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From: Eric D. <ede...@sy...> - 2017-08-23 17:28:21
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Hi Gerhard, thanks for this. I think we should consider and revise this a bit more before committing. Everyone, if you care about this topic, please see ongoing GitHub conversation: https://github.com/HUPO-PSI/psi-ms-CV/issues/7 thanks! Eric *From:* mayerg97 via Psidev-ms-dev [mailto: psi...@li...] *Sent:* Wednesday, August 23, 2017 4:58 AM *To:* psi...@li...; psi...@li...; Mass spectrometry standard development <psi...@li...> *Cc:* mayerg97 <ger...@ru...> *Subject:* [Psidev-ms-dev] Release candidate 4.0.15_rc1 of psi-ms.obo Dear proteomics community, attached there's the release candidate 4.0.15_rc1 of the psi-ms.obo file. It contains one new term for 'alternating polarity scans'. New CV terms in version 4.0.15_rc1 of psi-ms.obo: ================================================= ************ new term 'alternating polarity scans' [Term] id: MS:1002826 name: alternating polarity scans def: "Polarities of the scans are alternating." [PSI:PI] is_a: MS:1000465 ! scan polarity is_a: MS:1000808 ! chromatogram attribute 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 |
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From: mayerg97 <ger...@ru...> - 2017-08-23 11:57:58
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Dear proteomics community, attached there's the release candidate 4.0.15_rc1 of the psi-ms.obo file. It contains one new term for 'alternating polarity scans'. New CV terms in version 4.0.15_rc1 of psi-ms.obo: ================================================= ************ new term 'alternating polarity scans' [Term] id: MS:1002826 name: alternating polarity scans def: "Polarities of the scans are alternating." [PSI:PI] is_a: MS:1000465 ! scan polarity is_a: MS:1000808 ! chromatogram attribute 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/> |
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From: Juan A. V. <ju...@eb...> - 2017-08-21 15:49:52
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Dear all, In order to make some preparations for the “Bioinformatics Hub” during HUPO 2017 in Dublin, we would need to know who is planning to attend the event. I have created a Doodle poll to record this information. Please select those days where you are planning to go to the event. It does not mean that you will not be there all the time, but at least you are planning to spend some time there: http://doodle.com/poll/runkh2uwb5ztnmry <http://doodle.com/poll/runkh2uwb5ztnmry> It is important to highlight that for Sunday (September 17th), the event will not take place in the convention center. It will take place in the O’Brien Science Centre on the UCD Campus, as the other events planned for Sunday morning/early afternoon. So, extra arrangements need to be done for that day. We have been asked by the organisers to tell everyone that will be attending the event on Sunday to get registered properly for the "Bioinformatics Hub" (for planning the catering, among other reasons). To register, you need to send an e-mail to: HU...@co... <mailto:HU...@co...> I will also create an issue in the CompMS GitHub page, containing this information. This is the wiki page for the event. The content at this point is what we did in Taiwan last year: https://github.com/CompMS/Overview/wiki/HUPO-2017 <https://github.com/CompMS/Overview/wiki/HUPO-2017> Best regards, Juan P.S. Please send this e-mail to anyone that you think would be interested in attending. |
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From: mayerg97 <ger...@ru...> - 2017-08-08 10:05:59
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Dear proteomics community, attached there's the new version 4.0.14 of the psi-ms.obo file. It contains new terms for OpenMS file formats. New CV terms in version 4.0.14 of psi-ms.obo: ============================================= ************ new terms for OpenMS file formats [Term] id: MS:1002822 name: OpenMS file format def: "File format developed by the OpenMS team." [PMID: 27575624] is_a: MS:1001459 ! file format [Term] id: MS:1002823 name: idXML def: "OpenMS intermediate identification format." [PSI:PI] is_a: MS:1002822 ! OpenMS file format [Term] id: MS:1002824 name: featureXML def: "OpenMS feature file format." [PSI:PI] is_a: MS:1002822 ! OpenMS file format [Term] id: MS:1002825 name: consensusXML def: "OpenMS consensus map format." [PSI:PI] is_a: MS:1002822 ! OpenMS file format Changed CV terms in version 4.0.14 of psi-ms.obo: ================================================= ************ Changed name from ************ Andromeda result file --> Andromeda result format [Term] id: MS:1002576 name: Andromeda result format def: "Andromeda result file output format." [PSI:PI] is_a: MS:1001040 ! intermediate analysis format ************ Changed the definitions [Term] id: MS:1001421 name: pepXML format def: "The XML-based pepXML file format for encoding PSM information, created and maintained by the Trans-Proteomic Pipeline developers." [PSI:PI] is_a: MS:1001040 ! intermediate analysis format [Term] id: MS:1001422 name: protXML format def: "The XML-based protXML file format for encoding protein identifications, created and maintained by the Trans-Proteomic Pipeline developers." [PSI:PI] is_a: MS:1001040 ! intermediate analysis format 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/> |
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From: Neumann, S. <sne...@ip...> - 2017-08-04 07:48:06
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Hi, I am a bit unsure about this description as OpenMS *specific* formats, what if xcms would read/write that one day ? While we have prior examples (MGF ...) a slight modification could be "File format developed by the OpenMS team." I know that this is nitpicking, just wanted to share my 2c, and it's the OpenMS team and/or Gerd to decide. Yours, Steffen On Fri, 2017-07-21 at 09:32 +0200, mayerg97 via Psidev-ms-dev wrote: > Dear proteomics community, > > attached there's the release candidate 4.0.14_rc1 of the psi-ms.obo > file. > It contains new terms for OpenMS file formats. > > > New CV terms in version 4.0.14_rc1 of psi-ms.obo: > ================================================= > ************ new terms for OpenMS file formats > [Term] > id: MS:1002822 > name: OpenMS file format > def: "A file format specific for the OpenMS software." [PMID: > 27575624] > is_a: MS:1001459 ! file format > > [Term] > id: MS:1002823 > name: idXML > def: "OpenMS intermediate identification format." [PSI:PI] > is_a: MS:1002822 ! OpenMS file format > > [Term] > id: MS:1002824 > name: featureXML > def: "OpenMS feature file format." [PSI:PI] > is_a: MS:1002822 ! OpenMS file format > > [Term] > id: MS:1002825 > name: consensusXML > def: "OpenMS consensus map format." [PSI:PI] > is_a: MS:1002822 ! OpenMS file format > > > 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 > ------------------------------------------------------------------- > ----------- > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > Psidev-ms-dev mailing list > Psi...@li... > https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev -- IPB Halle AG Massenspektrometrie & Bioinformatik Dr. Steffen Neumann http://www.IPB-Halle.DE Weinberg 3 http://msbi.bic-gh.de 06120 Halle Tel. +49 (0) 345 5582 - 1470 +49 (0) 345 5582 - 0 sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409 |
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From: EuBIC developer's m. <eu...@gm...> - 2017-08-02 09:36:36
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*— EuBIC 2018 developer’s meeting – Save the date & call for project proposals —* We are pleased to announce that the upcoming EuBIC 2018 developer’s meeting will be held in Ghent, Belgium, on January 9-12, 2018. The EuBIC 2018 developer's meeting will bring together scientists active in the field of bioinformatics and computational proteomics. Date: January 9-12, 2018 Venue: Hotel Monasterium PoortAckere, Oude Houtlei 56, 9000 Gent, Belgium Website: http://uahost.uantwerpen.be/eubic18/ *Key dates* September 17, 2017: Project proposal submission deadline October 2, 2017: Announcement of selected projects October 2, 2017: Conference registration opens January 9-12, 2018: EuBIC 2018 developer's meeting in Ghent *Call for project proposals* The call for topics for the hackathon sessions during the EuBIC 2018 developer's meeting is now open! During the EuBIC 2018 developer’s meeting the participants will engage in a hackathon where they will develop bioinformatics tools and resources. The participants will break up into small groups to work together on these topics in an open, constructive, and productive atmosphere. You can now submit project proposals for inclusion into the EuBIC 2018 developer’s meeting program. Submit your project proposal before 17 September through the meeting website: http://uahost.uantwerpen.be/eubic18/submission.html *Topics* Hackathon projects can cover all topics in proteomics bioinformatics, including, but not limited to: - Tools - Extension of existing bioinformatics tools under the guidance of their original authors - Development of novel bioinformatics tools to solve open problems - Benchmarking - Compilation of gold-truth datasets - Collection of reference algorithmic implementations - Specification of benchmarking criteria - Workflows - Definition of formal protocols - Development of tutorials for bioinformatics software usage - Data analysis - (Re)analysis of publicly available proteomics datasets *More information* - Website: http://uahost.uantwerpen.be/eubic18/ - Social media hashtag: #EuBIC18 - Conference email: *eu...@gm... <eu...@gm...>* *Sponsorship* inquiries are welcome at *eu...@gm... <eu...@gm...>* We look forward to welcoming you in Ghent! On behalf of the organizing committee, Wout Bittremieux |
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From: Jones, A. <And...@li...> - 2017-08-01 09:42:54
