
is_a: PEFF:0000002 ! PEFF file header section term
xref: value-type:xsd\:string "The allowed value-type for this CV term."

[Term]
id: PEFF:0000014
name: DbDate
def: "OBSOLETE PEFF keyword for the database date (release or file date 
of the source) according to database provider." [PSI:PEFF]
comment: This term was obsoleted.
is_a: PEFF:0000002 ! PEFF file header section term
is_obsolete: true

[Term]
id: PEFF:0000015
name: NumberOfEntries
def: "PEFF keyword for the sumber of sequence entries in the database." 
[PSI:PEFF]
is_a: PEFF:0000002 ! PEFF file header section term
xref: value-type:xsd\:integer "The allowed value-type for this CV term."

[Term]
id: PEFF:0000016
name: Conversion
def: "PEFF keyword for the description of the conversion from original 
format to this current one." [PSI:PEFF]
is_a: PEFF:0000002 ! PEFF file header section term
xref: value-type:xsd\:string "The allowed value-type for this CV term."

[Term]
id: PEFF:0000017
name: SequenceType
def: "PEFF keyword for the molecular type of the sequences." [PSI:PEFF]
is_a: PEFF:0000002 ! PEFF file header section term
xref: value-type:xsd\:string "The allowed value-type for this CV term."
relationship: has_regexp PEFF:1002002 ! regular expression for PEFF 
molecular sequence type

[Term]
id: PEFF:0000018
name: SpecificKey
def: "PEFF keyword for database specific keywords not included in the 
current controlled vocabulary." [PSI:PEFF]
is_a: PEFF:0000002 ! PEFF file header section term
xref: value-type:xsd\:string "The allowed value-type for this CV term."

[Term]
id: PEFF:0000019
name: SpecificValue
def: "PEFF keyword for the specific values for a custom key." [PSI:PEFF]
is_a: PEFF:0000002 ! PEFF file header section term
xref: value-type:xsd\:string "The allowed value-type for this CV term."

[Term]
id: PEFF:0000020
name: DatabaseDescription
def: "PEFF keyword for the short description of the PEFF file." [PSI:PEFF]
is_a: PEFF:0000002 ! PEFF file header section term
xref: value-type:xsd\:string "The allowed value-type for this CV term."

[Term]
id: PEFF:0000021
name: GeneralComment
def: "PEFF keyword for a general comment." [PSI:PEFF]
is_a: PEFF:0000002 ! PEFF file header section term
xref: value-type:xsd\:string "The allowed value-type for this CV term."

[Term]
id: PEFF:0000022
name: ProteoformDb
def: "PEFF keyword that when set to 'true' indicates that the database 
contains complete proteoforms." [PSI:PEFF]
is_a: PEFF:0000002 ! PEFF file header section term
xref: value-type:xsd\:string "The allowed value-type for this CV term."

[Term]
id: PEFF:0000023
name: OptionalTagDef
def: "PEFF keyword for the short tag (abbreviation) and longer 
definition used to annotate a sequence annotation (such as variant or 
modification) in the OptionalTag location." [PSI:PEFF]
is_a: PEFF:0000002 ! PEFF file header section term
xref: value-type:xsd\:string "The allowed value-type for this CV term."

[Term]
id: PEFF:0000024
name: HasAnnotationIdentifiers
def: "PEFF keyword that when set to 'true' indicates that entries in the 
database have identifiers for each annotation." [PSI:PEFF]
is_a: PEFF:0000002 ! PEFF file header section term
xref: value-type:xsd\:string "The allowed value-type for this CV term."

[Term]
id: PEFF:0001001
name: DbUniqueId
def: "OBSOLETE Sequence database unique identifier." [PSI:PEFF]
comment: This term was made obsolete because decided in Heidelberg 
2018-04 that this is redundant.
is_a: PEFF:0000003 ! PEFF file sequence entry term
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_obsolete: true

[Term]
id: PEFF:0001002
name: PName
def: "PEFF keyword for the protein full name." [PSI:PEFF]
is_a: PEFF:0000003 ! PEFF file sequence entry term
xref: value-type:xsd\:string "The allowed value-type for this CV term."

[Term]
id: PEFF:0001003
name: NcbiTaxId
def: "PEFF keyword for the NCBI taxonomy identifier." [PSI:PEFF]
is_a: PEFF:0000003 ! PEFF file sequence entry term
xref: value-type:xsd\:int "The allowed value-type for this CV term."

[Term]
id: PEFF:0001004
name: TaxName
def: "PEFF keyword for the taxonomy name (latin or common name)." [PSI:PEFF]
is_a: PEFF:0000003 ! PEFF file sequence entry term
xref: value-type:xsd\:string "The allowed value-type for this CV term."

[Term]
id: PEFF:0001005
name: GName
def: "PEFF keyword for the gene name." [PSI:PEFF]
is_a: PEFF:0000003 ! PEFF file sequence entry term
xref: value-type:xsd\:string "The allowed value-type for this CV term."

[Term]
id: PEFF:0001006
name: Length
def: "PEFF keyword for the sequence length." [PSI:PEFF]
is_a: PEFF:0000003 ! PEFF file sequence entry term
xref: value-type:xsd\:int "The allowed value-type for this CV term."

[Term]
id: PEFF:0001007
name: SV
def: "PEFF keyword for the sequence version." [PSI:PEFF]
is_a: PEFF:0000003 ! PEFF file sequence entry term
xref: value-type:xsd\:string "The allowed value-type for this CV term."

[Term]
id: PEFF:0001008
name: EV
def: "PEFF keyword for the entry version." [PSI:PEFF]
is_a: PEFF:0000003 ! PEFF file sequence entry term
xref: value-type:xsd\:string "The allowed value-type for this CV term."

[Term]
id: PEFF:0001009
name: PE
def: "PEFF keyword for the Protein Evidence; A UniProtKB code 1-5." 
[PSI:PEFF]
is_a: PEFF:0000003 ! PEFF file sequence entry term
xref: value-type:xsd\:int "The allowed value-type for this CV term."

[Term]
id: PEFF:0001010
name: Processed
def: "PEFF keyword for information on how the full length original 
protein sequence can be processed into shorter components such as signal 
peptides and chains." [PSI:PEFF]
is_a: PEFF:0000003 ! PEFF file sequence entry term
xref: value-type:xsd\:string "The allowed value-type for this CV term."
relationship: has_regexp PEFF:1002001 ! regular expression for PEFF 
description line

[Term]
id: PEFF:0001011
name: Variant
def: "OBSOLETE Sequence variation (substitution, insertion, deletion)." 
[PSI:PEFF]
comment: This term was made obsolete in favor of VariantSimple and 
VariantComplex.
is_a: PEFF:0000003 ! PEFF file sequence entry term
xref: value-type:xsd\:string "The allowed value-type for this CV term."
relationship: has_regexp PEFF:1002001 ! regular expression for PEFF 
description line
is_obsolete: true

[Term]
id: PEFF:0001012
name: ModResPsi
def: "PEFF keyword for the modified residue with PSI-MOD identifier." 
[PSI:PEFF]
is_a: PEFF:0000003 ! PEFF file sequence entry term
xref: value-type:xsd\:string "The allowed value-type for this CV term."
relationship: has_regexp PEFF:1002001 ! regular expression for PEFF 
description line

[Term]
id: PEFF:0001013
name: ModRes
def: "PEFF keyword for the modified residue without aPSI-MOD or UniMod 
identifier." [PSI:PEFF]
is_a: PEFF:0000003 ! PEFF file sequence entry term
xref: value-type:xsd\:string "The allowed value-type for this CV term."
relationship: has_regexp PEFF:1002001 ! regular expression for PEFF 
description line

[Term]
id: PEFF:0001014
name: AltAC
def: "PEFF keyword for the Alternative Accession Code." [PSI:PEFF]
is_a: PEFF:0000003 ! PEFF file sequence entry term
xref: value-type:xsd\:string "The allowed value-type for this CV term."

[Term]
id: PEFF:0001015
name: SeqStatus
def: "PEFF keyword for the sequence status. Complete or Fragment." 
[PSI:PEFF]
is_a: PEFF:0000003 ! PEFF file sequence entry term
xref: value-type:xsd\:string "The allowed value-type for this CV term."
relationship: has_regexp PEFF:1002003 ! regular expression for PEFF 
sequence status

[Term]
id: PEFF:0001016
name: CC
def: "PEFF keyword for the entry associated comment." [PSI:PEFF]
is_a: PEFF:0000003 ! PEFF file sequence entry term
xref: value-type:xsd\:string "The allowed value-type for this CV term."

[Term]
id: PEFF:0001017
name: KW
def: "PEFF keyword for the entry associated keyword(s)." [PSI:PEFF]
is_a: PEFF:0000003 ! PEFF file sequence entry term
xref: value-type:xsd\:string "The allowed value-type for this CV term."

