Re: [Psidev-pi-dev] Release candidate 3.89.0_rc3 of psi-ms.obo

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Hi Gerhard,

Could you add a term for the new Sciex X500R QTOF?

[Term]
id: MS:1000xxx
name: X500R QTOF
def: "SCIEX X500R QTOF, a quadrupole - quadrupole - time-of-flight mass spectrometer." [PSI:MS]
is_a: MS:1000121 ! SCIEX instrument model

Thanks,
-Matt

On 6/3/2016 4:05 AM, mayerg97 wrote:
>
> Dear proteomics community,
>
> attached there's the release candidate 3.89.0_rc3 of the psi-ms.obo file.
>
>
> New CV terms in version 3.89.0_rc3 of psi-ms.obo:
> =================================================
> ************ Added a string value slot holding the molecular formula in Hill notation
> [Term]
> id: MS:1000336
> name: neutral loss
> def: "The loss of an uncharged species during a rearrangement process. The value slot holds the molecular formula in Hill notation of the 
> neutral loss molecule, see PMID: 21182243. This term must be used in conjunction with a child of the term MS:1002307 (fragmentation ion 
> type)." [PSI:MS]
> xref: value-type:xsd\:string "The allowed value-type for this CV term."
> is_a: MS:1001055 ! modification parameters
>
> ************ New terms for reporter ions
> ************ The mass can be specified in the value slot.
> [Term]
> id: MS:1002668
> name: frag: iTRAQ 4plex reporter ion
> def: "Standard reporter ion for iTRAQ 4Plex. The value slot holds the mass of the iTRAQ 4Plex reporter ion." [PSI:PI]
> xref: value-type:xsd\:int "The allowed value-type for this CV term."
> is_a: MS:1002307 ! fragmentation ion type
>
> [Term]
> id: MS:1002669
> name: frag: iTRAQ 8plex reporter ion
> def: "Standard reporter ion for iTRAQ 8Plex. The value slot holds the mass of the iTRAQ 8Plex reporter ion." [PSI:PI]
> xref: value-type:xsd\:int "The allowed value-type for this CV term."
> is_a: MS:1002307 ! fragmentation ion type
>
> [Term]
> id: MS:1002670
> name: frag: TMT reporter ion
> def: "Standard reporter ion for TMT. The value slot holds the mass of the iTRAQ 8Plex reporter ion and can be suffixed with either N or C, 
> indicating whether the mass difference is encoded at a Nitrogen or Carbon atom." [PSI:PI]
> xref: value-type:xsd\:string "The allowed value-type for this CV term."
> is_a: MS:1002307 ! fragmentation ion type
>
> [Term]
> id: MS:1002671
> name: frag: TMT ETD reporter ion
> def: "Standard reporter ion for TMT with ETD fragmentation. The value slot holds the mass of the iTRAQ 8Plex reporter ion and can be 
> suffixed with either N or C, indicating whether the mass difference is encoded at a Nitrogen or Carbon atom." [PSI:PI]
> xref: value-type:xsd\:string "The allowed value-type for this CV term."
> is_a: MS:1002307 ! fragmentation ion type
>
> [Term]
> id: MS:1002672
> name: no modification threshold
> def: "No statistical threshold for accepting or rejecting that a modification position." [PSI:PI]
> is_a: MS:1002555 ! PTM localization score threshold
>
> [Term]
> id: MS:1002673
> name: OpenXQuest
> def: "Cross-Linking MS search engine." [PSI:PI]
> is_a: MS:1000752 ! TOPP software
>
>
> Changed CV terms in version 3.89.0_rc3 of psi-ms.obo:
> =====================================================
> ************ Changed the regular expression to allow null for the interaction position
> [Term]
> id: MS:1002665
> name: regular expression for protein interaction scores derived from cross-linking
> def: "([:digit:]+[.][a|b]:([:digit:]+|null):[:digit:]+[.][:digit:]+([Ee][+-][0-9]+)*:(true|false]\{1\})" [PSI:PI]
> is_a: MS:1002479 ! regular expression
>
> ************ Obsoleted the following terms.
> [Term]
> id: MS:1002455
> name: H2O neutral loss
> def: "OBSOLETE Neutral loss of water." [PSI:PI]
> comment: This term was obsoleted because it should be replaced by MS:1000336 with value H2O.