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Just copying this message over from the mzTab for metabolomics Google group. Plan for mzTab workshop on 22nd and 23rd Aug at the EBI. Best wishes Andy ************* Hi all, It doesn't seem perfect but it seems that 22nd and 23rd August seems possible for most interested people. Can we hold those days everyone? Ken, I think you're now signed up for this list - can you tell me if there is an EBI room available for I guess around 10 people max on those days. I don't have a budget I can easily spend on this, can everyone cover their own costs to get to EBI and for lunches/dinners? I've started a google sheet for people to register at, where I will also add an agenda. Please put your name down and any notes about travel plans etc https://docs.google.com/spreadsheets/d/1R2fINJ5aXfQyTa0s0pTiISh7kpUgeozyqkqfkMn8PSI/edit?usp=sharing Any questions, drop me a mail or discuss here. cheers Andy From: Jones, Andy [mailto:And...@li...] Sent: 26 July 2017 10:42 To: psi...@li... Subject: [Psidev-pi-dev] mzTab 1.1 Hi all, I have started discussions with the EBI Metabolights team about possibly having a 1.5 or 2 day workshop there around 21st – 24th Aug to work on finishing mzTab 1.1, I have also posted this on the https://groups.google.com/forum/#!forum/mztab4metabolomics Google Group. Please reply through either list if you’re interested in joining, and which dates you’re free. Best wishes Andy |
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From: Martin E. <mar...@ru...> - 2017-07-28 15:09:58
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Dear colleague, dear member of the Proteomics community, please forward this message to potentially interested colleagues! The HUPO Proteomics Standards Initiative (PSI) develops standards for documentation and storage of Proteomics data (see http://www.psidev.info for an overview of activities). There has been a submission to the PSI Document Process by the Molecular Interactions workgroup updating the PSI-MI format to version 3.0.0 (from long-time stable XML 2.5, released 2005). The submission (incl. current version of the specification document) can be found here: http://www.psidev.info/PSI-MI-in-docproc After having passed a review of the PSI steering group with minor changes, the proposed document version 3.0.0 DRAFT now goes through 60-days public comments and external review phase (end: 29th September 2017). Purpose of the format (excerpt from the spec. doc.): The existing XML standard (PSI-MI XML2.5) has proven to be, and will continue to be, capable of capturing the vast majority of molecular interaction data, which are generated by techniques such as protein complementation assays, affinity capture, biophysical measurements and enzyme assays. However, use cases have arisen which cannot be adequately described within this XML schema, for example allosteric interactions, abstracted interactions and dynamic interactions. In order to meet these specialist use cases, a new version of the XML format has been developed, PSI-MI XML3.0. Specification document: attached and at http://www.psidev.info/PSI-MI-in-docproc Schema MIF300.xsd: https://github.com/HUPO-PSI/miXML/blob/master/3.0/src/MIF300.xsd Schema documentation (Schema browser): <https://rawgit.com/HUPO-PSI/miXML/master/3.0/doc/MIF300.html> https://rawgit.com/HUPO-PSI/miXML/master/3.0/doc/MIF300.html Schema documentation and use case examples (as Word docs.): See appendix documents at https://github.com/HUPO-PSI/miXML/tree/master/3.0/pub or <https://www.dropbox.com/sh/0oclv5c3xxluc1z/AACorWMii2v_MpwukezXi34Ca?dl=0> https://www.dropbox.com/sh/0oclv5c3xxluc1z/AACorWMii2v_MpwukezXi34Ca?dl=0 (details of appendices in the spec. doc. and below). PLEASE ADD COMMENTS to the submission page (http://www.psidev.info/PSI-MI-in-docproc) or send them directly to martin.eisenacher: at : rub.de for example regarding the following criteria: - That it is well formed that is, it is presented in accordance with the templates and is clearly written. - That it is sufficiently detailed and clearly contains and comprehensively describes the necessary and sufficient explanation of the format. - That the examples are in accordance with the specification.> > This message is to encourage you to contribute to the standards development activity by commenting on the material that is available online. We invite both positive and negative comments. If negative comments are being made, these could be on the relevance, clarity, correctness, appropriateness, etc, of the proposal as a whole or of specific parts of the proposal. If you do not feel well placed to comment on this document, but know someone who may be, please consider forwarding this request. There is no requirement that people commenting should have had any prior contact with the PSI. Many thanks for your valuable time and participation Martin Eisenacher (PSI Editor) 1. Appendices Example files showing how the schema meets each of the use cases listed in section 1.3. Note, all examples available in the IntAct database ( <http://www.ebi.ac.uk/intact> www.ebi.ac.uk/intact) unless otherwise stated 1.1 Appendix 1 Schema documentation for MIF300.xsd 1.2 Appendix 2 Example file showing the representation of all molecular interaction data from a single publication (PMID: 26919541) in PSI-MI XML3.0 note, includes use case 1.3k, rewrite of bibliography section 1.3 Appendix 3 Representation of a negative feature range (use case 1.3a) 1.4 Appendix 4 Representation of the sequence change caused by introduction of a mutation (use case 1.3b) 1.5 Appendix 5 Representation of multiple feature detection methods and feature roles (use cases 1.3c, 1.3d) 1.6 Appendix 6 Representation of kinetic parameters added at feature level (use case 1.3e) 1.7 Appendix 7 Representation of variable conditions (dynamic interactions) in an experiment (use case 1.3f) 1.8 Appendix 8 Representation of an abstracted interaction, a manually curated protein complex, in PSI-MI XML3.0 (use case 1.3g) 1.9 Appendix 9 Representation of a cooperative interaction in PSI-MI XML3.0 (Use case 1.3h) 1.10 Appendix 10 Representation of molecule sets i.e. cases where a participant may be one of a list of molecules (use case 1.3i) 1.11 Appendix 11 Representation of the systematic capture of the stoichiometry of molecules within an interaction (use case 1.3j) -- PD DR. MARTIN EISENACHER Department Leader DEPARTMENT Medical Bioinformatics Medizinisches Proteom-Center Ruhr-University Bochum Building ZKF E.141 | Universitätsstraße 150 | D-44801 Bochum Fon +49 (0)234 32-29288 | Fax +49 (0)234 32-14554 E-mail <mailto:mar...@ru...> mar...@ru... <http://www.medizinisches-proteom-center.de/> www.medizinisches-proteom-center.de |
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From: Jones, A. <And...@li...> - 2017-07-26 09:42:23
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Hi all, I have started discussions with the EBI Metabolights team about possibly having a 1.5 or 2 day workshop there around 21st - 24th Aug to work on finishing mzTab 1.1, I have also posted this on the https://groups.google.com/forum/#!forum/mztab4metabolomics Google Group. Please reply through either list if you're interested in joining, and which dates you're free. Best wishes Andy |
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From: mayerg97 <ger...@ru...> - 2017-07-21 07:32:59
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Dear proteomics community, attached there's the release candidate 4.0.14_rc1 of the psi-ms.obo file. It contains new terms for OpenMS file formats. New CV terms in version 4.0.14_rc1 of psi-ms.obo: ================================================= ************ new terms for OpenMS file formats [Term] id: MS:1002822 name: OpenMS file format def: "A file format specific for the OpenMS software." [PMID: 27575624] is_a: MS:1001459 ! file format [Term] id: MS:1002823 name: idXML def: "OpenMS intermediate identification format." [PSI:PI] is_a: MS:1002822 ! OpenMS file format [Term] id: MS:1002824 name: featureXML def: "OpenMS feature file format." [PSI:PI] is_a: MS:1002822 ! OpenMS file format [Term] id: MS:1002825 name: consensusXML def: "OpenMS consensus map format." [PSI:PI] is_a: MS:1002822 ! OpenMS file format 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/> |
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From: mayerg97 <ger...@ru...> - 2017-07-10 12:23:47
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Dear proteomics community, attached there's the new version 1.1.0 of the XLMOD.obo file for cross-linking reagents. It contains many new terms for cross-linker reagents, PTM's derived from them and new "cross-linking attribute"'s describing their properties, e.g. property_value: spacerLength: "x.y" xsd:float or information about their cleavability, labelling, handles used for click chemistry or enrichment, ... I used the following index ranges: ================================== reactive groups and attributes have ID's below XLMOD:01000 (mono-functional) cross-linker related PTM's have ID's above XLMOD:01000 label transfer reagents have ID's above XLMOD:01800 analogues of amino acids have ID's above XLMOD:01900 bi-functional cross-linker have ID's above XLMOD:02000 tri-functional cross-linker have ID's above XLMOD:03000 Of course the ID's of our old version (releases/2016-07-13) were not changed. Where available I added also cross-references to databases like PubChem, CAS, MDL, Beilstein, ChemSpider, ChemicalBook, ... I removed the chemical reaction-specificities from the cross-linkers to the reactive groups, which are now terms by their own, i.e. each cross-linker has now a relationship: has_reactive_group XLMOD:0xxxx ! ... Therefore the specificities have to be specified only once for each reactive group, which avoids unnecessary redundancies. I added also terms under the branch "label transfer reagents", which are not yet contained in PSI-MOD.obo / unimod.obo 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/> |
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From: mayerg97 <ger...@ru...> - 2017-07-03 08:59:37