[Term]
id: PEFF:0001018
name: GO
def: "PEFF keyword for the Gene Ontology code." [PSI:PEFF]
is_a: PEFF:0000003 ! PEFF file sequence entry term
xref: value-type:xsd\:string "The allowed value-type for this CV term."

[Term]
id: PEFF:0001019
name: XRef
def: "PEFF keyword for the cross-reference to an external resource." 
[PSI:PEFF]
is_a: PEFF:0000003 ! PEFF file sequence entry term
xref: value-type:xsd\:string "The allowed value-type for this CV term."

[Term]
id: PEFF:0001020
name: mature protein
def: "Portion of a newly synthesized protein that contributes to a final 
structure after other components such as signal peptides are removed." 
[PSI:PEFF]
is_a: PEFF:0001032 ! PEFF molecule processing keyword
xref: value-type:xsd\:string "The allowed value-type for this CV term."
relationship: has_regexp PEFF:1002001 ! regular expression for PEFF 
description line

[Term]
id: PEFF:0001021
name: signal peptide
def: "Short peptide present at the N-terminus of a newly synthesized 
protein that is cleaved off and is not part of the final mature 
protein." [PSI:PEFF]
is_a: PEFF:0001032 ! PEFF molecule processing keyword
xref: value-type:xsd\:string "The allowed value-type for this CV term."
relationship: has_regexp PEFF:1002001 ! regular expression for PEFF 
description line

[Term]
id: PEFF:0001022
name: transit peptide
def: "Short peptide present at the N-terminus of a newly synthesized 
protein that helps the protein through the membrane of its destination 
organelle." [PSI:PEFF]
is_a: PEFF:0001032 ! PEFF molecule processing keyword
xref: value-type:xsd\:string "The allowed value-type for this CV term."
relationship: has_regexp PEFF:1002001 ! regular expression for PEFF 
description line

[Term]
id: PEFF:0001023
name: Conflict
def: "PEFF keyword for the sequence conflict; a UniProtKB term." [PSI:PEFF]
is_a: PEFF:0000003 ! PEFF file sequence entry term
xref: value-type:xsd\:string "The allowed value-type for this CV term."
relationship: has_regexp PEFF:1002001 ! regular expression for PEFF 
description line

[Term]
id: PEFF:0001024
name: Crc64
def: "PEFF keyword for the Sequence checksum in crc64." [PSI:PEFF]
is_a: PEFF:0000003 ! PEFF file sequence entry term
xref: value-type:xsd\:string "The allowed value-type for this CV term."

[Term]
id: PEFF:0001025
name: Domain
def: "PEFF keyword for the sequence range of a domain." [PSI:PEFF]
is_a: PEFF:0000003 ! PEFF file sequence entry term
xref: value-type:xsd\:string "The allowed value-type for this CV term."

[Term]
id: PEFF:0001026
name: ID
def: "PEFF keyword for the UniProtKB specific Protein identifier ID; a 
UniProtKB term." [PSI:PEFF]
is_a: PEFF:0000003 ! PEFF file sequence entry term
xref: value-type:xsd\:string "The allowed value-type for this CV term."

[Term]
id: PEFF:0001027
name: ModResUnimod
def: "PEFF keyword for the modified residue with UniMod identifier." 
[PSI:PEFF]
is_a: PEFF:0000003 ! PEFF file sequence entry term
xref: value-type:xsd\:string "The allowed value-type for this CV term."
relationship: has_regexp PEFF:1002001 ! regular expression for PEFF 
description line

[Term]
id: PEFF:0001028
name: VariantSimple
def: "PEFF keyword for the simple sequence variation of a single amino 
acid change. A change to a stop codon is permitted with a * symbol. More 
complex variations must be encoded with the VariantComplex term." [PSI:PEFF]
is_a: PEFF:0000003 ! PEFF file sequence entry term
xref: value-type:xsd\:string "The allowed value-type for this CV term."
relationship: has_regexp PEFF:1002001 ! regular expression for PEFF 
description line

[Term]
id: PEFF:0001029
name: VariantComplex
def: "PEFF keyword for a sequence variation that is more complex than a 
single amino acid change or change to a stop codon." [PSI:PEFF]
is_a: PEFF:0000003 ! PEFF file sequence entry term
xref: value-type:xsd\:string "The allowed value-type for this CV term."
relationship: has_regexp PEFF:1002001 ! regular expression for PEFF 
description line

[Term]
id: PEFF:0001030
name: Proteoform
def: "PEFF keyword for the proteoforms of this protein, constructed as a 
set of annotation identifiers." [PSI:PEFF]
is_a: PEFF:0000003 ! PEFF file sequence entry term
xref: value-type:xsd\:string "The allowed value-type for this CV term."

[Term]
id: PEFF:0001031
name: DisulfideBond
def: "PEFF keyword for the disulfide bonds in this protein, constructed 
as a sets of annotation identifiers of two half-cystine modifications." 
[PSI:PEFF]
is_a: PEFF:0000003 ! PEFF file sequence entry term
xref: value-type:xsd\:string "The allowed value-type for this CV term."

[Term]
id: PEFF:0001032
name: PEFF molecule processing keyword
def: "PEFF keyword describing the type of processing event being 
described." [PSI:PEFF]
is_a: PEFF:0000003 ! PEFF file sequence entry term

[Term]
id: PEFF:0001033
name: Comment
def: "PEFF keyword for the individual protein entry comment. It is 
discouraged to put parsable information here. This is only for free-text 
commentary." [PSI:PEFF]
is_a: PEFF:0000003 ! PEFF file sequence entry term
xref: value-type:xsd\:string "The allowed value-type for this CV term."

[Term]
id: PEFF:0001034
name: maturation peptide
def: "Short peptide that is cleaved off a newly synthesized protein and 
generally immediately degraded in the process of protein maturation, and 
is not a signal peptide or transit peptide." [PSI:PEFF]
is_a: PEFF:0001032 ! PEFF molecule processing keyword
xref: value-type:xsd\:string "The allowed value-type for this CV term."
relationship: has_regexp PEFF:1002001 ! regular expression for PEFF 
description line

[Term]
id: PEFF:1002001
name: regular expression for each VariantSimple item
def: "([0-9]+|[A-Z*](|.+)?)." [PSI:PEFF]
is_a: MS:1002479 ! regular expression

[Term]
id: PEFF:1002002
name: regular expression for PEFF molecular sequence type
def: 
"(AA|NA|DNA|cDNA|RNA|RNAi|tRNA|rRNA|siRNA|mDNA|mRNA|snoRNA|ncRNA|EST|[a-z0-9A-Z]+)." 
[PSI:PEFF]
is_a: MS:1002479 ! regular expression

[Term]
id: PEFF:1002003
name: regular expression for PEFF sequence status
def: "(Complete|Fragment|[a-z0-9A-Z]+)." [PSI:PEFF]
is_a: MS:1002479 ! regular expression

Best Regards,
Gerhard

-- 

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

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

*PhD student*

*Medizinisches Proteom-Center*

*DEPARTMENT Medical Bioinformatics*

*Building *ZKF E.055 | Universitätsstraße 150 | D-44801 Bochum

*Fon *+49 (0)234 32-29272 | *Fax *+49 (0)234 32-14554

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

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

[Psidev-ms-dev] New version 4.1.16 of psi-ms.obo

[mayerg97 <ger...@ru...>]

Dear proteomics/metabolomics community,


the new version 4.1.16 of the psi-ms.obo file can be downloaded from
https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo

It contains two new digestion terms and new terms for
the IdentiPy software and the their scores.

In addition several terms are changed in order to remove redundant 
subclassing
(superfluous is_a relations are removed now).


New CV terms in version 4.1.16 of psi-ms.obo:
=============================================
************ New digestion terms
[Term]
id: MS:1002985
name: in-gel digestion
def: "Digestion of proteins separated by gel electrophoresis for mass 
spectrometric characterization of proteins and proteomes." [PSI:PI]
is_a: MS:1000831 ! sample preparation

[Term]
id: MS:1002986
name: in-solution digestion
def: "Digestion of proteins in solution for mass spectrometric 
characterization of proteins and proteomes." [PSI:PI]
is_a: MS:1000831 ! sample preparation

************ New search engine / score / software terms
[Term]
id: MS:1002987
name: IdentiPy
def: "IdentiPy." [PMID:29682971, https://bitbucket.org/levitsky/identipy]
is_a: MS:1001456 ! analysis software

[Term]
id: MS:1002988
name: IdentiPy:RHNS
def: "The IdentiPy result 'RHNS'." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001153 ! search engine specific score
relationship: has_order MS:1002108 ! higher score better

[Term]
id: MS:1002989
name: IdentiPy:hyperscore
def: "The IdentiPy result 'hyperscore'." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001153 ! search engine specific score
relationship: has_order MS:1002108 ! higher score better

[Term]
id: MS:1002990
name: ms_deisotope
def: "ms_deisotope, a library for deisotoping and charge state 
deconvolution of mass spectra." 
[https://github.com/mobiusklein/ms_deisotope]
is_a: MS:1001457 ! data processing software

