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From: mayerg97 <ger...@ru...> - 2016-05-13 09:41:14
Attachments:
psi-ms_3.88.0.7z
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Dear proteomics community, attached there's the new version 3.88.0 of the psi-ms.obo file. New CV terms in version 3.88.0 of psi-ms.obo: ============================================= ************ Two new instrument terms [Term] id: MS:1002666 name: impact II def: "Bruker Daltonics' impact II." [PSI:MS] is_a: MS:1001536 ! Bruker Daltonics micrOTOF series [Term] id: MS:1002667 name: impact HD def: "Bruker Daltonics' impact HD." [PSI:MS] is_a: MS:1001536 ! Bruker Daltonics micrOTOF series Changed CV terms in version 3.88.0 of psi-ms.obo: ================================================= ************ replaced the imports to pato and uo by PURL's import: http://purl.obolibrary.org/obo/pato.owl import: http://purl.obolibrary.org/obo/uo.owl ************ added is_a: MS:1001302 ! search engine specific input parameter [Term] id: MS:1002389 name: PIA workflow parameter def: "A parameter set for a single PIA analysis." [PSI:PI] is_a: MS:1002105 ! software specific input parameter is_a: MS:1001302 ! search engine specific input parameter 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 |
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From: mayerg97 <ger...@ru...> - 2016-05-24 13:56:12
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Hi all, how about the following terms? ************ New terms for neutral losses [Term] id: MS:1002668 name: HPO3 neutral loss def: "Neutral loss of phosphite." [PSI:PI] is_a: MS:1000336 ! neutral loss is_a: MS:1002473 ! ion series considered in search [Term] id: MS:1002669 name: CH4OS neutral loss def: "Neutral loss of methanesulfenic acid." [PSI:PI] is_a: MS:1000336 ! neutral loss is_a: MS:1002473 ! ion series considered in search [Term] id: MS:1002670 name: C3H9N neutral loss def: "Neutral loss of C3H9N." [PSI:PI] is_a: MS:1000336 ! neutral loss is_a: MS:1002473 ! ion series considered in search ************ New terms for reporter ions. The mass resp. type can be specified in the value slot. [Term] id: MS:1002671 name: frag: iTRAQ 4plex reporter ion def: "Standard reporter ion for iTRAQ 4Plex." [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:1002672 name: frag: iTRAQ 8plex reporter ion def: "Standard reporter ion for iTRAQ 8Plex." [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:1002673 name: frag: TMT reporter ion def: "Standard reporter ion for TMT." [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:1002674 name: frag: TMT ETD reporter ion def: "Standard reporter ion for TMT ETD." [PSI:PI] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002307 ! fragmentation ion type Best regards, Gerhard Am 24.05.2016 um 12:55 schrieb Harald Barsnes: > > Hi Gerhard, > > Thanks for adding the neutral losses CV terms. Would be great if you > could also add CV terms for the following reporter ions. > > > iTRAQ 4plex: > > Name: frag: iTRAQ 4plex 114 reporter ion > Description: Standard reporter ion for iTRAQ 4Plex 114. > > Name: frag: iTRAQ 4plex 115 reporter ion > Description: Standard reporter ion for iTRAQ 4Plex 115. > > Name: frag: iTRAQ 4plex 116 reporter ion > Description: Standard reporter ion for iTRAQ 4Plex 116. > > Name: frag: iTRAQ 4plex 117 reporter ion > Description: Standard reporter ion for iTRAQ 4Plex 117. > > > iTRAQ 8plex: > > Name: frag: iTRAQ 8plex 113 reporter ion > Description: Standard reporter ion for iTRAQ 8Plex 113. > > Name: frag: iTRAQ 8plex 114 reporter ion > Description: Standard reporter ion for iTRAQ 8Plex 114. > > Name: frag: iTRAQ 8plex 115 reporter ion > Description: Standard reporter ion for iTRAQ 8Plex 115. > > Name: frag: iTRAQ 8plex 116 reporter ion > Description: Standard reporter ion for iTRAQ 8Plex 116. > > Name: frag: iTRAQ 8plex 117 reporter ion > Description: Standard reporter ion for iTRAQ 8Plex 117. > > Name: frag: iTRAQ 8plex 118 reporter ion > Description: Standard reporter ion for iTRAQ 8Plex 118. > > Name: frag: iTRAQ 8plex 119 reporter ion > Description: Standard reporter ion for iTRAQ 8Plex 119. > > Name: frag: iTRAQ 8plex 121 reporter ion > Description: Standard