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Dear proteomics community, attached there's the new version 4.0.13 of the psi-ms.obo file. It contains terms for defining adduct ions and for ion mobility mass spectrometry (IM-MS). New CV terms in version 4.0.13 of psi-ms.obo: ============================================= ************ new terms for adduct ions [Term] id: MS:1002806 name: ion def: "An atomic or molecular species having a net positive or negative electric charge." [PSI:MS] relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Ontology [Term] id: MS:1002807 name: positive mode adduct ion def: "Adduct ion with positive ionization." [PSI:MS] is_a: MS:1000353 ! adduct ion [Term] id: MS:1002808 name: negative mode adduct ion def: "Adduct ion with negative ionization." [PSI:MS] is_a: MS:1000353 ! adduct ion [Term] id: MS:1002809 name: adduct ion attribute def: "Attribute describing an adduct formation." [PSI:PI] is_a: MS:1000547 ! object attribute [Term] id: MS:1002810 name: adduct ion mass def: "Mass of an adduct formation specified by the given value." [DOI:10.1016/S1044-0305(99)00089-6, http://fiehnlab.ucdavis.edu/staff/kind/Metabolomics/MS-Adduct-Calculator] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002809 ! adduct ion attribute [Term] id: MS:1002811 name: adduct ion isotope def: "Isotope of the matrix molecule M of an adduct formation." [PMID:18790129] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002809 ! adduct ion attribute [Term] id: MS:1002812 name: Regular expression for adduct ion formula def: "(\[[:digit:]{0,1}M([+][:digit:]{0,1}(H|K|(Na)|(Li)|(Cl)|(Br)|(NH3)|(NH4)|(CH3OH)|(IsoProp)|(DMSO)|(FA)|(Hac)|(TFA)|(NaCOOH)|(HCOOH)|(CF3COOH)|(ACN))){0,}([-][:digit:]{0,1}(H|(H2O)|(CH2)|(CH4)|(NH3)|(CO)|(CO2)|(COCH2)|(HCOOH)|(C2H4)|(C4H8)|(C3H2O3)|(C5H8O4)|(C6H10O4)|(C6H10O5)|(C6H8O6))){0,}\][:digit:]{0,1}[+-])." [PSI:PI] is_a: MS:1002479 ! regular expression [Term] id: MS:1002813 name: adduct ion formula def: "Adduct formation formula specified by the given value." [PMID:22111785, DOI:10.1016/S1044-0305(99)00089-6, http://fiehnlab.ucdavis.edu/staff/kind/Metabolomics/MS-Adduct-Calculator] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002809 ! adduct ion attribute relationship: has_regexp MS:1002812 ! (\[[:digit:]{0,1}M([+][:digit:]{0,1}(H|K|(Na)|(Li)|(Cl)|(Br)|(NH3)|(NH4)|(CH3OH)|(IsoProp)|(DMSO)|(FA)|(Hac)|(TFA)|(NaCOOH)|(HCOOH)|(CF3COOH)|(ACN))){0,}([-][:digit:]{0,1}(H|(H2O)|(CH2)|(CH4)|(NH3)|(CO)|(CO2)|(COCH2)|(HCOOH)|(C2H4)|(C4H8)|(C3H2O3)|(C5H8O4)|(C6H10O4)|(C6H10O5)|(C6H8O6))){0,}\][:digit:]{0,1}[+-]) ************ new terms for IM-MS [Term] id: MS:1002814 name: volt-second per square centimeter def: "An electrical mobility unit that equals the speed [cm/s] an ion reaches when pulled through a gas by a Voltage[V] over a certain distance [cm]." [PSI:PI] synonym: "Vs/cm^2" EXACT [] is_a: UO:0000000 ! unit [Term] id: MS:1002815 name: inverse reduced ion mobility def: "Ion mobility measurement for an ion or spectrum of ions as measured in an ion mobility mass spectrometer. This might refer to the central value of a bin into which all ions within a narrow range of mobilities have been aggregated." [PSI:MS] xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000455 ! ion selection attribute is_a: MS:1000503 ! scan attribute relationship: has_units MS:1002814 ! "volt-second per square centimeter" [Term] id: MS:1002816 name: mean ion mobility array def: "Array of drift times or inverse reduced ion mobilities, averaged from a matrix of binned m/z and ion mobility values, corresponding to a spectrum of individual peaks encoded with an m/z array." [PSI:MS] xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000513 ! binary data array relationship: has_units UO:0000028 ! millisecond relationship: has_units UO:0000010 ! second relationship: has_units MS:1002814 ! "volt-second per square centimeter" [Term] id: MS:1002817 name: Bruker TDF format def: "Bruker TDF raw file format." [PSI:MS] is_a: MS:1000560 ! mass spectrometer file format [Term] id: MS:1002818 name: Bruker TDF nativeID format def: "Native format defined by frame=xsd:nonNegativeInteger scan=xsd:nonNegativeInteger." [PSI:MS] is_a: MS:1000767 ! native spectrum identifier format [Term] id: MS:1002819 name: Bruker TDF nativeID format, combined spectra def: "Bruker TDF comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002646 ! native spectrum identifier format, combined spectra ************ some concrete ion species ************ are there other concrete ions species, which should be included here? [Term] id: MS:1002820 name: M+H ion def: "M+H ion from positive ion mode (M in the property ionMass denotes the mass of the neutral molecule)." [DOI:10.1016/S1044-0305(99)00089-6, http://fiehnlab.ucdavis.edu/staff/kind/Metabolomics/MS-Adduct-Calculator] property_value: ionMass: "M + 1.007276" xsd:string is_a: MS:1002807 ! positive mode adduct ion [Term] id: MS:1002821 name: M-H ion def: "M-H ion from negative ion mode (M in the property ionMass denotes the mass of the neutral molecule)." [DOI:10.1016/S1044-0305(99)00089-6, http://fiehnlab.ucdavis.edu/staff/kind/Metabolomics/MS-Adduct-Calculator] property_value: ionMass: "M - 1.007276" xsd:string is_a: MS:1002808 ! negative mode adduct ion Changed CV terms in version 4.0.13 of psi-ms.obo: ================================================= ************ Reactivated the obsolete term 'adduct ion' [Term] id: MS:1000353 name: adduct ion def: "Ion formed by the interaction of an ion with one or more atoms or molecules to form an ion containing all the constituent atoms of the precursor ion as well as the additional atoms from the associated atoms or molecules." [PSI:MS] is_a: MS:1002806 ! ion 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/> |
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From: Yasset Perez-R. <yp...@eb...> - 2017-06-27 10:11:06
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For example the current pride-mod library in PRIDE needs to handle three different providers: UNIMOD, PSI-MS and PSI-MOD. On 27/06/2017 11:08, Yasset Perez-Riverol wrote: > > Why not adding this into PSI-MS as a section as you already did. It > would be great to have this only in one place. We have already > fragment neutral loss in the PSI-MS > http://www.ebi.ac.uk/ols/ontologies/ms/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FMS_1001524 > . I recommend to extend only this concept and do not create another > Obo file, for two main reasons: > > - Is not recommended in any of our file formats. > > - It is something will not growth more than a ~100 terms, then we > need to mantain another file just for a few number of terms. > > - It will be in two files the same information in PSI-MS and XLMOD > obo, we will need to take care of sync, etc. > > Hope you understand my points. > > Regards > > Yasset > > > On 27/06/2017 10:58, Jones, Andy wrote: >> >> It is stand-alone for the moment – for encoding cross-linking >> reagents that didn’t fit easily into other mod CVs (PSI-MOD or >> Unimod) for different reasons >> >> *From:*Yasset Perez-Riverol [mailto:yp...@eb...] >> *Sent:* 27 June 2017 10:53 >> *To:* mayerg97 <ger...@ru...>; >> psi...@li...; >> psi...@li...; Mass spectrometry standard >> development <psi...@li...>; Lutz Fischer >> <lfi...@st...>; le...@im... >> *Subject:* Re: [Psidev-ms-vocab] [Psidev-pi-dev] Release candidate >> 1.1.0_rc1 of XLMOD.obo >> >> Is this a new PTM ontology or this will be under PSI-MS? >> >> On 27/06/2017 10:49, mayerg97 via Psidev-pi-dev wrote: >> >> Dear proteomics community, >> >> attached there's the release candidate 1.1.0_rc1 of the XLMOD.obo >> file >> for cross-linking reagents. >> >> It contains many new terms for cross-linker reagents, PTM's >> derived from >> them and new "cross-linking attribute"'s describing their >> properties, e.g. >> property_value: spacerLength: "x.y" xsd:float >> or information about their cleavability, labelling, handles used >> for click chemistry or enrichment, ... >> >> I used the following index ranges: >> =========================== >> reactive groups and attributes have ID's below XLMOD:01000 >> (mono-functional) cross-linker related PTM's have ID's above >> XLMOD:01000 >> label transfer reagents have ID's above XLMOD:01800 >> analogues of amino acids have ID's above XLMOD:01900 >> bi-functional cross-linker have ID's above XLMOD:02000 >> tri-functional cross-linker have ID's above XLMOD:03000 >> >> Of course the ID's of our old version (releases/2016-07-13) were >> not changed. >> >> Where available I added also cross-references to databases >> like PubChem, CAS, MDL, Beilstein, ChemSpider, ChemicalBook, ... >> >> I removed the chemical reaction-specificities from the >> cross-linkers to the >> reactive groups, which are now terms by their own, i.e. each >> cross-linker has now a >> relationship: has_reactive_group XLMOD:0xxxx ! ... >> >> Therefore the specificities have to be specified only once for >> each reactive group, >> which avoids unnecessary redundancies. >> >> I added also terms under the branch "label transfer reagents", >> which are not yet contained in PSI-MOD.obo / unimod.obo >> >> 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/> >> >> >> >> >> ------------------------------------------------------------------------------ >> >> Check out the vibrant tech community on one of the world's most >> >> engaging tech sites, Slashdot.org!http://sdm.link/slashdot >> >> >> >> >> _______________________________________________ >> >> Psidev-pi-dev mailing list >> >> Psi...@li... >> <mailto:Psi...@li...> >> >> https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev >> >> >> >> -- >> Yasset Perez-Riverol PhD. >> Project Leader: PRIDE Resources >> Proteomics Services Team, PRIDE Group >> European Bioinformatics Institute (EMBL-EBI) >> Wellcome Trust Genome Campus >> Hinxton >> Cambridge CB10 1SD >> United Kingdom >> Twitter: @ypriverol >> >> >> ------------------------------------------------------------------------------ >> Check out the vibrant tech community on one of the world's most >> engaging tech sites, Slashdot.org!http://sdm.link/slashdot >> >> >> _______________________________________________ >> Psidev-pi-dev mailing list >> Psi...@li... >> https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev > > -- > Yasset Perez-Riverol PhD. > Project Leader: PRIDE Resources > Proteomics Services Team, PRIDE Group > European Bioinformatics Institute (EMBL-EBI) > Wellcome Trust Genome Campus > Hinxton > Cambridge CB10 1SD > United Kingdom > Twitter: @ypriverol > > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > > > _______________________________________________ > Psidev-pi-dev mailing list > Psi...@li... > https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev -- Yasset Perez-Riverol PhD. Project Leader: PRIDE Resources Proteomics Services Team, PRIDE Group European Bioinformatics Institute (EMBL-EBI) Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD United Kingdom Twitter: @ypriverol |
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From: Yasset Perez-R. <yp...@eb...> - 2017-06-27 10:08:20