[Term]
id: MS:1002991
name: python-psims
def: "python-psims, a library for generating mzML and mzIdentML." 
[https://github.com/mobiusklein/psims]
is_a: MS:1002333 ! conversion software



Changed CV terms in version 4.1.16 of psi-ms.obo:
*********** REMOVED REDUNDANT SUBCLASSINGS **********
=================================================

************ Removed the redundant is_a: MS:1001457 ! data processing 
software
************ for the following three terms
[Term]
id: MS:1002334
name: ProCon
def: "Java software designed to convert one of several proteomics 
identification results formats into mzIdentML or PRIDE XML." [PSI:PI, 
http://www.medizinisches-proteom-center.de/procon]
is_a: MS:1002333 ! conversion software

[Term]
id: MS:1002335
name: PRIDE Converter2
def: "Java software designed to convert one of several proteomics 
identification results formats into PRIDE XML." [PMID:22949509]
is_a: MS:1002333 ! conversion software

[Term]
id: MS:1002387
name: PIA
def: "PIA - Protein Inference Algorithms, a toolbox for protein 
inference and identification analysis." [PSI:PI, 
http://www.medizinisches-proteom-center.de/pia]
is_a: MS:1002414 ! postprocessing software
is_a: MS:1001456 ! analysis software

************ Removed the redundant is_a: MS:1001833 ! quantitation 
analysis summary
************ for the following ten terms
[Term]
id: MS:1001837
name: iTRAQ quantitation analysis
def: "Quantification analysis using the SCIEX amine-reactive isobaric 
tags for relative and absolute quantification (iTRAQ) labelling 
workflow, wherein 2-8 reporter ions are measured in MS2 spectra near in 
the 114-121 m/z range." [PSI:PI, PMID:15385600]
is_a: MS:1002009 ! isobaric label quantitation analysis

[Term]
id: MS:1002010
name: TMT quantitation analysis
def: "Quantitation analysis using the Thermo Fisher amine-reactive 
tandem mass tag (TMT) labelling workflow, wherein 2-10 reporter ions are 
measured in MS2 spectra in the 126-131 m/z." [PSI:PI, PMID:12713048]
is_a: MS:1002009 ! isobaric label quantitation analysis

[Term]
id: MS:1002212
name: IPTL quantitation analysis
def: "Quantification analysis using a labelling strategy where both 
peptide termini are labelled so that the peptides from different 
labelling schema are isobaric." [PSI:PI, PMID:19655813]
is_a: MS:1002009 ! isobaric label quantitation analysis

[Term]
id: MS:1002756
name: iodoTMT quantitation analysis
def: "Quantitation analysis using the Thermo Fisher sulfhydryl-reactive 
iodo tandem mass tag (iodoTMT) labelling workflow." [PSI:PI, PMID:24926564]
is_a: MS:1002009 ! isobaric label quantitation analysis

[Term]
id: MS:1002757
name: glyco-TMT quantitation analysis
def: "Quantitation analysis using the Thermo Fisher carbonyl-reactive 
glyco-tandem mass tag (glyco-TMT) labelling workflow." [PSI:PI, 
PMID:22455665]
is_a: MS:1002009 ! isobaric label quantitation analysis

[Term]
id: MS:1002758
name: aminoxyTMT quantitation analysis
def: "Quantitation analysis using the Thermo Fisher carbonyl-reactive 
aminoxy tandem mass tag (aminoxyTMT) labelling workflow." [PSI:PI, 
PMID:25337643]
is_a: MS:1002009 ! isobaric label quantitation analysis

[Term]
id: MS:1002759
name: hydrazideTMT quantitation analysis
def: "Quantitation analysis using the Thermo Fisher carbonyl-reactive 
hydrazide tandem mass tag (hydrazide-TMT) labelling workflow." [PSI:PI, 
PMID:25337643]
is_a: MS:1002009 ! isobaric label quantitation analysis

[Term]
id: MS:1002760
name: iTRAQH quantitation analysis
def: "Quantification analysis using the carbonyl-reactive isobaric tags 
for relative and absolute quantification hydrazide (iTRAQH) labelling 
workflow." [PSI:PI, PMID:22926130]
is_a: MS:1002009 ! isobaric label quantitation analysis

[Term]
id: MS:1002761
name: DiART quantitation analysis
def: "Quantification analysis using the amine-reactive deuterium 
isobaric amine reactive tag (DiART) labelling workflow." [PSI:PI, 
PMID:20715779]
is_a: MS:1002009 ! isobaric label quantitation analysis

[Term]
id: MS:1002762
name: DiLeu quantitation analysis
def: "Quantification analysis using the amine-reactive dimethyl leucine 
(DiLeu) tag labelling workflow." [PSI:PI, PMID:20715779]
is_a: MS:1002009 ! isobaric label quantitation analysis

************ Removed the redundant is_a: MS:1001459 ! file format
[Term]
id: MS:1000914
name: tab delimited text format
def: "A file format that has two or more columns of tabular data where 
each column is separated by a TAB character." [PSI:MS]
is_a: MS:1001040 ! intermediate analysis format

************ Removed the redundant is_a: MS:1001455 ! acquisition software
************ Removed the redundant is_a: MS:1001456 ! analysis software
************ Removed the redundant is_a: MS:1001457 ! data processing 
software
[Term]
id: MS:1001878
name: MALDI Solutions Microbial Identification
def: "Shimadzu Biotech software for data acquisition, processing, and 
analysis." [PSI:MS]
is_a: MS:1001558 ! MALDI Solutions

************ Removed the redundant is_a: MS:1001405 ! spectrum 
identification result details
[Term]
id: MS:1001114
name: retention time(s)
def: "OBSOLETE Retention time of the spectrum from the source file." 
[PSI:PI]
comment: This term was made obsolete because scan start time 
(MS:1000016) should be used instead.
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001105 ! peptide sequence-level identification attribute
relationship: has_units UO:0000010 ! second
relationship: has_units UO:0000031 ! minute
is_obsolete: true

************ Removed a blank in the dbxref
[Term]
id: MS:1002822
name: OpenMS file format
def: "File format developed by the OpenMS team." [PMID:27575624]
is_a: MS:1001459 ! file format

Best Regards,
Gerhard

-- 

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

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

*PhD student*

*Medizinisches Proteom-Center*

*DEPARTMENT Medical Bioinformatics*

*Building *ZKF E.055 | Universitätsstraße 150 | D-44801 Bochum

*Fon *+49 (0)234 32-29272 | *Fax *+49 (0)234 32-14554

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

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

[Psidev-ms-dev] Release candidate 4.1.16_rc1 of psi-ms.obo

[mayerg97 <ger...@ru...>]

Dear proteomics/metabolomics community,

following are new terma and changes for the release candidate 4.1.16_rc1 of
the psi-ms.obo file. It contains two new digestion terms and new terms for
the IdentiPy software and the their scores.

In addition several terms are chanegd in order to remove redundant 
subclassing
(superfluous is_a relations are removed now).


New CV terms in version 4.1.16_rc1 of psi-ms.obo:
=================================================
************ New digestion terms
[Term]
id: MS:1002985
name: in-gel digestion
def: "Digestion of proteins separated by gel electrophoresis for mass 
spectrometric characterization of proteins and proteomes." [PSI:PI]
is_a: MS:1000831 ! sample preparation

[Term]
id: MS:1002986
name: in-solution digestion
def: "Digestion of proteins in solution for mass spectrometric 
characterization of proteins and proteomes." [PSI:PI]
is_a: MS:1000831 ! sample preparation

************ New search engine / score / software terms
[Term]
id: MS:1002987
name: IdentiPy
def: "IdentiPy." [PMID:29682971, https://bitbucket.org/levitsky/identipy]
is_a: MS:1001456 ! analysis software

[Term]
id: MS:1002988
name: IdentiPy:RHNS
def: "The IdentiPy result 'RHNS'." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001153 ! search engine specific score
relationship: has_order MS:1002108 ! higher score better

[Term]
id: MS:1002989
name: IdentiPy:hyperscore
def: "The IdentiPy result 'hyperscore'." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001153 ! search engine specific score
relationship: has_order MS:1002108 ! higher score better

[Term]
id: MS:1002990
name: ms_deisotope
def: "ms_deisotope, a library for deisotoping and charge state 
deconvolution of mass spectra." 
[https://github.com/mobiusklein/ms_deisotope]
is_a: MS:1001457 ! data processing software

[Term]
id: MS:1002991
name: python-psims
def: "python-psims, a library for generating mzML and mzIdentML." 
[https://github.com/mobiusklein/psims]
is_a: MS:1002333 ! conversion software



Changed CV terms in version 4.1.16_rc1 of psi-ms.obo:
*********** REMOVED REDUNDANT SUBCLASSINGS **********
=====================================================