reporter ion for iTRAQ 8Plex 121. > > > TMT: > > Name: frag: TMT 126 reporter ion > Description: Standard reporter ion for TMT 126. > > Name: frag: TMT 127N reporter ion > Description: Standard reporter ion for TMT 127N. > > Name: frag: TMT 127C reporter ion > Description: Standard reporter ion for TMT 127C. > > Name: frag: TMT 128N reporter ion > Description: Standard reporter ion for TMT 128N. > > Name: frag: TMT 128C reporter ion > Description: Standard reporter ion for TMT 128C. > > Name: frag: TMT 128N reporter ion > Description: Standard reporter ion for TMT 128N. > > Name: frag: TMT 128C reporter ion > Description: Standard reporter ion for TMT 128C. > > Name: frag: TMT 130N reporter ion > Description: Standard reporter ion for TMT 130N. > > Name: frag: TMT 130C reporter ion > Description: Standard reporter ion for TMT 130C. > > Name: frag: TMT 131 reporter ion > Description: Standard reporter ion for TMT 131. > > Name: frag: TMT 126 ETD reporter ion > Description: Standard reporter ion for TMT 126 ETD. > > Name: frag: TMT 127N ETD reporter ion > Description: Standard reporter ion for TMT 127N ETD. > > Name: frag: TMT 127C ETD reporter ion > Description: Standard reporter ion for TMT 127C ETD. > > Name: frag: TMT 128N ETD reporter ion > Description: Standard reporter ion for TMT 128N ETD. > > Name: frag: TMT 128C ETD reporter ion > Description: Standard reporter ion for TMT 128C ETD. > > Name: frag: TMT 129N ETD reporter ion > Description: Standard reporter ion for TMT 129N ETD. > > Name: frag: TMT 129C ETD reporter ion > Description: Standard reporter ion for TMT 129C ETD. > > Name: frag: TMT 130N ETD reporter ion > Description: Standard reporter ion for TMT 130N ETD. > > Name: frag: TMT 130C ETD reporter ion > Description: Standard reporter ion for TMT 130C ETD. > > Name: frag: TMT 131 ETD reporter ion > Description: Standard reporter ion for TMT 131 ETD. > > > All should be children of MS:1002307 (fragmentation ion type). > > > Thanks in advance. > > Best regards, > Harald > -- *--* *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 |
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From: Eric D. <ede...@sy...> - 2016-05-24 16:01:39
Attachments:
image002.jpg
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Hi Gerhard, many thanks for adjusting this. Regarding the reporter ions, what does “mass resp. type” mean? If there is a value that must be supplied, the term name and definition really should be about that value. Thanks, Eric *From:* mayerg97 [mailto:ger...@ru...] *Sent:* Tuesday, May 24, 2016 6:56 AM *To:* Harald Barsnes; psi...@li...; psi...@li...; psi...@li... *Subject:* Re: [Psidev-ms-dev] PSI-MS: reporter ion cv terms Hi all, how about the following terms? ************ New terms for neutral losses [Term] id: MS:1002668 name: HPO3 neutral loss def: "Neutral loss of phosphite." [PSI:PI] is_a: MS:1000336 ! neutral loss is_a: MS:1002473 ! ion series considered in search [Term] id: MS:1002669 name: CH4OS neutral loss def: "Neutral loss of methanesulfenic acid." [PSI:PI] is_a: MS:1000336 ! neutral loss is_a: MS:1002473 ! ion series considered in search [Term] id: MS:1002670 name: C3H9N neutral loss def: "Neutral loss of C3H9N." [PSI:PI] is_a: MS:1000336 ! neutral loss is_a: MS:1002473 ! ion series considered in search ************ New terms for reporter ions. The mass resp. type can be specified in the value slot. [Term] id: MS:1002671 name: frag: iTRAQ 4plex reporter ion def: "Standard reporter ion for iTRAQ 4Plex." [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:1002672 name: frag: iTRAQ 8plex reporter ion def: "Standard reporter ion for iTRAQ 8Plex." [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:1002673 name: frag: TMT reporter ion def: "Standard reporter ion for TMT." [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:1002674 name: frag: TMT ETD reporter ion def: "Standard reporter ion for TMT ETD." [PSI:PI] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002307 ! fragmentation ion type Best regards, Gerhard Am 24.05.2016 um 12:55 schrieb Harald Barsnes: Hi Gerhard, Thanks for adding the neutral losses CV terms. Would be great if you could also add CV terms for the following reporter ions. iTRAQ 