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Why not adding this into PSI-MS as a section as you already did. It would be great to have this only in one place. We have already fragment neutral loss in the PSI-MS http://www.ebi.ac.uk/ols/ontologies/ms/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FMS_1001524 . I recommend to extend only this concept and do not create another Obo file, for two main reasons: - Is not recommended in any of our file formats. - It is something will not growth more than a ~100 terms, then we need to mantain another file just for a few number of terms. - It will be in two files the same information in PSI-MS and XLMOD obo, we will need to take care of sync, etc. Hope you understand my points. Regards Yasset On 27/06/2017 10:58, Jones, Andy wrote: > > It is stand-alone for the moment – for encoding cross-linking reagents > that didn’t fit easily into other mod CVs (PSI-MOD or Unimod) for > different reasons > > *From:*Yasset Perez-Riverol [mailto:yp...@eb...] > *Sent:* 27 June 2017 10:53 > *To:* mayerg97 <ger...@ru...>; > psi...@li...; > psi...@li...; Mass spectrometry standard > development <psi...@li...>; Lutz Fischer > <lfi...@st...>; le...@im... > *Subject:* Re: [Psidev-ms-vocab] [Psidev-pi-dev] Release candidate > 1.1.0_rc1 of XLMOD.obo > > Is this a new PTM ontology or this will be under PSI-MS? > > On 27/06/2017 10:49, mayerg97 via Psidev-pi-dev wrote: > > Dear proteomics community, > > attached there's the release candidate 1.1.0_rc1 of the XLMOD.obo file > for cross-linking reagents. > > It contains many new terms for cross-linker reagents, PTM's > derived from > them and new "cross-linking attribute"'s describing their > properties, e.g. > property_value: spacerLength: "x.y" xsd:float > or information about their cleavability, labelling, handles used > for click chemistry or enrichment, ... > > I used the following index ranges: > =========================== > reactive groups and attributes have ID's below XLMOD:01000 > (mono-functional) cross-linker related PTM's have ID's above > XLMOD:01000 > label transfer reagents have ID's above XLMOD:01800 > analogues of amino acids have ID's above XLMOD:01900 > bi-functional cross-linker have ID's above XLMOD:02000 > tri-functional cross-linker have ID's above XLMOD:03000 > > Of course the ID's of our old version (releases/2016-07-13) were > not changed. > > Where available I added also cross-references to databases > like PubChem, CAS, MDL, Beilstein, ChemSpider, ChemicalBook, ... > > I removed the chemical reaction-specificities from the > cross-linkers to the > reactive groups, which are now terms by their own, i.e. each > cross-linker has now a > relationship: has_reactive_group XLMOD:0xxxx ! ... > > Therefore the specificities have to be specified only once for > each reactive group, > which avoids unnecessary redundancies. > > I added also terms under the branch "label transfer reagents", > which are not yet contained in PSI-MOD.obo / unimod.obo > > 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/> > > > > > ------------------------------------------------------------------------------ > > Check out the vibrant tech community on one of the world's most > > engaging tech sites, Slashdot.org!http://sdm.link/slashdot > > > > > _______________________________________________ > > Psidev-pi-dev mailing list > > Psi...@li... > <mailto:Psi...@li...> > > https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev > > > > -- > Yasset Perez-Riverol PhD. > Project Leader: PRIDE Resources > Proteomics Services Team, PRIDE Group > European Bioinformatics Institute (EMBL-EBI) > Wellcome Trust Genome Campus > Hinxton > Cambridge CB10 1SD > United Kingdom > Twitter: @ypriverol > > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > > > _______________________________________________ > Psidev-pi-dev mailing list > Psi...@li... > https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev -- Yasset Perez-Riverol PhD. Project Leader: PRIDE Resources Proteomics Services Team, PRIDE Group European Bioinformatics Institute (EMBL-EBI) Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD United Kingdom Twitter: @ypriverol |
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From: Jones, A. <And...@li...> - 2017-06-27 09:58:42
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It is stand-alone for the moment – for encoding cross-linking reagents that didn’t fit easily into other mod CVs (PSI-MOD or Unimod) for different reasons From: Yasset Perez-Riverol [mailto:yp...@eb...] Sent: 27 June 2017 10:53 To: mayerg97 <ger...@ru...>; psi...@li...; psi...@li...; Mass spectrometry standard development <psi...@li...>; Lutz Fischer <lfi...@st...>; le...@im... Subject: Re: [Psidev-ms-vocab] [Psidev-pi-dev] Release candidate 1.1.0_rc1 of XLMOD.obo Is this a new PTM ontology or this will be under PSI-MS? On 27/06/2017 10:49, mayerg97 via Psidev-pi-dev wrote: Dear proteomics community, attached there's the release candidate 1.1.0_rc1 of the XLMOD.obo file for cross-linking reagents. It contains many new terms for cross-linker reagents, PTM's derived from them and new "cross-linking attribute"'s describing their properties, e.g. property_value: spacerLength: "x.y" xsd:float or information about their cleavability, labelling, handles used for click chemistry or enrichment, ... I used the following index ranges: =========================== reactive groups and attributes have ID's below XLMOD:01000 (mono-functional) cross-linker related PTM's have ID's above XLMOD:01000 label transfer reagents have ID's above XLMOD:01800 analogues of amino acids have ID's above XLMOD:01900 bi-functional cross-linker have ID's above XLMOD:02000 tri-functional cross-linker have ID's above XLMOD:03000 Of course the ID's of our old version (releases/2016-07-13) were not changed. Where available I added also cross-references to databases like PubChem, CAS, MDL, Beilstein, ChemSpider, ChemicalBook, ... I removed the chemical reaction-specificities from the cross-linkers to the reactive groups, which are now terms by their own, i.e. each cross-linker has now a relationship: has_reactive_group XLMOD:0xxxx ! ... Therefore the specificities have to be specified only once for each reactive group, which avoids unnecessary redundancies. I added also terms under the branch "label transfer reagents", which are not yet contained in PSI-MOD.obo / unimod.obo 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/> ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot _______________________________________________ Psidev-pi-dev mailing list Psi...@li...<mailto:Psi...@li...> https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev -- Yasset Perez-Riverol PhD. Project Leader: PRIDE Resources Proteomics Services Team, PRIDE Group European Bioinformatics Institute (EMBL-EBI) Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD United Kingdom Twitter: @ypriverol |
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From: Yasset Perez-R. <yp...@eb...> - 2017-06-27 09:53:10
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Is this a new PTM ontology or this will be under PSI-MS? On 27/06/2017 10:49, mayerg97 via Psidev-pi-dev wrote: > > Dear proteomics community, > > attached there's the release candidate 1.1.0_rc1 of the XLMOD.obo file > for cross-linking reagents. > > It contains many new terms for cross-linker reagents, PTM's derived from > them and new "cross-linking attribute"'s describing their properties, e.g. > property_value: spacerLength: "x.y" xsd:float > or information about their cleavability, labelling, handles used > for click chemistry or enrichment, ... > > I used the following index ranges: > =========================== > reactive groups and attributes have ID's below XLMOD:01000 > (mono-functional) cross-linker related PTM's have ID's above XLMOD:01000 > label transfer reagents have ID's above XLMOD:01800 > analogues of amino acids have ID's above XLMOD:01900 > bi-functional cross-linker have ID's above XLMOD:02000 > tri-functional cross-linker have ID's above XLMOD:03000 > > Of course the ID's of our old version (releases/2016-07-13) were not > changed. > > Where available I added also cross-references to databases > like PubChem, CAS, MDL, Beilstein, ChemSpider, ChemicalBook, ... > > I removed the chemical reaction-specificities from the cross-linkers > to the > reactive groups, which are now terms by their own, i.e. each > cross-linker has now a > relationship: has_reactive_group XLMOD:0xxxx ! ... > > Therefore the specificities have to be specified only once for each > reactive group, > which avoids unnecessary redundancies. > > I added also terms under the branch "label transfer reagents", > which are not yet contained in PSI-MOD.obo / unimod.obo > > 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/> > > > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > > > _______________________________________________ > Psidev-pi-dev mailing list > Psi...@li... > https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev -- Yasset Perez-Riverol PhD. Project Leader: PRIDE Resources Proteomics Services Team, PRIDE Group European Bioinformatics Institute (EMBL-EBI) Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD United Kingdom Twitter: @ypriverol |
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From: mayerg97 <ger...@ru...> - 2017-06-27 09:49:51
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Dear proteomics community, attached there's the release candidate 1.1.0_rc1 of the XLMOD.obo file for cross-linking reagents. It contains many new terms for cross-linker reagents, PTM's derived from them and new "cross-linking attribute"'s describing their properties, e.g. property_value: spacerLength: "x.y" xsd:float or information about their cleavability, labelling, handles used for click chemistry or enrichment, ... I used the following index ranges: =========================== reactive groups and attributes have ID's below XLMOD:01000 (mono-functional) cross-linker related PTM's have ID's above XLMOD:01000 label transfer reagents have ID's above XLMOD:01800 analogues of amino acids have ID's above XLMOD:01900 bi-functional cross-linker have ID's above XLMOD:02000 tri-functional cross-linker have ID's above XLMOD:03000 Of course the ID's of our old version (releases/2016-07-13) were not changed. Where available I added also cross-references to databases like PubChem, CAS, MDL, Beilstein, ChemSpider, ChemicalBook, ... I removed the chemical reaction-specificities from the cross-linkers to the reactive groups, which are now terms by their own, i.e. each cross-linker has now a relationship: has_reactive_group XLMOD:0xxxx ! ... Therefore the specificities have to be specified only once for each reactive group, which avoids unnecessary redundancies. I added also terms under the branch "label transfer reagents", which are not yet contained in PSI-MOD.obo / unimod.obo 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/> |