************ Removed the redundant is_a: MS:1001457 ! data processing 
software
************ for the following three terms
[Term]
id: MS:1002334
name: ProCon
def: "Java software designed to convert one of several proteomics 
identification results formats into mzIdentML or PRIDE XML." [PSI:PI, 
http://www.medizinisches-proteom-center.de/procon]
is_a: MS:1002333 ! conversion software

[Term]
id: MS:1002335
name: PRIDE Converter2
def: "Java software designed to convert one of several proteomics 
identification results formats into PRIDE XML." [PMID:22949509]
is_a: MS:1002333 ! conversion software

[Term]
id: MS:1002387
name: PIA
def: "PIA - Protein Inference Algorithms, a toolbox for protein 
inference and identification analysis." [PSI:PI, 
http://www.medizinisches-proteom-center.de/pia]
is_a: MS:1002414 ! postprocessing software
is_a: MS:1001456 ! analysis software

************ Removed the redundant is_a: MS:1001833 ! quantitation 
analysis summary
************ for the following ten terms
[Term]
id: MS:1001837
name: iTRAQ quantitation analysis
def: "Quantification analysis using the SCIEX amine-reactive isobaric 
tags for relative and absolute quantification (iTRAQ) labelling 
workflow, wherein 2-8 reporter ions are measured in MS2 spectra near in 
the 114-121 m/z range." [PSI:PI, PMID:15385600]
is_a: MS:1002009 ! isobaric label quantitation analysis

[Term]
id: MS:1002010
name: TMT quantitation analysis
def: "Quantitation analysis using the Thermo Fisher amine-reactive 
tandem mass tag (TMT) labelling workflow, wherein 2-10 reporter ions are 
measured in MS2 spectra in the 126-131 m/z." [PSI:PI, PMID:12713048]
is_a: MS:1002009 ! isobaric label quantitation analysis

[Term]
id: MS:1002212
name: IPTL quantitation analysis
def: "Quantification analysis using a labelling strategy where both 
peptide termini are labelled so that the peptides from different 
labelling schema are isobaric." [PSI:PI, PMID:19655813]
is_a: MS:1002009 ! isobaric label quantitation analysis

[Term]
id: MS:1002756
name: iodoTMT quantitation analysis
def: "Quantitation analysis using the Thermo Fisher sulfhydryl-reactive 
iodo tandem mass tag (iodoTMT) labelling workflow." [PSI:PI, PMID:24926564]
is_a: MS:1002009 ! isobaric label quantitation analysis

[Term]
id: MS:1002757
name: glyco-TMT quantitation analysis
def: "Quantitation analysis using the Thermo Fisher carbonyl-reactive 
glyco-tandem mass tag (glyco-TMT) labelling workflow." [PSI:PI, 
PMID:22455665]
is_a: MS:1002009 ! isobaric label quantitation analysis

[Term]
id: MS:1002758
name: aminoxyTMT quantitation analysis
def: "Quantitation analysis using the Thermo Fisher carbonyl-reactive 
aminoxy tandem mass tag (aminoxyTMT) labelling workflow." [PSI:PI, 
PMID:25337643]
is_a: MS:1002009 ! isobaric label quantitation analysis

[Term]
id: MS:1002759
name: hydrazideTMT quantitation analysis
def: "Quantitation analysis using the Thermo Fisher carbonyl-reactive 
hydrazide tandem mass tag (hydrazide-TMT) labelling workflow." [PSI:PI, 
PMID:25337643]
is_a: MS:1002009 ! isobaric label quantitation analysis

[Term]
id: MS:1002760
name: iTRAQH quantitation analysis
def: "Quantification analysis using the carbonyl-reactive isobaric tags 
for relative and absolute quantification hydrazide (iTRAQH) labelling 
workflow." [PSI:PI, PMID:22926130]
is_a: MS:1002009 ! isobaric label quantitation analysis

[Term]
id: MS:1002761
name: DiART quantitation analysis
def: "Quantification analysis using the amine-reactive deuterium 
isobaric amine reactive tag (DiART) labelling workflow." [PSI:PI, 
PMID:20715779]
is_a: MS:1002009 ! isobaric label quantitation analysis

[Term]
id: MS:1002762
name: DiLeu quantitation analysis
def: "Quantification analysis using the amine-reactive dimethyl leucine 
(DiLeu) tag labelling workflow." [PSI:PI, PMID:20715779]
is_a: MS:1002009 ! isobaric label quantitation analysis

************ Removed the redundant is_a: MS:1001459 ! file format
[Term]
id: MS:1000914
name: tab delimited text format
def: "A file format that has two or more columns of tabular data where 
each column is separated by a TAB character." [PSI:MS]
is_a: MS:1001040 ! intermediate analysis format

************ Removed the redundant is_a: MS:1001455 ! acquisition software
************ Removed the redundant is_a: MS:1001456 ! analysis software
************ Removed the redundant is_a: MS:1001457 ! data processing 
software
[Term]
id: MS:1001878
name: MALDI Solutions Microbial Identification
def: "Shimadzu Biotech software for data acquisition, processing, and 
analysis." [PSI:MS]
is_a: MS:1001558 ! MALDI Solutions

************ Removed the redundant is_a: MS:1001405 ! spectrum 
identification result details
[Term]
id: MS:1001114
name: retention time(s)
def: "OBSOLETE Retention time of the spectrum from the source file." 
[PSI:PI]
comment: This term was made obsolete because scan start time 
(MS:1000016) should be used instead.
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001105 ! peptide sequence-level identification attribute
relationship: has_units UO:0000010 ! second
relationship: has_units UO:0000031 ! minute
is_obsolete: true

Best Regards,
Gerhard

-- 

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

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

*PhD student*

*Medizinisches Proteom-Center*

*DEPARTMENT Medical Bioinformatics*

*Building *ZKF E.055 | Universitätsstraße 150 | D-44801 Bochum

*Fon *+49 (0)234 32-29272 | *Fax *+49 (0)234 32-14554

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

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

Re: [Psidev-ms-dev] [HUPO-PSI/psi-ms-CV] New class suggestions for PSI-MS (#19)

[mayerg97 <ger...@ru...>]

Dear Jane,

we have already in psi-ms.obo a term for MS2 search:
[Term]
id: MS:1001083
name: ms-ms search
def: "An MS2 search (with fragment ions)." [PSI:PI]
is_a: MS:1001080 ! search type

For the other two terms I propose:

[Term]
id: MS:1002985
name: in-gel digestion
def: "Digestion of proteins separated by gel electrophoresis for mass 
spectrometric characterization of proteins and proteomes." [PSI:PI]
is_a: MS:1000831 ! sample preparation

[Term]
id: MS:1002986
name: in-solution digestion
def: "Digestion of proteins in solution for mass spectrometric 
characterization of proteins and proteomes." [PSI:PI]
is_a: MS:1000831 ! sample preparation

Best regards,
Gerhard


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

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

*PhD student*

*Medizinisches Proteom-Center*

*DEPARTMENT Medical Bioinformatics*

*Building *ZKF E.055 | Universitätsstraße 150 | D-44801 Bochum

*Fon *+49 (0)234 32-29272 | *Fax *+49 (0)234 32-14554

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

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

[Psidev-ms-dev] New version 4.1.15 of psi-ms.obo

[mayerg97 <ger...@ru...>]

Dear proteomics/metabolomics community,

since it was urgent, the next new version 4.1.15 (exceptionally without 
a release candidate)
of the psi-ms.obo file can be downloaded from
https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo
It contains a new term for the Andromeda .apl file format.


New CV terms in version 4.1.15 of psi-ms.obo:
=============================================
[Term]
id: MS:1002996
name: Andromeda:apl file format
def: "Peak list file format of the Andromeda search engine." [PSI:PI]
is_a: MS:1000560 ! mass spectrometer file format


Best Regards,
Gerhard
-- 

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

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

*PhD student*

*Medizinisches Proteom-Center*

*DEPARTMENT Medical Bioinformatics*

*Building *ZKF E.055 | Universitätsstraße 150 | D-44801 Bochum

*Fon *+49 (0)234 32-29272 | *Fax *+49 (0)234 32-14554

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

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

[Psidev-ms-dev] New version 4.1.14 of psi-ms.obo

[mayerg97 <ger...@ru...>]

Dear proteomics/metabolomics community,


the new version 4.1.14 of the psi-ms.obo file can be downloaded from
https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo
It contains a new term for Andromeda scoring.


