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

[Psidev-pi-dev] New version 3.89.0 of psi-ms.obo

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

Dear proteomics community,

attached there's the new version 3.89.0 of the psi-ms.obo file.
It contains a generic neutral loss term and terms for reporter ions.


New CV terms in version 3.89.0 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 
integer mass of the iTRAQ 4Plex reporter ion, e.g. 114." [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 
integer mass of the iTRAQ 8Plex reporter ion, e.g. 113." [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 integer 
mass of the TMT reporter ion and can be suffixed with either N or C, 
indicating whether the mass difference is encoded at a Nitrogen or 
Carbon atom, e.g. 127N." [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 integer mass of the TMT ETD reporter ion and can be 
suffixed with either N or C, indicating whether the mass difference is 
encoded at a Nitrogen or Carbon atom, e.g. 127C." [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

[Term]
id: MS:1002674
name: X500R QTOF
def: "SCIEX X500R QTOF, a quadrupole - quadrupole - time-of-flight mass 
spectrometer." [PSI:MS]
is_a: MS:1000121 ! SCIEX instrument model


Changed CV terms in version 3.89.0 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 ************
************ 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*

*PhD student*

*Medizinisches Proteom-Center*

*DEPARTMENT Medical Bioinformatics*

*Building *ZKF E.049a | Universitätsstraße 150 | D-44801 Bochum

*Fon *+49 (0)234 32-21006 | *Fax *+49 (0)234 32-14554

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

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

RUB Logo

ANNOUNCEMENT de.NBI summer school September 2016:

*Analysis of Mass-Spectrometric Data - *

*Big Data Bioinformatics in Proteomics and Metabolomics*

http://www.denbi.de/index.php/11-training-cat/95-lss2016

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

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

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*
>
> *PhD student*
>
> *Medizinisches Proteom-Center*
>
> *DEPARTMENT Medical Bioinformatics*
>
> *Building *ZKF E.049a | Universitätsstraße 150 | D-44801 Bochum
>
> *Fon *+49 (0)234 32-21006 | *Fax *+49 (0)234 32-14554
>
> *E-mail***ger...@ru...
>
> www.medizinisches-proteom-center.de
>
> RUB Logo
>
> ANNOUNCEMENT de.NBI summer school September 2016:
>
> *Analysis of Mass-Spectrometric Data - *
>
> *Big Data Bioinformatics in Proteomics and Metabolomics*
>
> <http://www.denbi.de/index.php/11-training-cat/95-lss2016>http://www.denbi.de/index.php/11-training-cat/95-lss2016
>

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

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

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*

*PhD student*

*Medizinisches Proteom-Center*

*DEPARTMENT Medical Bioinformatics*

*Building *ZKF E.049a | Universitätsstraße 150 | D-44801 Bochum

*Fon *+49 (0)234 32-21006 | *Fax *+49 (0)234 32-14554

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

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

RUB Logo

ANNOUNCEMENT de.NBI summer school September 2016:

*Analysis of Mass-Spectrometric Data - *

*Big Data Bioinformatics in Proteomics and Metabolomics*

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[Psidev-pi-dev] [HUPO-PSI/mzIdentML] mzIdentMLValidator_GUI_v1.4.17-SNAPSHOT: - Prevent NullPointerExceptions for missing CV values in PersonObject…

[Mathias W. <not...@gi...>]

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Re: [Psidev-pi-dev] [HUPO-PSI/mzIdentML] Build of validator (#21)

[Mathias W. <not...@gi...>]

I updated the release to the current and fixed the link on the start page to the release page. 
@germa if you could create a github release (https://github.com/HUPO-PSI/psi-ms-CV/releases/new) when you release a new version of the validator, welcome page will always point to the most recent validator.

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Re: [Psidev-pi-dev] [HUPO-PSI/mzIdentML] generic neutral loss term with value slot for the formula (#34)

[andrewrobertjones <not...@gi...>]

Agreed to this change

e.g.

<cvParam name = "neutral loss" value = "H2O"/>

@germa  Can you action this, and I will add this to the spec doc

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Re: [Psidev-pi-dev] [HUPO-PSI/mzIdentML] Validator: too strict on "cross-link spectrum identification item" values (#31)

[andrewrobertjones <not...@gi...>]

Discussed the correct behaviour should be to check 2 or 4 having the same value --> 4 for the case of stable isotopes only

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Re: [Psidev-pi-dev] [HUPO-PSI/mzIdentML] Encoding of cross-linker as part of SearchModifications (#30)

[andrewrobertjones <not...@gi...>]

Discussed on the call today - generally this seems sensible, I will provisionally add this to the spec doc

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Re: [Psidev-pi-dev] [HUPO-PSI/mzIdentML] Build of validator (#21)

[Mathias W. <not...@gi...>]

I just saw that Yasset already built github releases for the validator :smiley:

So for a better accessibility, we would just have to update the releases and link to the release site from the repository start page.

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Re: [Psidev-pi-dev] [HUPO-PSI/mzIdentML] Build of validator (#21)

[Mathias W. <not...@gi...>]

In the telco I was referring to that: https://github.com/HUPO-PSI/psi-ms-CV/releases

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[Psidev-pi-dev] [HUPO-PSI/mzIdentML] generic neutral loss term with value slot for the formula (#34)

[Gerhard M. <not...@gi...>]

Should we define a generic neutral loss term as proposed by Steffen Neumann,
see https://sourceforge.net/p/psidev/mailman/psidev-ms-vocab/?viewmonth=201605&viewday=25

and should be the terms
id: MS:1002455 ! H2O neutral loss, 
id: MS:1002456 ! NH3 neutral loss and 
id: MS:1002457 !  H3PO4 neutral loss
then be made obsolete?