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From: mayerg97 <ger...@ru...> - 2017-06-23 11:45:30
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Dear proteomics and metabolomics community, attached there's the release candidate 4.0.13_rc1 of the psi-ms.obo file. It contains terms for defining adduct ions and for ion mobility mass spectrometry (IM-MS). New CV terms in version 4.0.13_rc1 of psi-ms.obo: ================================================= ************ new terms for adduct ions [Term] id: MS:1002806 name: ion def: "An atomic or molecular species having a net positive or negative electric charge." [PSI:MS] relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Ontology [Term] id: MS:1002807 name: positive mode adduct ion def: "Adduct ion with positive ionization." [PSI:MS] is_a: MS:1000353 ! adduct ion [Term] id: MS:1002808 name: negative mode adduct ion def: "Adduct ion with negative ionization." [PSI:MS] is_a: MS:1000353 ! adduct ion [Term] id: MS:1002809 name: adduct ion attribute def: "Attribute describing an adduct formation." [PSI:PI] is_a: MS:1000547 ! object attribute [Term] id: MS:1002810 name: adduct ion mass def: "Mass of an adduct formation specified by the given value." [DOI:10.1016/S1044-0305(99)00089-6, http://fiehnlab.ucdavis.edu/staff/kind/Metabolomics/MS-Adduct-Calculator] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002809 ! adduct ion attribute [Term] id: MS:1002811 name: adduct ion isotope def: "Isotope of the matrix molecule M of an adduct formation." [PMID:18790129] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002809 ! adduct ion attribute [Term] id: MS:1002812 name: Regular expression for adduct ion formula def: "(\[[:digit:]{0,1}M([+][:digit:]{0,1}(H|K|(Na)|(Cl)|(Br)|(NH3)|(NH4)|(CH3OH)|(IsoProp)|(DMSO)|(FA)|(Hac)|(TFA)|(NaCOOH)|(HCOOH)|(CF3COOH)|(ACN))){0,}([-][:digit:]{0,1}(H|(H2O)|(CH2)|(CH4)|(NH3)|(CO)|(CO2)|(COCH2)|(HCOOH)|(C2H4)|(C4H8)|(C3H2O3)|(C5H8O4)|(C6H10O4)|(C6H10O5)|(C6H8O6))){0,}\][:digit:]{0,1}[+-])." [PSI:PI] is_a: MS:1002479 ! regular expression [Term] id: MS:1002813 name: adduct ion formula def: "Adduct formation formula specified by the given value." [PMID:22111785, DOI:10.1016/S1044-0305(99)00089-6, http://fiehnlab.ucdavis.edu/staff/kind/Metabolomics/MS-Adduct-Calculator] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002809 ! adduct ion attribute relationship: has_regexp MS:1002812 ! (\[[:digit:]{0,1}M([+][:digit:]{0,1}(H|K|(Na)|(Cl)|(Br)|(NH3)|(NH4)|(CH3OH)|(IsoProp)|(DMSO)|(FA)|(Hac)|(TFA)|(NaCOOH)|(HCOOH)|(CF3COOH)|(ACN))){0,}([-][:digit:]{0,1}(H|(H2O)|(CH2)|(CH4)|(NH3)|(CO)|(CO2)|(COCH2)|(HCOOH)|(C2H4)|(C4H8)|(C3H2O3)|(C5H8O4)|(C6H10O4)|(C6H10O5)|(C6H8O6))){0,}\][:digit:]{0,1}[+-]) ************ new terms for IM-MS [Term] id: MS:1002814 name: volt-second per square centimeter def: "An electrical mobility unit that equals the speed [cm/s] an ion reaches when pulled through a gas by a Voltage[V] over a certain distance [cm]." [PSI:PI] synonym: "Vs/cm^2" EXACT [] is_a: UO:0000000 ! unit [Term] id: MS:1002815 name: inverse reduced ion mobility def: "Ion mobility measurement for an ion or spectrum of ions as measured in an ion mobility mass spectrometer. This might refer to the central value of a bin into which all ions within a narrow range of mobilities have been aggregated." [PSI:MS] xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000455 ! ion selection attribute is_a: MS:1000503 ! scan attribute relationship: has_units MS:1002814 ! "volt-second per square centimeter" [Term] id: MS:1002816 name: mean ion mobility array def: "Array of drift times or inverse reduced ion mobilities, averaged from a matrix of binned m/z and ion mobility values, corresponding to a spectrum of individual peaks encoded with an m/z array." [PSI:MS] xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000513 ! binary data array relationship: has_units UO:0000028 ! millisecond relationship: has_units UO:0000010 ! second relationship: has_units MS:1002814 ! "volt-second per square centimeter" [Term] id: MS:1002817 name: Bruker TDF format def: "Bruker TDF raw file format." [PSI:MS] is_a: MS:1000560 ! mass spectrometer file format [Term] id: MS:1002818 name: Bruker TDF nativeID format def: "Native format defined by frame=xsd:nonNegativeInteger scan=xsd:nonNegativeInteger." [PSI:MS] is_a: MS:1000767 ! native spectrum identifier format [Term] id: MS:1002819 name: Bruker TDF nativeID format, combined spectra def: "Bruker TDF comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002646 ! native spectrum identifier format, combined spectra ************ some concrete ion species ************ are there other concrete ions species, which should be included here? [Term] id: MS:1002820 name: M+H ion def: "M+H ion from positive ion mode (M in the property ionMass denotes the mass of the neutral molecule)." [DOI:10.1016/S1044-0305(99)00089-6, http://fiehnlab.ucdavis.edu/staff/kind/Metabolomics/MS-Adduct-Calculator] property_value: ionMass: "M + 1.007276" xsd:string is_a: MS:1002807 ! positive mode adduct ion [Term] id: MS:1002821 name: M-H ion def: "M-H ion from negative ion mode (M in the property ionMass denotes the mass of the neutral molecule)." [DOI:10.1016/S1044-0305(99)00089-6, http://fiehnlab.ucdavis.edu/staff/kind/Metabolomics/MS-Adduct-Calculator] property_value: ionMass: "M - 1.007276" xsd:string is_a: MS:1002808 ! negative mode adduct ion Changed CV terms in version 4.0.13_rc1 of psi-ms.obo: ===================================================== ************ Reactivated the obsolete term 'adduct ion' [Term] id: MS:1000353 name: adduct ion def: "Ion formed by the interaction of an ion with one or more atoms or molecules to form an ion containing all the constituent atoms of the precursor ion as well as the additional atoms from the associated atoms or molecules." [PSI:MS] is_a: MS:1002806 ! ion 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/> |
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From: mayerg97 <ger...@ru...> - 2017-06-19 14:04:26
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Dear Steffen and Michael, in principle one could specify the adduct ions more generic, but even then the problem remains that one has to adapt the RegEx if one wants to cover e.g. other neutral losses. [Term] id: MS:1000353 name: adduct ion def: "Ion formed by the interaction of an ion with one or more atoms or molecules to form an ion containing all the constituent atoms of the precursor ion as well as the additional atoms from the associated atoms or molecules." [PSI:MS] is_a: MS:1002806 ! ion [Term] id: MS:1002806 name: ion def: "An atomic or molecular species having a net positive or negative electric charge." [PSI:MS] relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Ontology [Term] id: MS:1002856 name: adduct ion formula def: "Adduct formation formula specified by the given value." [PMID:22111785, DOI:10.1016/S1044-0305(99)00089-6, http://fiehnlab.ucdavis.edu/staff/kind/Metabolomics/MS-Adduct-Calculator] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1000353 ! adduct ion relationship: has_regexp MS:1002857 ! (\[[:digit:]{0,1}M([+][:digit:]{0,1}(H|K|(Na)|(Cl)|(Br)|(NH3)|(NH4)|(CH3OH)|(IsoProp)|(DMSO)|(FA)|(Hac)|(TFA)|(NaCOOH)|(HCOOH)|(CF3COOH)|(ACN))){0,}([-]\d{0,1}(H|(H2O)|(CH2)|(CH4)|(NH3)|(CO)|(CO2)|(COCH2)|(HCOOH)|(C2H4)|(C4H8)|(C3H2O3)|(C5H8O4)|(C6H10O4)|(C6H10O5)|(C6H8O6))){0,}\]\d{0,1}[+-]) [Term] id: MS:1002857 name: Regular expression for adduct ion formula def: "(\[[:digit:]{0,1}M([+][:digit:]{0,1}(H|K|(Na)|(Cl)|(Br)|(NH3)|(NH4)|(CH3OH)|(IsoProp)|(DMSO)|(FA)|(Hac)|(TFA)|(NaCOOH)|(HCOOH)|(CF3COOH)|(ACN))){0,}([-]\d{0,1}(H|(H2O)|(CH2)|(CH4)|(NH3)|(CO)|(CO2)|(COCH2)|(HCOOH)|(C2H4)|(C4H8)|(C3H2O3)|(C5H8O4)|(C6H10O4)|(C6H10O5)|(C6H8O6))){0,}\]\d{0,1}[+-])" [PSI:PI] is_a: MS:1002479 ! regular expression [Term] id: MS:1002858 name: adduct ion attribute def: "Attribute describing an adduct formation." [PSI:PI] is_a: MS:1000547 ! object attribute [Term] id: MS:1002859 name: adduct ion mass def: "Mass of an adduct formation specified by the given value." [DOI:10.1016/S1044-0305(99)00089-6, http://fiehnlab.ucdavis.edu/staff/kind/Metabolomics/MS-Adduct-Calculator] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002858 ! adduct ion attribute [Term] id: MS:1002860 name: adduct ion isotope def: "Isotope of the matrix molecule M of an adduct formation." [PMID:18790129] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002858 ! adduct ion attribute Best regards, Gerhard Mayer Am 14.06.2017 um 15:24 schrieb Witting, Michael, Dr. via Psidev-ms-vocab: > Hi Gerd, Hi Steffen, > > and if we are currently talking about such things: What about isotopes? We > might think about something like M+1, M+2, M+3 with a value that can specify > more exact which isotope, if you have the resolution e.g. M+1 could be 13C > or 15N or M+2, 13C2 or 34S. > > Best regards, > > Michael > > -----Ursprüngliche Nachricht----- > Von: Neumann, Steffen [mailto:sne...@ip...] > Gesendet: Mittwoch, 14. Juni 2017 15:20 > An: psi...@li...; ger...@ru...; > psi...@li...; psi...@li...; > joe...@wa...; mzt...@go... > Cc: mic...