New CV terms in version 4.1.14 of psi-ms.obo:
=============================================
[Term]
id: MS:1002995
name: Andromeda:PEP
def: "Posterior error probability of the best identified peptide of the 
Andromeda search engine." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive
relationship: has_order MS:1002108 ! higher score better

Best Regards,
Gerhard

-- 

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

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

*PhD student*

*Medizinisches Proteom-Center*

*DEPARTMENT Medical Bioinformatics*

*Building *ZKF E.055 | Universitätsstraße 150 | D-44801 Bochum

*Fon *+49 (0)234 32-29272 | *Fax *+49 (0)234 32-14554

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

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

Re: [Psidev-ms-dev] Standardize representation for MS^e and AIF

[Hannes R. <han...@gm...>]

Hi Matt

I would suggest to go with Option 1 since in most other DIA settings,
the high energy scans are treated as MS2 with a isolation window that
specifies which (if any) ions were isolated. Using the scan window as
the isolation window is not *quite* correct since it is possible that
you fragment something that is *not* in the scan window but then
produces fragment ions (e.g. you scan from 0 to 2000 m/z but in your
high energy scan you also fragment a 3000 m/z analyte that produces a
signal at 1800 m/z which you pick up in your high energy scan).

I think setting low energy = MS1 and high energy = MS2 makes most
sense to me, having a new spectrum type does not seem warrented to me.

Best

Hannes

On Mon, Sep 17, 2018 at 10:16 AM, Chambers, Matthew
<mat...@gm...> wrote:
> Hi Eric, you were in the discussion of this issue in the private thread with
> the Waters folks. Do you have a preference for one of the options below, or
> another to suggest?
>
> On 8/14/2018 5:07 PM, Chambers, Matthew wrote:
>
> Hi all,
>
> Over the last few months there have been quite a few users asking me about
> how to distinguish the low and high energy levels in MSe[1]. It seems most
> users expect them to correspond to MS1 and MS2 (most of the users were
> actually reporting all MSe scans being the same MS level as a bug). As far
> as I know, reporting both low and high energy MSe spectra as MS1 is the
> current standard approach. But it seems obvious that users need a way to
> distinguish between the low and high energy spectra, so something needs to
> change with mzML. I see a few options and there may be others.
>
> 1. Keep the existing schema: continue treating low energy spectra as MS1,
> but treat high energy spectra as MSn (ms2) with an isolationWindow the same
> width as the scanWindow, and add a bogus selectedIon in the middle of the
> window.
>
> 2. Change the schema: make isolationWindow and selectedIonList optional so
> collision energy can be stored in the activation element without specifying
> bogus window/ion information.
>
> 3. Change the schema: allow the activation element in either the <scan>
> element or the <precursor> element? This would avoid the need to have a
> "precursor" for a spectrum which really doesn't have one.
>
> With either option 2 or 3, there are a few aspects to decide:
>   a. Should low energy MSe spectra be considered MS1 or MSn (ms2)? If MS1,
> should they still have an activation element in order to preserve collision
> energy info?
>   b. If low energy spectra are treated as MS1, should high energy spectra be
> considered MS1 or MSn (ms2)? High energy spectra certainly need the
> activation element.
>   c. Should MSe spectra get their own spectrum type instead of trying to
> shoehorn them into MS1/MSn? Perhaps a general term like "broadband
> fragmentation spectrum"?
>
> It's not clear to me which option is the best, but if I had to choose I'd
> probably pick 1. Because it won't force schema-validating parsers to update,
> and old software will still be able to read the new files (but that would
> only be a good thing in SOME cases; in other cases the software should
> probably give an error that it can't handle that kind of data).
>
> This has been an outstanding issue for mzML for a while. I hope we can
> finally get it resolved.
>
> Thanks,
> -Matt
>
>
> [1] Briefly, MSe is a data-independent-acquisition method where all ions are
> fragmented simultaneously rather than isolating any specific precursors.
> It's up to the analyzing software to make sense of the resulting complex
> spectra by looking at how the peaks change over time. The technique may or
> may not be combined with ion mobility separation (HDMSe). The spectra are
> acquired in an every-other-scan scheme, i.e. low-high-low-high-low-high. Low
> energy spectra have very little collision energy, but it's not exactly zero.
>
>
>
>
> _______________________________________________
> Psidev-ms-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
>

Re: [Psidev-ms-dev] Standardize representation for MS^e and AIF

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

Hi Eric, you were in the discussion of this issue in the private thread with the Waters folks. Do you have a preference for one of the 
options below, or another to suggest?

On 8/14/2018 5:07 PM, Chambers, Matthew wrote:
> Hi all,
>
> Over the last few months there have been quite a few users asking me about how to distinguish the low and high energy levels in MS^e [1]. 
> It seems most users expect them to correspond to MS1 and MS2 (most of the users were actually reporting all MS^e scans being the same MS 
> level as a bug). As far as I know, reporting both low and high energy MS^e spectra as MS1 is the current standard approach. But it seems 
> obvious that users need a way to distinguish between the low and high energy spectra, so something needs to change with mzML. I see a few 
> options and there may be others.
>
> 1. Keep the existing schema: continue treating low energy spectra as MS1, but treat high energy spectra as MSn (ms2) with an 
> isolationWindow the same width as the scanWindow, and add a bogus selectedIon in the middle of the window.
>
> 2. Change the schema: make isolationWindow and selectedIonList optional so collision energy can be stored in the activation element 
> without specifying bogus window/ion information.
>
> 3. Change the schema: allow the activation element in either the <scan> element or the <precursor> element? This would avoid the need to 
> have a "precursor" for a spectrum which really doesn't have one.
>
> With either option 2 or 3, there are a few aspects to decide:
>   a. Should low energy MS^e spectra be considered MS1 or MSn (ms2)? If MS1, should they still have an activation element in order to 
> preserve collision energy info?
>   b. If low energy spectra are treated as MS1, should high energy spectra be considered MS1 or MSn (ms2)? High energy spectra certainly 
> need the activation element.
>   c. Should MS^e spectra get their own spectrum type instead of trying to shoehorn them into MS1/MSn? Perhaps a general term like 
> "broadband fragmentation spectrum"?
>
> It's not clear to me which option is the best, but if I had to choose I'd probably pick 1. Because it won't force schema-validating 
> parsers to update, and old software will still be able to read the new files (but that would only be a good thing in SOME cases; in other 
> cases the software should probably give an error that it can't handle that kind of data).
>
> This has been an outstanding issue for mzML for a while. I hope we can finally get it resolved.
>
> Thanks,
> -Matt
>
>
> [1] Briefly, MS^e is a data-independent-acquisition method where all ions are fragmented simultaneously rather than isolating any specific 
> precursors. It's up to the analyzing software to make sense of the resulting complex spectra by looking at how the peaks change over time. 
> The technique may or may not be combined with ion mobility separation (HDMS^e ). The spectra are acquired in an every-other-scan scheme, 
> i.e. low-high-low-high-low-high. Low energy spectra have very little collision energy, but it's not exactly zero.

[Psidev-ms-dev] Release candidate 4.1.14_rc1 of psi-ms.obo

[mayerg97 <ger...@ru...>]

Dear proteomics/metabolomics community,

following are new and changed terms for the release candidate 4.1.14_rc1 
of the psi-ms.obo file.
It contains a new term for Andromeda.

New CV terms in version 4.1.14_rc1 of psi-ms.obo:
=================================================
[Term]
id: MS:1002995
name: Andromeda:PEP
def: "Posterior error probability of the best identified peptide of the 
Andromeda search engine." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive
relationship: has_order MS:1002108 ! higher score better

Best Regards,
Gerhard

-- 

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

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

*PhD student*

*Medizinisches Proteom-Center*

*DEPARTMENT Medical Bioinformatics*

*Building *ZKF E.055 | Universitätsstraße 150 | D-44801 Bochum

*Fon *+49 (0)234 32-29272 | *Fax *+49 (0)234 32-14554

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

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

[Psidev-ms-dev] New version 4.1.13 of psi-ms.obo

[mayerg97 <ger...@ru...>]

Dear proteomics/metabolomics community,


the new version 4.1.13 of the psi-ms.obo file can be downloaded from
https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo
It contains new terms for de novo software.

New CV terms in version 4.1.13 of psi-ms.obo:
=============================================
************ New terms for de novo software
[Term]
id: MS:1002982
name: PepNovo
def: "PepNovo tool for de novo peptide sequencing." [PMID:15858974]
is_a: MS:1001456 ! analysis software

[Term]
id: MS:1002983
name: pNovo
def: "pNovo tool for de novo peptide sequencing and identification using 
HCD spectra." [PMID:20329752]
is_a: MS:1001456 ! analysis software

[Term]
id: MS:1002984
name: Novor
def: "Novor real-time peptide de novo sequencing software tool." 
[PMID:26122521]
is_a: MS:1001456 ! analysis software


Changed CV terms in version 4.1.13 of psi-ms.obo:
=================================================
************ Changed value slot from xsd\:date to xsd\:dateTime
[Term]
id: MS:1000747
name: completion time
def: "The time that a data processing action was finished." [PSI:MS]
xref: value-type:xsd\:dateTime "The allowed value-type for this CV term."
is_a: MS:1000630 ! data processing parameter

[Term]
id: MS:1002435
name: data processing start time
def: "The time that a data processing action was started." [PSI:MS]
xref: value-type:xsd\:dateTime "The allowed value-type for this CV term."
is_a: MS:1000630 ! data processing parameter

Best Regards,
Gerhard

-- 

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

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

*PhD student*

*Medizinisches Proteom-Center*

*DEPARTMENT Medical Bioinformatics*

*Building *ZKF E.055 | Universitätsstraße 150 | D-44801 Bochum

*Fon *+49 (0)234 32-29272 | *Fax *+49 (0)234 32-14554

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

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

[Psidev-ms-dev] Release candidate 4.1.13_rc1 of psi-ms.obo

[mayerg97 <ger...@ru...>]

Dear proteomics/metabolomics community,


following are new and changed terms for the release candidate 4.1.13_rc1 
of the psi-ms.obo file.
It contains new terms for de novo software.