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Re: [Psidev-pi-dev] [HUPO-PSI/mzIdentML] Proteogenomics encoding (#4)

[F. G. <not...@gi...>]

Closed #4.

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[Psidev-pi-dev] mzid call today

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

Hi all,

Apologies for the short notice. Assuming people can join, let's have an mzid 1.2 call at 4pm UK today (1st June): http://www.timeanddate.com/worldclock/fixedtime.html?iso=20160601T16&p1=301

We will work through the issue list: https://github.com/HUPO-PSI/mzIdentML/issues as far as possible. Please check in any updates to example files, and report back whether the validator appears to be catching both good and bad examples correctly.
Best wishes
Andy

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Re: [Psidev-pi-dev] [HUPO-PSI/mzIdentML] Cross-Linking fragment annotations (#32)

[Mathias W. <not...@gi...>]

**One idea** would be to allow strings in the values of ```<FragmentArray>``` elements and by convention let these strings be accessions to CVs defined in the ```<Measurement>```.

**The other** would be to introduce an additional abstraction of ```<FragmentArray>``` for ```<FragmentCVREFArray>```.  ```<Measurement>``` for these would have to be allowed to carry several cv, one for each possible type of annotation flag.

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Re: [Psidev-pi-dev] [HUPO-PSI/mzIdentML] Cross-Linking fragment annotations (#32)

[Mathias W. <not...@gi...>]

If we would decide to introduce CVs like frag: y ion - alpha, ... this would also add to the bloat of the file, as there would be more  ```<IonType>``` elements. This would also bloat the CV.

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Re: [Psidev-pi-dev] [HUPO-PSI/mzIdentML] Cross-Linking fragment annotations (#32)

[Mathias W. <not...@gi...>]

For any software it would not make much sense to rip apart the annotations to one spectrum - and puzzle it back together.  - Though this would solve the problem of denoting alpha/beta, not so for ci/xi ions.

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Re: [Psidev-pi-dev] [HUPO-PSI/mzIdentML] moved annotations from initial OXQ example to separate file (#33)

[Mathias W. <not...@gi...>]

Merged #33.

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[Psidev-pi-dev] [HUPO-PSI/mzIdentML] removed annotations from initial example (#33)

[Mathias W. <not...@gi...>]

You can view, comment on, or merge this pull request online at:

  https://github.com/HUPO-PSI/mzIdentML/pull/33

-- Commit Summary --

  * removed annotations from initial example

-- File Changes --

    M examples/1_2examples/crosslinking/OpenxQuest_example.mzid (344)

-- Patch Links --

https://github.com/HUPO-PSI/mzIdentML/pull/33.patch
https://github.com/HUPO-PSI/mzIdentML/pull/33.diff

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[Psidev-pi-dev] [HUPO-PSI/mzIdentML] Cross-Linking fragment annotations (#32)

[Eugen N. <not...@gi...>]

We are trying to implement fragment annotations for cross-linked peptides in OpenMS and uploaded an example file under examples/1_2examples/crosslinking/OpenxQuest_example.mzid.

In the case of cross-linking we have fragments resulting from cleavages of both peptides in one spectrum. Therefore distributing the annotations between several SIIs would make further usage e.g. visualization of these annotations more complicated and the separation would not be possible in more complex fragmentation patterns, e.g. cross-linked fragments where both peptides were cleaved. So we would prefer to store the annotations for one PSM under one SII, e.g. the light alpha case.

The example suggests adapting FragmentArray to also carry strings (words) or have an additional array carrying these (not in the example). 
The specific CVs we would need are:
One Array for "cross-link chain" containing CV strings for "donor" or "acceptor" for each fragment.
One Array for "cross-link ion category" containing CV strings for "common ion" or "cross-linked ion" for each fragment.
The example file shows roughly how that could look like.

Another way to do it would be to introduce additional IonTypes and therefore separate these types into different arrays. In that case we would need all four combinations of donor/receiver with common/cross-linked


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Re: [Psidev-pi-dev] [HUPO-PSI/mzIdentML] MS:1002404 (count of identified proteins) ought to be a child of MS:1001184 (search statistics)? (#8)

[Gerhard M. <not...@gi...>]

Closed #8.

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Re: [Psidev-pi-dev] [HUPO-PSI/mzIdentML] MS:1002404 (count of identified proteins) ought to be a child of MS:1001184 (search statistics)? (#8)

[Gerhard M. <not...@gi...>]

Solved now.

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[Psidev-pi-dev] [HUPO-PSI/mzIdentML] Validator: too strict on "cross-link spectrum identification item" values (#31)

[Eugen N. <not...@gi...>]

The CV accession="MS:1002511" name="cross-link spectrum identification item" must have the same value for SIIs that represent a pair of cross-linked peptides.
Currently the validator only allows exactly two equal values, but we have 4 SIIs for the same cross-link when using isotope labelled linkers.

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Re: [Psidev-pi-dev] [HUPO-PSI/mzIdentML] Manual annotation of PSMs (#14)

[Eugen N. <not...@gi...>]

Closed #14.

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Re: [Psidev-pi-dev] [HUPO-PSI/mzIdentML] Error in PeptideLevelStatsObjectRule (#29)

[Gerhard M. <not...@gi...>]

Closed #29.

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Re: [Psidev-pi-dev] [HUPO-PSI/mzIdentML] Error in PeptideLevelStatsObjectRule (#29)

[Gerhard M. <not...@gi...>]

Fixed in version 1.4.17

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