@he...; Schober, Daniel > Betreff: Re: [Psidev-ms-dev] List of ion species, anyone ? > > Hi Gerd, > > Michael Witting and I also had already started a simple list, but a problem > might be that there will always be one ion type missing. > It also depends on the sample and analytical conditions, e.g. M+3H would be > fairly uncommon. > > Michael has a good set of literature describing adducts, and Tobias Kind in > UC Davies has a nice collection at > http://fiehnlab.ucdavis.edu/staff/kind/Metabolomics/MS-Adduct-Calculator > > In the R package CAMERA (see below) we defined them in a combinatorial way, > and comes up with ~134 combinations (considering neutral losses common in > metabolomics). > So in addition to a fixed list, it would be great to have more generic > annotation terms. like > > [Term] > id: MS:10028XX > name: adduct ion formula > def: "Adduct formation with specified ion." [PSI:MS] > xref: value-type:xsd\:string "The allowed value-type for this CV term." > is_a: MS:1002806 ! adduct ion type > > And we'd need examples how to put the generic adduct ion into the > value="..." of the cvParam something like > > "+3H", "+Cl", "-H" > > and similar we want to annotate cluster ions like > > "M", "2M" > > and neutral losses > > "-H20", "-H20-H20", "-C6H10O5" > > So both a short list of "common" (in metabolomics/proteomics) ion species > plus some more generic approach make sense, striking a balance between > simplicity and general applicability. > > > Yours, > Steffen > > library(CAMERA) > r <- new("ruleSet"); > r2 <- setDefaultLists(r) ; > r3 <- readLists(r2) ; > r4 <- setDefaultParams(r3) ; > r5 <- generateRules(r4) > r5@rules["name"] > > name > 1 [M+H]+ > 2 [M+2H]2+ > 3 [M+3H]3+ > 4 [M+H+Na]2+ > 5 [M+H+K]2+ > 6 [M+Na]+ > ... > 42 [2M+2Na+K-H]2+ > 43 [2M+3Na+K-H]3+ > 44 [2M+Na+2K-H]2+ > 45 [2M+2Na+2K-H]3+ > 47 [2M+2K-H]+ > ... > 93 [M+H-NH3]+ > 94 [M+2H-NH3]2+ > 95 [M+3H-NH3]3+ > 96 [M+H-H20]+ > 97 [M+2H-H20]2+ > 98 [M+3H-H20-H20]3+ > 99 [M+H-CH4]+ > 100 [M+2H-CH4]2+ > 101 [M+3H-CH4]3+ > ... > 128 [M+3H-C6H10O4]3+ > 129 [M+H-C6H10O5]+ > ... > 134 [M+3H-C6H8O6]3+ > > > > > On Fri, 2017-06-09 at 10:41 +0200, mayerg97 wrote: >> Hi Joel and Steffen, >> dear metabolomics and proteomics community, >> >> would the following terms fit for you purposes? >> >> [Term] >> id: MS:1002806 >> name: adduct ion type >> def: "Adduct ion type resulting from ionization in ESI-MS or other >> soft ionization techniques." [PSI:MS] >> is_a: MS:1001249 ! search input details >> >> [Term] >> id: MS:1002807 >> name: positive mode adduct ion type >> def: "Adduct ion type from positive ion mode." [PSI:MS] >> is_a: MS:1002806 ! adduct ion type >> >> [Term] >> id: MS:1002808 >> name: negative mode adduct ion type >> def: "Adduct ion type from negative ion mode." [PSI:MS] >> is_a: MS:1002806 ! adduct ion type >> >> [Term] >> id: MS:1002809 >> name: M+3H ion >> def: "M+3H ion in positive ion mode (M in the property ionMass >> denotes the mass of the neutral molecule)." [http://fiehnlab.ucdavis. >> edu/staff/kind/Metabolomics/MS-Adduct-Calculator, >> http://dx.doi.org/10.1016/S1044-0305(99)00089-6] >> property_value: ionMass: "M/3 + 1.007276" xsd:string >> is_a: MS:1002807 ! positive mode adduct ion type >> >> ... analogous for the other positive mode adduct ions >> >> [Term] >> id: MS:10028xy >> name: M-3H ion >> def: "M-3H ion in negative ion mode (M in the property ionMass >> denotes the mass of the neutral molecule)." [http://fiehnlab.ucdavis. >> edu/staff/kind/Metabolomics/MS-Adduct-Calculator, >> http://dx.doi.org/10.1016/S1044-0305(99)00089-6] >> property_value: ionMass: "M/3 - 1.007276 " xsd:string >> is_a: MS:1002808 ! negative mode adduct ion type >> >> ... analogous for the other negative mode ions >> >> Best regards, >> Gerhard Mayer >> >> Am 05.01.2017 um 13:08 schrieb Joel Rein: >>> Hi Steffen, >>> >>> I'd be very keen to see such a list developed/help with the RFC. >>> I think Tobias Kind's list (http://fiehnlab.ucdavis.edu/staff/kind/ >>> Metabolomics/MS-Adduct-Calculator/) would be a useful list to >>> include. >>> >>> Cheers, >>> Joel >>> >>> On Wednesday, January 4, 2017 at 8:06:12 PM UTC, Steffen Neumann >>> wrote: >>>> Hi, >>>> >>>> are there any efforts to collect ion species for psi-ms.obo, >>>> such as [M+H]+ or [M-Cl]- ? >>>> >>>> I was able to find "(M+H)+" in [1], but nothing in psi-ms.obo. >>>> I know a few groups interested in such a list, and would be >>>> happy to collect terms and send a proposal to Gerhard for >>>> inclusion. >>>> >>>> If there are no proposals or suggestions, I would start-off >>>> the stuff Michael Witting has collected, and come back with an >>>> RFC. >>>> >>>> Yours, >>>> Steffen >>>> >>>> >>>> [1] http://www.ebi.ac.uk/ols/ontologies/pride/terms?iri=http%3A%2 >>>> F%2Fpurl.obolibrary.org%2Fobo%2FPRIDE_0000051 >>>> >>> >>> ----------------------------------------------------------------- >>> ------------- >>> Check out the vibrant tech community on one of the world's most >>> engaging tech sites, SlashDot.org! http://sdm.link/slashdot >>> >>> >>> _______________________________________________ >>> Psidev-ms-dev mailing list >>> Psi...@li... >>> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev >> -- >> -------------------------------------------------------------------- >> 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 -- *--------------------------------------------------------------------* *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/> |
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From: Neumann, S. <sne...@ip...> - 2017-06-14 13:20:26
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Hi Gerd, Michael Witting and I also had already started a simple list, but a problem might be that there will always be one ion type missing. It also depends on the sample and analytical conditions, e.g. M+3H would be fairly uncommon. Michael has a good set of literature describing adducts, and Tobias Kind in UC Davies has a nice collection at http://fiehnlab.ucdavis.edu/staff/kind/Metabolomics/MS-Adduct-Calculator In the R package CAMERA (see below) we defined them in a combinatorial way, and comes up with ~134 combinations (considering neutral losses common in metabolomics). So in addition to a fixed list, it would be great to have more generic annotation terms. like [Term] id: MS:10028XX name: adduct ion formula def: "Adduct formation with specified ion." [PSI:MS] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002806 ! adduct ion type And we'd need examples how to put the generic adduct ion into the value="..." of the cvParam something like "+3H", "+Cl", "-H" and similar we want to annotate cluster ions like "M", "2M" and neutral losses "-H20", "-H20-H20", "-C6H10O5" So both a short list of "common" (in metabolomics/proteomics) ion species plus some more generic approach make sense, striking a balance between simplicity and general applicability. Yours, Steffen library(CAMERA) r <- new("ruleSet"); r2 <- setDefaultLists(r) ; r3 <- readLists(r2) ; r4 <- setDefaultParams(r3) ; r5 <- generateRules(r4) r5@rules["name"] name 1 [M+H]+ 2 [M+2H]2+ 3 [M+3H]3+ 4 [M+H+Na]2+ 5 [M+H+K]2+ 6 [M+Na]+ ... 42 [2M+2Na+K-H]2+ 43 [2M+3Na+K-H]3+ 44 [2M+Na+2K-H]2+ 45 [2M+2Na+2K-H]3+ 47 [2M+2K-H]+ ... 93 [M+H-NH3]+ 94 [M+2H-NH3]2+ 95 [M+3H-NH3]3+ 96 [M+H-H20]+ 97 [M+2H-H20]2+ 98 [M+3H-H20-H20]3+ 99 [M+H-CH4]+ 100 [M+2H-CH4]2+ 101 [M+3H-CH4]3+ ... 128 [M+3H-C6H10O4]3+ 129 [M+H-C6H10O5]+ ... 134 [M+3H-C6H8O6]3+ On Fri, 2017-06-09 at 10:41 +0200, mayerg97 wrote: > Hi Joel and Steffen, > dear metabolomics and proteomics community, > > would the following terms fit for you purposes? > > [Term] > id: MS:1002806 > name: adduct ion type > def: "Adduct ion type resulting from ionization in ESI-MS or other > soft ionization techniques." [PSI:MS] > is_a: MS:1001249 ! search input details > > [Term] > id: MS:1002807 > name: positive mode adduct ion type > def: "Adduct ion type from positive ion mode." [PSI:MS] > is_a: MS:1002806 ! adduct ion type > > [Term] > id: MS:1002808 > name: negative mode adduct ion type > def: "Adduct ion type from negative ion mode." [PSI:MS] > is_a: MS:1002806 ! adduct ion type > > [Term] > id: MS:1002809 > name: M+3H ion > def: "M+3H ion in positive ion mode (M in the property ionMass > denotes the mass of the neutral molecule)." [http://fiehnlab.ucdavis. > edu/staff/kind/Metabolomics/MS-Adduct-Calculator, > http://dx.doi.org/10.1016/S1044-0305(99)00089-6] > property_value: ionMass: "M/3 + 1.007276" xsd:string > is_a: MS:1002807 ! positive mode adduct ion type > > ... analogous for the other positive mode adduct ions > > [Term] > id: MS:10028xy > name: M-3H ion > def: "M-3H ion in negative ion mode (M in the property ionMass > denotes the mass of the neutral molecule)." [http://fiehnlab.ucdavis. > edu/staff/kind/Metabolomics/MS-Adduct-Calculator, > http://dx.doi.org/10.1016/S1044-0305(99)00089-6] > property_value: ionMass: "M/3 - 1.007276 " xsd:string > is_a: MS:1002808 ! negative mode adduct ion type > > ... analogous for the other negative mode ions > > Best regards, > Gerhard Mayer > > Am 05.01.2017 um 13:08 schrieb Joel Rein: > > Hi Steffen, > > > > I'd be very keen to see such a list developed/help with the RFC. > > I think Tobias Kind's list (http://fiehnlab.ucdavis.edu/staff/kind/ > > Metabolomics/MS-Adduct-Calculator/) would be a useful list to > > include. > > > > Cheers, > > Joel > > > > On Wednesday, January 4, 2017 at 8:06:12 PM UTC, Steffen Neumann > > wrote: > > > Hi, > > > > > > are there any efforts to collect ion species for psi-ms.obo, > > > such as [M+H]+ or [M-Cl]- ? > > > > > > I was able to find "(M+H)+" in [1], but nothing in psi-ms.obo. > > > I know a few groups interested in such a list, and would be > > > happy to collect terms and send a proposal to Gerhard for > > > inclusion. > > > > > > If there are no proposals or suggestions, I would start-off > > > the stuff Michael Witting has collected, and come back with an > > > RFC. > > > > > > Yours, > > > Steffen > > > > > > > > > [1] http://www.ebi.ac.uk/ols/ontologies/pride/terms?iri=http%3A%2 > > > F%2Fpurl.obolibrary.org%2Fobo%2FPRIDE_0000051 > > > > > > > > > ----------------------------------------------------------------- > > ------------- > > Check out the vibrant tech community on one of the world's most > > engaging tech sites, SlashDot.org! http://sdm.link/slashdot > > > > > > _______________________________________________ > > Psidev-ms-dev mailing list > > Psi...@li... > > https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev > > -- > -------------------------------------------------------------------- > 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 -- IPB Halle AG Massenspektrometrie & Bioinformatik Dr. Steffen Neumann http://www.IPB-Halle.DE Weinberg 3 http://msbi.bic-gh.de 06120 Halle Tel. +49 (0) 345 5582 - 1470 +49 (0) 345 5582 - 0 sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409 |
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From: Schober, D. <dsc...@ip...> - 2017-06-09 10:59:41
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Dear all,
First, my admittedly picky view on the matter, having my formal
ontology hat on (which I wear less and less often these days) ...