New CV terms in version 4.1.13_rc1 of psi-ms.obo:
=================================================
************ New terms for de novo software
[Term]
id: MS:1002982
name: PepNovo
def: "PepNovo tool for de novo peptide sequencing." [PMID:15858974]
is_a: MS:1001456 ! analysis software

[Term]
id: MS:1002983
name: pNovo
def: "pNovo tool for de novo peptide sequencing and identification using 
HCD spectra." [PMID:20329752]
is_a: MS:1001456 ! analysis software

[Term]
id: MS:1002984
name: Novor
def: "Novor real-time peptide de novo sequencing software tool." 
[PMID:26122521]
is_a: MS:1001456 ! analysis software


Changed CV terms in version 4.1.13_rc1 of psi-ms.obo:
=====================================================
************ Changed value slot form xsd\:date to xsd\:dateTime
[Term]
id: MS:1000747
name: completion time
def: "The time that a data processing action was finished." [PSI:MS]
xref: value-type:xsd\:dateTime "The allowed value-type for this CV term."
is_a: MS:1000630 ! data processing parameter

[Term]
id: MS:1002435
name: data processing start time
def: "The time that a data processing action was started." [PSI:MS]
xref: value-type:xsd\:dateTime "The allowed value-type for this CV term."
is_a: MS:1000630 ! data processing parameter

Best Regards,
Gerhard

-- 

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

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

*PhD student*

*Medizinisches Proteom-Center*

*DEPARTMENT Medical Bioinformatics*

*Building *ZKF E.055 | Universitätsstraße 150 | D-44801 Bochum

*Fon *+49 (0)234 32-29272 | *Fax *+49 (0)234 32-14554

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

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

[Psidev-ms-dev] Standardize representation for MS^e and AIF

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

Hi all,

Over the last few months there have been quite a few users asking me about how to distinguish the low and high energy levels in MS^e [1]. It 
seems most users expect them to correspond to MS1 and MS2 (most of the users were actually reporting all MS^e scans being the same MS level 
as a bug). As far as I know, reporting both low and high energy MS^e spectra as MS1 is the current standard approach. But it seems obvious 
that users need a way to distinguish between the low and high energy spectra, so something needs to change with mzML. I see a few options 
and there may be others.

1. Keep the existing schema: continue treating low energy spectra as MS1, but treat high energy spectra as MSn (ms2) with an isolationWindow 
the same width as the scanWindow, and add a bogus selectedIon in the middle of the window.

2. Change the schema: make isolationWindow and selectedIonList optional so collision energy can be stored in the activation element without 
specifying bogus window/ion information.

3. Change the schema: allow the activation element in either the <scan> element or the <precursor> element? This would avoid the need to 
have a "precursor" for a spectrum which really doesn't have one.

With either option 2 or 3, there are a few aspects to decide:
   a. Should low energy MS^e spectra be considered MS1 or MSn (ms2)? If MS1, should they still have an activation element in order to 
preserve collision energy info?
   b. If low energy spectra are treated as MS1, should high energy spectra be considered MS1 or MSn (ms2)? High energy spectra certainly 
need the activation element.
   c. Should MS^e spectra get their own spectrum type instead of trying to shoehorn them into MS1/MSn? Perhaps a general term like 
"broadband fragmentation spectrum"?

It's not clear to me which option is the best, but if I had to choose I'd probably pick 1. Because it won't force schema-validating parsers 
to update, and old software will still be able to read the new files (but that would only be a good thing in SOME cases; in other cases the 
software should probably give an error that it can't handle that kind of data).

This has been an outstanding issue for mzML for a while. I hope we can finally get it resolved.

Thanks,
-Matt


[1] Briefly, MS^e is a data-independent-acquisition method where all ions are fragmented simultaneously rather than isolating any specific 
precursors. It's up to the analyzing software to make sense of the resulting complex spectra by looking at how the peaks change over time. 
The technique may or may not be combined with ion mobility separation (HDMS^e ). The spectra are acquired in an every-other-scan scheme, 
i.e. low-high-low-high-low-high. Low energy spectra have very little collision energy, but it's not exactly zero.
^

[Psidev-ms-dev] New version 4.1.12 of psi-ms.obo

[mayerg97 <ger...@ru...>]

Dear proteomics/metabolomics community,

the new version 4.1.12 of the psi-ms.obo file can be downloaded from
https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo

It contains a new term for the Proline software.


New CV terms in version 4.1.12 of psi-ms.obo:
=============================================
[Term]
id: MS:1002981
name: Proline
def: "The Proline software suite for mass spectrometry based 
proteomics." [http://www.profiproteomics.fr/proline/]
is_a: MS:1001456 ! analysis software


Best Regards,
Gerhard

-- 

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

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

*PhD student*

*Medizinisches Proteom-Center*

*DEPARTMENT Medical Bioinformatics*

*Building *ZKF E.055 | Universitätsstraße 150 | D-44801 Bochum

*Fon *+49 (0)234 32-29272 | *Fax *+49 (0)234 32-14554

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

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

[Psidev-ms-dev] Tool Training for Proteomics in Bochum

[Julian U. <jul...@ru...>]

Dear colleague,
dear member of the proteomics community,

we would like to call your attention to the training course
    "Tool Training for Proteomics"
which we will be hosted on 16th October 2018 at Ruhr University Bochum
as part of the de.NBI (www.denbi.de) training programme.

Besides the tool based sessions we offer a "bring your own data" session
to discuss and try out analysis strategies of your own special data.

As the number of participants is limited, please register soon at
http://l.rub.de/20f01037 if you are interested.

Further information about the course is available at the
registration page and soon also at http://www.denbi.de/training-courses.

If you have any questions don’t hesitate to contact us via
bio...@ru...

Please also forward this message to potentially interested colleagues.

Best regards,
    Julian Uszkoreit

Re: [Psidev-ms-dev] New version 1.1.4 of XLMOD.obo

[mayerg97 <ger...@ru...>]

Sorry, that was the wrong link, here is the corrected one:

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

Best regards,

Gerhard


Am 13.07.2018 um 13:42 schrieb mayerg97:
>
> Dear proteomics/metabolomics community,
>
> the new version 1.1.4 of the XLMOD.obo file can be downloaded from
> https://raw.githubusercontent.com/HUPO-PSI/mzIdentML/master/cv/XLMOD.obo
>
> It contains many new terms for GCMS and LCMS derivatization reagents.
>
> Best Regards,
> Gerhard
>
> -- 
>
> *--------------------------------------------------------------------*
>
> *Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER*
>
> *PhD student*
>
> *Medizinisches Proteom-Center*
>
> *DEPARTMENT Medical Bioinformatics*
>
> *Building *ZKF E.055 | Universitätsstraße 150 | D-44801 Bochum
>
> *Fon *+49 (0)234 32-29272 | *Fax *+49 (0)234 32-14554
>
> *E-mail***ger...@ru... <mailto:ger...@ru...>
>
> www.medizinisches-proteom-center.de 
> <http://www.medizinisches-proteom-center.de/>
>

-- 

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

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

*PhD student*

*Medizinisches Proteom-Center*

*DEPARTMENT Medical Bioinformatics*

*Building *ZKF E.055 | Universitätsstraße 150 | D-44801 Bochum

*Fon *+49 (0)234 32-29272 | *Fax *+49 (0)234 32-14554

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

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

[Psidev-ms-dev] New version 1.1.4 of XLMOD.obo

[mayerg97 <ger...@ru...>]

Dear proteomics/metabolomics community,

the new version 1.1.4 of the XLMOD.obo file can be downloaded from
https://raw.githubusercontent.com/HUPO-PSI/mzIdentML/master/cv/XLMOD.obo

It contains many new terms for GCMS and LCMS derivatization reagents.

Best Regards,
Gerhard

-- 

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

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

*PhD student*

*Medizinisches Proteom-Center*

*DEPARTMENT Medical Bioinformatics*

*Building *ZKF E.055 | Universitätsstraße 150 | D-44801 Bochum

*Fon *+49 (0)234 32-29272 | *Fax *+49 (0)234 32-14554

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

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

[Psidev-ms-dev] New version 4.1.11 of psi-ms.obo

[mayerg97 <ger...@ru...>]

Dear proteomics/metabolomics community,

the new version 4.1.11 of the psi-ms.obo file can be downloaded from
https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo

It contains some further terms for specifying lipidomics tools in mzTab-L.