> is_a: MS:1000336 ! neutral loss
> is_a: MS:1002473 ! ion series considered in search
> is_obsolete: true
>
> [Term]
> id: MS:1002456
> name: NH3 neutral loss
> def: "OBSOLETE Neutral loss of ammonia." [PSI:PI]
> comment: This term was obsoleted because it should be replaced by MS:1000336 with value NH3.
> is_a: MS:1000336 ! neutral loss
> is_a: MS:1002473 ! ion series considered in search
> is_obsolete: true
>
> [Term]
> id: MS:1002457
> name: H3PO4 neutral loss
> def: "OBSOLETE Neutral loss of phosphoric acid." [PSI:PI]
> comment: This term was obsoleted because it should be replaced by MS:1000336 with value H3PO4.
> is_a: MS:1000336 ! neutral loss
> is_a: MS:1002473 ! ion series considered in search
> is_obsolete: true
>
> ************ REARRANGEMENT OF PSM-level result details BRANCH ************ (see attached figure)
> ************ The following two terms moved from
> ************ is_a: MS:1001872 ! distinct peptide-level e-value
> ************ to is_a: MS:1002353 ! PSM-level e-value
> [Term]
> id: MS:1001328
> name: OMSSA:evalue
> def: "OMSSA E-value." [PSI:PI]
> xref: value-type:xsd\:double "The allowed value-type for this CV term."
> is_a: MS:1001143 ! search engine specific score for PSMs
> is_a: MS:1001153 ! search engine specific score
> is_a: MS:1002353 ! PSM-level e-value
>
> [Term]
> id: MS:1001330
> name: X\!Tandem:expect
> def: "The X!Tandem expectation value." [PSI:PI]
> xref: value-type:xsd\:double "The allowed value-type for this CV term."
> is_a: MS:1001143 ! search engine specific score for PSMs
> is_a: MS:1001153 ! search engine specific score
> is_a: MS:1002353 ! PSM-level e-value
>
> ************ The following two terms moved from
> ************ is_a: MS:1001870 ! distinct peptide-level p-value
> ************ to is_a: MS:1002352 ! PSM-level p-value
> [Term]
> id: MS:1001329
> name: OMSSA:pvalue
> def: "OMSSA p-value." [PSI:PI]
> xref: value-type:xsd\:double "The allowed value-type for this CV term."
> is_a: MS:1001143 ! search engine specific score for PSMs
> is_a: MS:1001153 ! search engine specific score
> is_a: MS:1002352 ! PSM-level p-value
>
> [Term]
> id: MS:1001396
> name: Phenyx:PepPvalue
> def: "The p-value of a peptide sequence match in Phenyx." [PSI:PI]
> xref: value-type:xsd\:double "The allowed value-type for this CV term."
> is_a: MS:1001143 ! search engine specific score for PSMs
> is_a: MS:1001153 ! search engine specific score
> is_a: MS:1002352 ! PSM-level p-value
>
> ************ The following two terms moved from
> ************ is_a: MS:1002347 ! PSM-level identification confidence metric
> ************ to is_a: MS:1001092 ! peptide identification confidence metric
> [Term]
> id: MS:1001872
> name: distinct peptide-level e-value
> def: "Estimation of the e-value for distinct peptides once redundant identifications of the same peptide have been removed (id est 
> multiple PSMs have been collapsed to one entry)." [PSI:PI]
> xref: value-type:xsd\:double "The allowed value-type for this CV term."
> MS:1001092 ! peptide identification confidence metric
> relationship: has_domain MS:1002306 ! value greater than zero
>
> [Term]
> id: MS:1001870
> name: distinct peptide-level p-value
> def: "Estimation of the p-value for distinct peptides once redundant identifications of the same peptide have been removed (id est 
> multiple PSMs have been collapsed to one entry)." [PSI:PI]
> xref: value-type:xsd\:double "The allowed value-type for this CV term."
> MS:1001092 ! peptide identification confidence metric
> relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive
>
>
> Best Regards,
> Gerhard
>
> -- 
>
> *--*
>
> *Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER*
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> *PhD student*
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