Aside my usual ontological aversions against epistemic intrusion a la
M+3H *ion* /is_a/ *search input details* (rather than a molecule/ion), I
think the presented pattern will do, given the pragmatic mz CV design.
Another design principle I am not really comfortable with is that the
essentials of a class are captured in the definition by selected
extrinsic rather than essential intrinsic properties, i.e. in this case
that Ion classes like "positive mode adduct ion type" are defined via
the mode of an Instrument-run that detected them ("Adduct ion type from
positive ion mode."). A more intrinsic definition would be via the
ionisation level of the adduct itself.
These are just comments, and Gerhard knows the CV structure and design
principles much better.
Best regards,
Daniel Schober
Am 09.06.2017 um 10:41 schrieb mayerg97:
> Hi Joel and Steffen,
> dear metabolomics and proteomics community,
>
> would the following terms fit for you purposes?
>
> [Term]
> id: MS:1002806
> name: adduct ion type
> def: "Adduct ion type resulting from ionization in ESI-MS or other
> soft ionization techniques." [PSI:MS]
> is_a: MS:1001249 ! search input details
>
> [Term]
> id: MS:1002807
> name: positive mode adduct ion type
> def: "Adduct ion type from positive ion mode." [PSI:MS]
> is_a: MS:1002806 ! adduct ion type
>
> [Term]
> id: MS:1002808
> name: negative mode adduct ion type
> def: "Adduct ion type from negative ion mode." [PSI:MS]
> is_a: MS:1002806 ! adduct ion type
>
> [Term]
> id: MS:1002809
> name: M+3H ion
> def: "M+3H ion in positive ion mode (M in the property ionMass denotes
> the mass of the neutral molecule)."
> [http://fiehnlab.ucdavis.edu/staff/kind/Metabolomics/MS-Adduct-Calculator,
> http://dx.doi.org/10.1016/S1044-0305(99)00089-6]
> property_value: ionMass: "M/3 + 1.007276" xsd:string
> is_a: MS:1002807 ! positive mode adduct ion type
>
> ... analogous for the other positive mode adduct ions
>
> [Term]
> id: MS:10028xy
> name: M-3H ion
> def: "M-3H ion in negative ion mode (M in the property ionMass denotes
> the mass of the neutral molecule)."
> [http://fiehnlab.ucdavis.edu/staff/kind/Metabolomics/MS-Adduct-Calculator,
> http://dx.doi.org/10.1016/S1044-0305(99)00089-6]
> property_value: ionMass: "M/3 - 1.007276 " xsd:string
> is_a: MS:1002808 ! negative mode adduct ion type
>
> ... analogous for the other negative mode ions
>
> Best regards,
> Gerhard Mayer
>
> Am 05.01.2017 um 13:08 schrieb Joel Rein:
>> Hi Steffen,
>>
>> I'd be very keen to see such a list developed/help with the RFC.
>> I think Tobias Kind's list
>> (http://fiehnlab.ucdavis.edu/staff/kind/Metabolomics/MS-Adduct-Calculator/)
>> would be a useful list to include.
>>
>> Cheers,
>> Joel
>>
>> On Wednesday, January 4, 2017 at 8:06:12 PM UTC, Steffen Neumann wrote:
>>
>> Hi,
>>
>> are there any efforts to collect ion species for psi-ms.obo,
>> such as [M+H]+ or [M-Cl]- ?
>>
>> I was able to find "(M+H)+" in [1], but nothing in psi-ms.obo.
>> I know a few groups interested in such a list, and would be
>> happy to collect terms and send a proposal to Gerhard for inclusion.
>>
>> If there are no proposals or suggestions, I would start-off
>> the stuff Michael Witting has collected, and come back with an RFC.
>>
>> Yours,
>> Steffen
>>
>>
>> [1]
>> http://www.ebi.ac.uk/ols/ontologies/pride/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FPRIDE_0000051
>> <http://www.ebi.ac.uk/ols/ontologies/pride/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FPRIDE_0000051>
>>
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, SlashDot.org!http://sdm.link/slashdot
>>
>>
>> _______________________________________________
>> Psidev-ms-dev mailing list
>> Psi...@li...
>> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
>
> --
>
> *--------------------------------------------------------------------*
>
> *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/>
>
--
Dr. Daniel Schober
Senior Ontologist, Data manager
Leibniz Institute of Plant Biochemistry, http://www.IPB-Halle.de
Dept. for Stress and Developmental Biology Bioinformatics & Mass Spectrometry
Weinberg 3 Tel. +49 (0) 345 5582 - 1476
06120 Halle
|
|
From: mayerg97 <ger...@ru...> - 2017-06-09 08:41:28
|
Hi Joel and Steffen, dear metabolomics and proteomics community, would the following terms fit for you purposes? [Term] id: MS:1002806 name: adduct ion type def: "Adduct ion type resulting from ionization in ESI-MS or other soft ionization techniques." [PSI:MS] is_a: MS:1001249 ! search input details [Term] id: MS:1002807 name: positive mode adduct ion type def: "Adduct ion type from positive ion mode." [PSI:MS] is_a: MS:1002806 ! adduct ion type [Term] id: MS:1002808 name: negative mode adduct ion type def: "Adduct ion type from negative ion mode." [PSI:MS] is_a: MS:1002806 ! adduct ion type [Term] id: MS:1002809 name: M+3H ion def: "M+3H ion in positive ion mode (M in the property ionMass denotes the mass of the neutral molecule)." [http://fiehnlab.ucdavis.edu/staff/kind/Metabolomics/MS-Adduct-Calculator, http://dx.doi.org/10.1016/S1044-0305(99)00089-6] property_value: ionMass: "M/3 + 1.007276" xsd:string is_a: MS:1002807 ! positive mode adduct ion type ... analogous for the other positive mode adduct ions [Term] id: MS:10028xy name: M-3H ion def: "M-3H ion in negative ion mode (M in the property ionMass denotes the mass of the neutral molecule)." [http://fiehnlab.ucdavis.edu/staff/kind/Metabolomics/MS-Adduct-Calculator, http://dx.doi.org/10.1016/S1044-0305(99)00089-6] property_value: ionMass: "M/3 - 1.007276 " xsd:string is_a: MS:1002808 ! negative mode adduct ion type ... analogous for the other negative mode ions Best regards, Gerhard Mayer Am 05.01.2017 um 13:08 schrieb Joel Rein: > Hi Steffen, > > I'd be very keen to see such a list developed/help with the RFC. > I think Tobias Kind's list > (http://fiehnlab.ucdavis.edu/staff/kind/Metabolomics/MS-Adduct-Calculator/) > would be a useful list to include. > > Cheers, > Joel > > On Wednesday, January 4, 2017 at 8:06:12 PM UTC, Steffen Neumann wrote: > > Hi, > > are there any efforts to collect ion species for psi-ms.obo, > such as [M+H]+ or [M-Cl]- ? > > I was able to find "(M+H)+" in [1], but nothing in psi-ms.obo. > I know a few groups interested in such a list, and would be > happy to collect terms and send a proposal to Gerhard for inclusion. > > If there are no proposals or suggestions, I would start-off > the stuff Michael Witting has collected, and come back with an RFC. > > Yours, > Steffen > > > [1] > http://www.ebi.ac.uk/ols/ontologies/pride/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FPRIDE_0000051 > <http://www.ebi.ac.uk/ols/ontologies/pride/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FPRIDE_0000051> > > > > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, SlashDot.org! http://sdm.link/slashdot > > > _______________________________________________ > Psidev-ms-dev mailing list > Psi...@li... > https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev -- *--------------------------------------------------------------------* *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/> |
|
From: Jones, A. <And...@li...> - 2017-06-08 11:53:00
|
Hi all, Sandra has asked if anyone would be interested in writing a tutorial article for Current Protocols in Bioinformatics. Given that mzid 1.2 is now just published, it would seem timely to write a new tutorial on working with the standard in practice, support in commercial and free tools, and a guide for developers on new features – similar to the 10 minute guide we wrote (but didn’t publish for mzid 1.1). I am happy to coordinate an article but would appreciate some help from volunteers wanting to write some text. Reply to me off the list if you’re interested and we can discuss feasibility and timescales. Best wishes Andy From: Sandra Orchard [mailto:or...@eb...] Sent: 02 May 2017 16:36 To: Jones, Andy <jo...@li...> Subject: Publicising the PI workgroups output Hi Andy I hope you've recovered from your promotion to the dizzy heights of PSI Chair. I was intending to talk to you in Beijing about a possible article that someone in your group could write, but never seemed to have the time. I have been asked to edit and update the section on Proteomics in Current Protocols in Bioinformatics and thought it would be a possible opportunity to push some of the tools built on the standards, or alternatively an updated version of the article Faviel wrote some years ago on how to develop tools in the first place. I'd be interested to hear if you can think of anything we could showcase - accompanied by a volunteer to do so. The Current Protocols in Bioinformatics target audience is molecular biologists who have an interest in applying bioinformatic tools to their own work. In general it provides tutorial-like protocols to lead the biologists through one or more resources to achieve various tasks. The articles are PubMed indexed so can be a useful addition to a lab member's CV. If you can think of something we could do in this area, then I'd put you in contact with Dr. Ann Boyle, our Developmental Editor. She can provide additional details about CPBI, the table of contents, and the expected format, as well as discuss a mutually agreeable deadline. I look forward to hearing from you soon. Sandra -- Sandra Orchard Molecular Interactions Team Leader European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD United Kingdom phone: 01223 494675 fax: 01223 494468 email: or...@eb...<mailto:or...@eb...> |