New CV terms in version 4.1.11 of psi-ms.obo:
=============================================
[Term]
id: MS:1002977
name: ALEX123
def: "Analysis of lipid experiments 123, a calculator with m/z values of 
intact lipid molecules (MS1) and their fragment ions at the MS2 and MS3 
level." [PMID:29786091]
is_a: MS:1002964 ! lipidomics analysis software
is_a: MS:1001457 ! data processing software

id: MS:1002978
name: LIMSA
def: "Software tool for the quantitative analysis of mass spectrometric 
lipidome data." [PMID:17165823]
is_a: MS:1002964 ! lipidomics analysis software
is_a: MS:1001457 ! data processing software

id: MS:1002979
name: LOBSTAHS
def: "Adduct-Based lipidomics software for the discovery and 
identification of oxidative stress biomarkers." [PMID:27322848]
is_a: MS:1002964 ! lipidomics analysis software
is_a: MS:1001457 ! data processing software

id: MS:1002980
name: LipidQA
def: "Lipid qualitative/quantitative analysis software for 
identification and quantitation of complex lipid molecular species." 
[PMID:17720531]
is_a: MS:1002964 ! lipidomics analysis software
is_a: MS:1001457 ! data processing software


Changed CV terms in version 4.1.11 of psi-ms.obo:
=================================================
************ Changed the definition
[Term]
id: MS:1002976
name: ALEX
def: "Analysis of lipid experiments, a calculator for m/z values of 
intact lipid molecules (MS1)." [PMID:24244551]
is_a: MS:1002964 ! lipidomics analysis software
is_a: MS:1001457 ! data processing software

Best Regards,
Gerhard

-- 

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

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

*PhD student*

*Medizinisches Proteom-Center*

*DEPARTMENT Medical Bioinformatics*

*Building *ZKF E.055 | Universitätsstraße 150 | D-44801 Bochum

*Fon *+49 (0)234 32-29272 | *Fax *+49 (0)234 32-14554

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

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

[Psidev-ms-dev] Release candidate 4.1.11_rc1 of psi-ms.obo

[mayerg97 <ger...@ru...>]

Dear proteomics/metabolomics community,

following are new terms from the release candidate 4.1.11_rc1 of the 
psi-ms.obo file.
It contains some further terms for specifying lipidomics tools in mzTab-L.


New CV terms in version 4.1.11_rc1 of psi-ms.obo:
=================================================
[Term]
id: MS:1002977
name: ALEX123
def: "Analysis of lipid experiments 123, a calculator with m/z values of 
intact lipid molecules (MS1) and their fragment ions at the MS2 and MS3 
level." [PMID:29786091]
is_a: MS:1002964 ! lipidomics analysis software
is_a: MS:1001457 ! data processing software

id: MS:1002978
name: LIMSA
def: "Software tool for the quantitative analysis of mass spectrometric 
lipidome data." [PMID:17165823]
is_a: MS:1002964 ! lipidomics analysis software
is_a: MS:1001457 ! data processing software

id: MS:1002979
name: LOBSTAHS
def: "Adduct-Based lipidomics software for the discovery and 
identification of oxidative stress biomarkers." [PMID:27322848]
is_a: MS:1002964 ! lipidomics analysis software
is_a: MS:1001457 ! data processing software

id: MS:1002980
name: LipidQA
def: "Lipid qualitative/quantitative analysis software for 
identification and quantitation of complex lipid molecular species." 
[PMID:17720531]
is_a: MS:1002964 ! lipidomics analysis software
is_a: MS:1001457 ! data processing software


Changed CV terms in version 4.1.11_rc1 of psi-ms.obo:
=====================================================
************ Changed the definition
[Term]
id: MS:1002976
name: ALEX
def: "Analysis of lipid experiments, a calculator for m/z values of 
intact lipid molecules (MS1)." [PMID:24244551]
is_a: MS:1002964 ! lipidomics analysis software
is_a: MS:1001457 ! data processing software

Best Regards,
Gerhard

-- 

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

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

*PhD student*

*Medizinisches Proteom-Center*

*DEPARTMENT Medical Bioinformatics*

*Building *ZKF E.055 | Universitätsstraße 150 | D-44801 Bochum

*Fon *+49 (0)234 32-29272 | *Fax *+49 (0)234 32-14554

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

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

[Psidev-ms-dev] New version 4.1.10 of psi-ms.obo

[mayerg97 <ger...@ru...>]

Dear proteomics/metabolomics community,

the new version 4.1.10 of the psi-ms.obo file can be downloaded from
https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo
It contains new terms for specifying lipidomics tools in mzTab-L.

New CV terms in version 4.1.10 of psi-ms.obo:
=============================================
[Term]
id: MS:1002962
name: mean
def: "The arithmetic mean." [PSI:PI]
is_a: MS:1002882 ! study variable average function

[Term]
id: MS:1002963
name: variation coefficient
def: "The coefficient of variation." [PSI:PI]
is_a: MS:1002884 ! study variable variation function

[Term]
id: MS:1002964
name: lipidomics analysis software
def: "Lipidomics analysis software." [PSI:PI]
is_a: MS:1002878 ! small molecule analysis software

[Term]
id: MS:1002965
name: Lipid Data Analyzer
def: "Lipid Data Analyzer software for lipid quantification." 
[PMID:29058722]
is_a: MS:1002964 ! lipidomics analysis software
is_a: MS:1001457 ! data processing software

[Term]
id: MS:1002966
name: chrom format
def: "The Lipid Data Analyzer native chrom format." [PSI:PI]
is_a: MS:1000560 ! mass spectrometer file format

[Term]
id: MS:1002967
name: LipidHunter
def: "Software for identification of phospholipids by high-throughput 
processing of LC-MS and shotgun lipidomics datasets." [PMID:28753264]
is_a: MS:1002964 ! lipidomics analysis software
is_a: MS:1001457 ! data processing software

[Term]
id: MS:1002968
name: LipidXplorer
def: "Software for consensual cross-platform lipidomics." [PMID:22272252]
is_a: MS:1002964 ! lipidomics analysis software
is_a: MS:1001457 ! data processing software

[Term]
id: MS:1002969
name: LipidMatch
def: "An automated workflow for rule-based lipid identification using 
untargeted high-resolution tandem mass spectrometry data." [PMID:28693421]
is_a: MS:1002964 ! lipidomics analysis software
is_a: MS:1001457 ! data processing software

[Term]
id: MS:1002970
name: Greazy
def: "Open-source software for automated phospholipid tandem mass 
spectrometry identification." [PMID:27186799]
is_a: MS:1002964 ! lipidomics analysis software
is_a: MS:1001457 ! data processing software

[Term]
id: MS:1002971
name: LipidBlast
def: "LC-MS-based lipidomics and automated identification of lipids 
using the LipidBlast in-silico MS/MS library." [PMID:28660581]
is_a: MS:1002964 ! lipidomics analysis software
is_a: MS:1001457 ! data processing software

[Term]
id: MS:1002972
name: Lipid-Pro
def: "A computational lipid identification solution for untargeted 
lipidomics on data-independent acquisition tandem mass spectrometry 
platforms." [PMID:25433698]
is_a: MS:1002964 ! lipidomics analysis software
is_a: MS:1001457 ! data processing software

[Term]
id: MS:1002973
name: LipidFinder
def: "A computational workflow for the discovery of lipids for the 
identification of eicosanoid-phosphoinositides in platelets." 
[PMID:28405621]
is_a: MS:1002964 ! lipidomics analysis software
is_a: MS:1001457 ! data processing software

[Term]
id: MS:1002974
name: LipiDex
def: "An integrated software package for high-confidence lipid 
identification." [PMID:29705063]
is_a: MS:1002964 ! lipidomics analysis software
is_a: MS:1001457 ! data processing software

[Term]
id: MS:1002975
name: LIQUID
def: "An-open source software for identifying lipids in LC-MS/MS-based 
lipidomics data." [PMID:28158427]
is_a: MS:1002964 ! lipidomics analysis software
is_a: MS:1001457 ! data processing software

[Term]
id: MS:1002976
name: ALEX
def: "Analysis of lipid experiments, a software framework for the 
analysis of high-resolution shotgun lipidomics data." [PMID:24244551]
is_a: MS:1002964 ! lipidomics analysis software
is_a: MS:1001457 ! data processing software


Changed CV terms in version 4.1.10 of psi-ms.obo:
=================================================
No changed terms

Best Regards,
Gerhard

-- 

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

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

*PhD student*

*Medizinisches Proteom-Center*

*DEPARTMENT Medical Bioinformatics*

*Building *ZKF E.055 | Universitätsstraße 150 | D-44801 Bochum

*Fon *+49 (0)234 32-29272 | *Fax *+49 (0)234 32-14554

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

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

[Psidev-ms-dev] Release candidate 4.1.10_rc1 of psi-ms.obo

[mayerg97 <ger...@ru...>]

Dear proteomics/metabolomics community,

following are new terms from the release candidate 4.1.10_rc1 of the 
psi-ms.obo file.
It contains new terms for specifying lipidomics tools in mzTab-L.