4plex: Name: frag: iTRAQ 4plex 114 reporter ion Description: Standard reporter ion for iTRAQ 4Plex 114. Name: frag: iTRAQ 4plex 115 reporter ion Description: Standard reporter ion for iTRAQ 4Plex 115. Name: frag: iTRAQ 4plex 116 reporter ion Description: Standard reporter ion for iTRAQ 4Plex 116. Name: frag: iTRAQ 4plex 117 reporter ion Description: Standard reporter ion for iTRAQ 4Plex 117. iTRAQ 8plex: Name: frag: iTRAQ 8plex 113 reporter ion Description: Standard reporter ion for iTRAQ 8Plex 113. Name: frag: iTRAQ 8plex 114 reporter ion Description: Standard reporter ion for iTRAQ 8Plex 114. Name: frag: iTRAQ 8plex 115 reporter ion Description: Standard reporter ion for iTRAQ 8Plex 115. Name: frag: iTRAQ 8plex 116 reporter ion Description: Standard reporter ion for iTRAQ 8Plex 116. Name: frag: iTRAQ 8plex 117 reporter ion Description: Standard reporter ion for iTRAQ 8Plex 117. Name: frag: iTRAQ 8plex 118 reporter ion Description: Standard reporter ion for iTRAQ 8Plex 118. Name: frag: iTRAQ 8plex 119 reporter ion Description: Standard reporter ion for iTRAQ 8Plex 119. Name: frag: iTRAQ 8plex 121 reporter ion Description: Standard reporter ion for iTRAQ 8Plex 121. TMT: Name: frag: TMT 126 reporter ion Description: Standard reporter ion for TMT 126. Name: frag: TMT 127N reporter ion Description: Standard reporter ion for TMT 127N. Name: frag: TMT 127C reporter ion Description: Standard reporter ion for TMT 127C. Name: frag: TMT 128N reporter ion Description: Standard reporter ion for TMT 128N. Name: frag: TMT 128C reporter ion Description: Standard reporter ion for TMT 128C. Name: frag: TMT 128N reporter ion Description: Standard reporter ion for TMT 128N. Name: frag: TMT 128C reporter ion Description: Standard reporter ion for TMT 128C. Name: frag: TMT 130N reporter ion Description: Standard reporter ion for TMT 130N. Name: frag: TMT 130C reporter ion Description: Standard reporter ion for TMT 130C. Name: frag: TMT 131 reporter ion Description: Standard reporter ion for TMT 131. Name: frag: TMT 126 ETD reporter ion Description: Standard reporter ion for TMT 126 ETD. Name: frag: TMT 127N ETD reporter ion Description: Standard reporter ion for TMT 127N ETD. Name: frag: TMT 127C ETD reporter ion Description: Standard reporter ion for TMT 127C ETD. Name: frag: TMT 128N ETD reporter ion Description: Standard reporter ion for TMT 128N ETD. Name: frag: TMT 128C ETD reporter ion Description: Standard reporter ion for TMT 128C ETD. Name: frag: TMT 129N ETD reporter ion Description: Standard reporter ion for TMT 129N ETD. Name: frag: TMT 129C ETD reporter ion Description: Standard reporter ion for TMT 129C ETD. Name: frag: TMT 130N ETD reporter ion Description: Standard reporter ion for TMT 130N ETD. Name: frag: TMT 130C ETD reporter ion Description: Standard reporter ion for TMT 130C ETD. Name: frag: TMT 131 ETD reporter ion Description: Standard reporter ion for TMT 131 ETD. All should be children of MS:1002307 (fragmentation ion type). Thanks in advance. Best regards, Harald -- *--* *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 [image: 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 |
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From: Steffen N. <sne...@ip...> - 2016-05-25 13:28:38
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Hi, I'd be a bit hesitant to have one term per neutral loss. The Table 2 in http://pubs.acs.org/doi/full/10.1021/ac101825k#tbl2-fn1 contains already >30 neutral losses, and it is not complete ... What about a generic neutral loss that has a value which is a formula ? Yours, Steffen On Di, 2016-05-24 at 15:55 +0200, mayerg97 wrote: > ************ New terms for neutral losses > [Term] > id: MS:1002668 > name: HPO3 neutral loss > def: "Neutral loss of phosphite." [PSI:PI] > is_a: MS:1000336 ! neutral loss > is_a: MS:1002473 ! ion series considered in search > ... > name: CH4OS neutral loss > name: C3H9N neutral loss -- IPB Halle AG Massenspektrometrie & Bioinformatik Dr. Steffen Neumann http://www.IPB-Halle.DE Weinberg 3 Tel. +49 (0) 345 5582 - 1470 06120 Halle +49 (0) 345 5582 - 0 sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409 |
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