|
From: mayerg97 <ger...@ru...> - 2017-05-26 13:50:09
|
Dear proteomics community, attached there's the new version 4.0.12 of the psi-ms.obo file. It contains new terms for Agilent instruments. New CV terms in version 4.0.12 of psi-ms.obo: ============================================= [Term] id: MS:1002783 name: 6550 iFunnel Q-TOF LC/MS def: "The 6550 Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer." [PSI:MS] is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1002784 name: 6550A iFunnel Q-TOF LC/MS def: "The 6550A Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer." [PSI:MS] is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1002785 name: 6520B Q-TOF LC/MS def: "The 6520B Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer." [PSI:MS] is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1002786 name: 6530A Q-TOF LC/MS def: "The 6530A Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer." [PSI:MS] is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1002787 name: 6530B Q-TOF LC/MS def: "The 6530B Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer." [PSI:MS] is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1002788 name: 6538 Q-TOF LC/MS def: "The 6538 Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer." [PSI:MS] is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1002789 name: 6540 Q-TOF LC/MS def: "The 6540 Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer." [PSI:MS] is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1002790 name: 6542 Q-TOF LC/MS def: "The 6542 Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer." [PSI:MS] is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1002791 name: 6545 Q-TOF LC/MS def: "The 6545 Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer." [PSI:MS] is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1002792 name: 6560 Q-TOF LC/MS def: "The 6560 Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer." [PSI:MS] is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1002793 name: 6570 Q-TOF LC/MS def: "The 6570 Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer." [PSI:MS] is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1002794 name: 6120B Quadrupole LC/MS def: "The 6120B Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a single quadrupole mass spectrometer from the 6100 Series of Agilent mass spectrometers." [PSI:MS] is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1002795 name: 6150 Quadrupole LC/MS def: "The 6150 Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a single quadrupole mass spectrometer from the 6100 Series of Agilent mass spectrometers." [PSI:MS] is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1002796 name: 6224 Time-of-Flight LC/MS def: "The 6224 Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer." [PSI:MS] is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1002797 name: 6230A Time-of-Flight LC/MS def: "The 6230A Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer." [PSI:MS] is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1002798 name: 6230B Time-of-Flight LC/MS def: "The 6230B Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer." [PSI:MS] is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1002799 name: 6430 Triple Quadrupole LC/MS def: "The 6430 Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer." [PSI:MS] is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1002800 name: 6495A Triple Quadrupole LC/MS def: "The 6495A Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer." [PSI:MS] is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1002801 name: 6495B Triple Quadrupole LC/MS def: "The 6495B Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer." [PSI:MS] is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1002802 name: 7000A Triple Quadrupole GC/MS def: "The 7000A Quadrupole GC/MS system is a Agilent gas chromatography instrument combined with a Agilent triple quadrupole mass spectrometer." [PSI:MS] is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1002803 name: 7000B Triple Quadrupole GC/MS def: "The 7000B Quadrupole GC/MS system is a Agilent gas chromatography instrument combined with a Agilent triple quadrupole mass spectrometer." [PSI:MS] is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1002804 name: 7800 Quadrupole ICP-MS def: "The 7800 Quadrupole ICP-MS system is a Agilent inductively couple plasma instrument combined with a Agilent quadrupole mass spectrometer." [PSI:MS] is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1002805 name: 8800 Triple Quadrupole ICP-MS def: "The 8800 Quadrupole ICP-MS system is a Agilent inductively couple plasma instrument combined with a Agilent quadrupole mass spectrometer." [PSI:MS] is_a: MS:1000490 ! Agilent instrument model Changed CV terms in version 4.0.12 of psi-ms.obo: ================================================= ************ 6120 --> 6120A [Term] id: MS:1000469 name: 6120A Quadrupole LC/MS def: "The 6120A Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a single quadrupole mass spectrometer from the 6100 Series of Agilent mass spectrometers. 6120 quadrupole mass spectrometer has m/z range of 10-1500, 2500 u/s scan speed and utilizes multiple signal acquisition." [PSI:MS] is_a: MS:1000490 ! Agilent instrument model ************ 6520 --> 6520A [Term] id: MS:1000677 name: 6520A Quadrupole Time-of-Flight LC/MS def: "The 6520A Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. This time of flight mass spectrometer has a m/z range of 50-12000, mass accuracy of less than 2 ppm and resolution greater than 26,000 at m/z 2722. It has multiple ion sources and can be used with multimode ion sources." [PSI:MS] is_a: MS:1000490 ! Agilent instrument model 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/> |
|
From: Martin E. <mar...@ru...> - 2017-05-18 10:56:25
|
Dear colleague,
dear member of the Proteomics community,
this is a reminder, that the 60-days public comments
and external review phase ends in two weeks on 31st May!
See below for details of your contribution.
Many thanks for your valuable time and participation
Martin Eisenacher (PSI Editor)
--
PD DR. MARTIN EISENACHER
Department Leader
DEPARTMENT Medical Bioinformatics
Medizinisches Proteom-Center
Ruhr-University Bochum
Building ZKF E.141 | Universitätsstraße 150 | D-44801 Bochum
Fon +49 (0)234 32-29288 | Fax +49 (0)234 32-14554
E-mail <mailto:mar...@ru...> mar...@ru...
<http://www.medizinisches-proteom-center.de/>
www.medizinisches-proteom-center.de
Von: Martin Eisenacher [mailto:mar...@ru...]
Gesendet: Donnerstag, 30. März 2017 09:50
An: 'psi...@li...'
<psi...@li...>; 'psi...@li...'
<psi...@li...>; 'psi...@li...'
<psi...@li...>; 'ps...@eb...'
<ps...@eb...>; 'psi...@eb...' <psi...@eb...>
Betreff: HUPO PSI recommendation document (file format proBAM), 60-days
public review
Dear colleague,
dear member of the Proteomics community,
please forward this message to potentially interested colleagues!
The HUPO Proteomics Standards Initiative (PSI) develops standards
for documentation and storage of Proteomics data (see
http://www.psidev.info for an overview of activities).
A recommendation document specifying the proBAM file format
has been submitted to the PSI document process.
The submission can be found here:
http://www.psidev.info/proBAM-in-docproc
After having passed a 30-day review of the PSI steering group
with minor changes, the proposed document version 1.0.0 DRAFT
now goes through 60-days public comments and external
review phase (end: 31st May 2017).
The format represents output from proteogenomic studies,
mapping the MS-based proteomics PSM information to
the genome. Background: The proBAM format builds upon the structure of the
original SAM/BAM format (http://samtools.github.io/hts-specs/SAMv1.pdf)
by extending it with other mandatory fields to accommodate unique features
on MS-based proteomics peptide-spectrum matches (PSMs) information.
PLEASE ADD COMMENTS to the submission page
(http://www.psidev.info/proBAM-in-docproc)
or send them directly to martin.eisenacher: at : rub.de for
example regarding the following criteria:
- That it is well formed that is, it is presented in accordance with the
templates and is clearly written.
- That it is sufficiently detailed and clearly contains and comprehensively
describes the necessary and sufficient explanation of the format.
- That the examples are in accordance with the specification.> >
This message is to encourage you to contribute to the standards
development activity by commenting on the material that is
available online. We invite both positive and negative comments.
If negative comments are being made, these could be on the relevance,
clarity, correctness, appropriateness, etc, of the proposal as
a whole or of specific parts of the proposal.
If you do not feel well placed to comment on this document, but
know someone who may be, please consider forwarding this request.
There is no requirement that people commenting should have had any
prior contact with the PSI.
Many thanks for your valuable time and participation
Martin Eisenacher (PSI Editor)
--
PD DR. MARTIN EISENACHER
Department Leader
DEPARTMENT Medical Bioinformatics
Medizinisches Proteom-Center
Ruhr-University Bochum
Building ZKF E.141 | Universitätsstraße 150 | D-44801 Bochum
Fon +49 (0)234 32-29288 | Fax +49 (0)234 32-14554
E-mail <mailto:mar...@ru...> mar...@ru...
<http://www.medizinisches-proteom-center.de/>
www.medizinisches-proteom-center.de
|
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