New CV terms in version 4.1.10_rc1 of psi-ms.obo:
=================================================
[Term]
id: MS:1002962
name: mean
def: "The arithmetic mean." [PSI:PI]
is_a: MS:1002882 ! study variable average function

[Term]
id: MS:1002963
name: variation coefficient
def: "The coefficient of variation." [PSI:PI]
is_a: MS:1002884 ! study variable variation function

[Term]
id: MS:1002964
name: lipidomics analysis software
def: "Lipidomics analysis software." [PSI:PI]
is_a: MS:1002878 ! small molecule analysis software

[Term]
id: MS:1002965
name: Lipid Data Analyzer
def: "Lipid Data Analyzer software for lipid quantification." 
[PMID:29058722]
is_a: MS:1002964 ! lipidomics analysis software
is_a: MS:1001457 ! data processing software

[Term]
id: MS:1002966
name: chrom format
def: "The Lipid Data Analyzer native chrom format." [PSI:PI]
is_a: MS:1000560 ! mass spectrometer file format

[Term]
id: MS:1002967
name: LipidHunter
def: "Software for identification of phospholipids by high-throughput 
processing of LC-MS and shotgun lipidomics datasets." [PMID:28753264]
is_a: MS:1002964 ! lipidomics analysis software
is_a: MS:1001457 ! data processing software

[Term]
id: MS:1002968
name: LipidXplorer
def: "Software for consensual cross-platform lipidomics." [PMID:22272252]
is_a: MS:1002964 ! lipidomics analysis software
is_a: MS:1001457 ! data processing software

[Term]
id: MS:1002969
name: LipidMatch
def: "An automated workflow for rule-based lipid identification using 
untargeted high-resolution tandem mass spectrometry data." [PMID:28693421]
is_a: MS:1002964 ! lipidomics analysis software
is_a: MS:1001457 ! data processing software

[Term]
id: MS:1002970
name: Greazy
def: "Open-source software for automated phospholipid tandem mass 
spectrometry identification." [PMID:27186799]
is_a: MS:1002964 ! lipidomics analysis software
is_a: MS:1001457 ! data processing software

[Term]
id: MS:1002971
name: LipidBlast
def: "LC-MS-based lipidomics and automated identification of lipids 
using the LipidBlast in-silico MS/MS library." [PMID:28660581]
is_a: MS:1002964 ! lipidomics analysis software
is_a: MS:1001457 ! data processing software

[Term]
id: MS:1002972
name: Lipid-Pro
def: "A computational lipid identification solution for untargeted 
lipidomics on data-independent acquisition tandem mass spectrometry 
platforms." [PMID:25433698]
is_a: MS:1002964 ! lipidomics analysis software
is_a: MS:1001457 ! data processing software

[Term]
id: MS:1002973
name: LipidFinder
def: "A computational workflow for the discovery of lipids for the 
identification of eicosanoid-phosphoinositides in platelets." 
[PMID:28405621]
is_a: MS:1002964 ! lipidomics analysis software
is_a: MS:1001457 ! data processing software

[Term]
id: MS:1002974
name: LipiDex
def: "An integrated software package for high-confidence lipid 
identification." [PMID:29705063]
is_a: MS:1002964 ! lipidomics analysis software
is_a: MS:1001457 ! data processing software

[Term]
id: MS:1002975
name: LIQUID
def: "An-open source software for identifying lipids in LC-MS/MS-based 
lipidomics data." [PMID:28158427]
is_a: MS:1002964 ! lipidomics analysis software
is_a: MS:1001457 ! data processing software

[Term]
id: MS:1002976
name: ALEX
def: "Analysis of lipid experiments, a software framework for the 
analysis of high-resolution shotgun lipidomics data." [PMID:24244551]
is_a: MS:1002964 ! lipidomics analysis software
is_a: MS:1001457 ! data processing software


Changed CV terms in version 4.1.10_rc1 of psi-ms.obo:
=====================================================
No changed terms

Best Regards,
Gerhard

-- 

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

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

*PhD student*

*Medizinisches Proteom-Center*

*DEPARTMENT Medical Bioinformatics*

*Building *ZKF E.055 | Universitätsstraße 150 | D-44801 Bochum

*Fon *+49 (0)234 32-29272 | *Fax *+49 (0)234 32-14554

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

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

[Psidev-ms-dev] New version 4.1.9 of psi-ms.obo

[mayerg97 <ger...@ru...>]

Dear proteomics/metabolomics community,

the new version 4.1.9 of the psi-ms.obo file can be downloaded from
https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo

It contains new terms for isomer, isotopomer, isotopologue and their peaks
as well as name changes for the PEFF regular expression terms.


New CV terms in version 4.1.9 of psi-ms.obo:
============================================
[Term]
id: MS:1002955
name: hr-ms compound identification confidence level
def: "Refined High Resolution mass spectrometry confidence level for 
annotation of identified compounds as proposed by Schymanski et al. The 
value slot can have the values 'Level 1', 'Level 2', 'Level 2a', 'Level 
2b', 'Level 3', 'Level 4', and 'Level 5'." [PMID:24476540]
xref: value-type:xsd:string "The allowed value-type for this CV term."
is_a: MS:1002895 ! small molecule identification attribute

[Term]
id: MS:1002956
name: isotopic ion MS peak
def: "A mass spectrometry peak that represents one or more isotopic 
ions. The value slot contains a description of the represented isotope 
set, e.g. 'M+1 peak'." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1000231 ! peak

[Term]
id: MS:1002957
name: isotopomer MS peak
def: "The described isotopomer mass spectrometric signal. The value slot 
contains a description of the represented isotopomer, e.g. '13C peak', 
'15N peak', '2H peak', '18O peak' or '31P peak'." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002956 ! isotopic ion MS peak

[Term]
id: MS:1002958
name: isotopologue MS peak
def: "The described isotopologue mass spectrometric signal. The value 
slot contains a description of the represented isotopologue, e.g. '13C1 
peak' or '15N1 peak'." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002956 ! isotopic ion MS peak

[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."
relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass 
Spectrometry Ontology

[Term]
id: MS:1002960
name: isotopomer
def: "An isomer that differs from another only in the spatial 
distribution of the constitutive isotopic atoms." 
[https://goldbook.iupac.org/html/I/I03352.html]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002959 ! isomer

[Term]
id: MS:1002961
name: isotopologue
def: "A molecular entity that differs only in isotopic composition 
(number of isotopic substitutions)." 
[https://goldbook.iupac.org/html/I/I03351.html]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002959 ! isomer



Changed CV terms in version 4.1.9 of psi-ms.obo:
================================================
************ Obsoleted the following term
[Term]
id: MS:1002897
name: isotopomer peak
def: "OBSOLETE Identifies a peak when no de-isotoping has been 
performed. The value slot reports the isotopomer peak, e.g. '2H', '13C', 
'15N', '18O', '31P'." [PSI:PI]
comment: This term was obsoleted because it was replaced by the more 
exact terms terms MS:1002956 'isotopic ion MS peak', MS:1002957 
'isotopomer MS peak' and MS:1002958 'isotopologue MS peak' instead.
xref: value-type:xsd:string "The allowed value-type for this CV term."
is_a: MS:1000231 ! peak
is_obsolete: true

************ Exchanged the name and definition for the PEFF regular 
expression
************ terms PEFF:1002001, PEFF:1002002 and PEFF:1002003 in order 
to make
************ the psi-ms.obo file loadable in OBO-Edit again (currently the
************ validator exits with an error message special characters 
are not
************ allowed in names).
[Term]
id: PEFF:1002001
name: regular expression for PEFF description line
def: "([0-9]+|[0-9]+|[a-zA-Z0-9]*)." [PSI:PEFF]
is_a: MS:1002479 ! regular expression

[Term]
id: PEFF:1002002
name: regular expression for PEFF molecular sequence type
def: 
"(AA|NA|DNA|cDNA|RNA|RNAi|tRNA|rRNA|siRNA|mDNA|mRNA|snoRNA|ncRNA|EST|[a-z0-9A-Z]+)." 
[PSI:PEFF]
is_a: MS:1002479 ! regular expression

[Term]
id: PEFF:1002003
name: regular expression for PEFF sequence status
def: "(Complete|Fragment|[a-z0-9A-Z]+)." [PSI:PEFF]
is_a: MS:1002479 ! regular expression

Best Regards,
Gerhard

-- 

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

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

*PhD student*

*Medizinisches Proteom-Center*

*DEPARTMENT Medical Bioinformatics*

*Building *ZKF E.055 | Universitätsstraße 150 | D-44801 Bochum

*Fon *+49 (0)234 32-29272 | *Fax *+49 (0)234 32-14554

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

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