1. Johannes Griss jgriss@ebi.ac.uk PSI Meeting Heidelberg, April 2011 EBI is an Outstation of the European Molecular Biology Laboratory. mzTab Proposal for A Simple Data Format for Proteomics Results

2. Johannes Griss jgriss@ebi.ac.uk PSI Meeting Heidelberg, April 2011 Current Situation The necessity of standard data formats has become generally accepted Proteomics techniques are constantly evolving Proposed standard formats had to become very complex to adequately capture proteomics data mzIdentML for identification data mzQuantML for quantitative data An effective use of these data formats requires sophisticated bioinformatic knowledge Many researchers are still used to use MS Excel to “look” at their data

3. Johannes Griss jgriss@ebi.ac.uk PSI Meeting Heidelberg, April 2011 Communication of Proteomics Results Proteomics resources require a mechanism to simply/efficiently exchange basic proteomics results Collaboration with colleagues from other scientific fields is increasingly important Necessity to share proteomics results with researchers outside of proteomics Need to make proteomics data easily accessible

4. Johannes Griss jgriss@ebi.ac.uk PSI Meeting Heidelberg, April 2011 Potential Current Problems Currently proposed standard formats are difficult to use without the JAVA APIs “Complete” standard formats are too complex and big to quickly share the essential results Quick, f.e. Perl scripts for specific research questions are not easily possible Large amount of potential innovation could be lost Reading files requires special software Further processing of the data (f.e. with statistical) tools is not easily possible No standard tools to read / write mz*ML files available Custom built software required for many use cases otherwise fulfilled by “Excel & friends”

5. Johannes Griss jgriss@ebi.ac.uk PSI Meeting Heidelberg, April 2011 mzTab - Aim To provide a simple and efficient way of exchanging proteomics data Which protein / peptide was identified in a given experimental setting Easy to update and maintain Easy to use by the proteomics community, systems biologists as well as providers of knowledge bases

6. Johannes Griss jgriss@ebi.ac.uk PSI Meeting Heidelberg, April 2011 mzTab – Target Audience Proteomics repositories (f.e. PRIDE, PeptideAtlas) Knowledge base resources (f.e. UniProt, HPRD) Researchers outside of proteomics Researchers analyzing proteomics data with limited bioinformatic knowledge / support

7. Johannes Griss jgriss@ebi.ac.uk PSI Meeting Heidelberg, April 2011 mzTab – proposed concept A tab-delimited file format Goals Content should be “readable” using MS Excel Should contain minimal information for proteomics repositories / knowledge bases to exchange data Data should be easily accessible using f.e. scripting languages One file should be able to contain multiple experiments / proteins from different resources Aim: To represent the result of a query to f.e. PRIDE using this format Provide a simplisitic summary of proteomics results Every entry contains a reference to the source data (in mzIdentML / mzQuantML format)

8. Johannes Griss jgriss@ebi.ac.uk PSI Meeting Heidelberg, April 2011 mzTab – proposed concept What the format does NOT aim at: Replace mzIdentML or mzQuantML Contain the complete data of a proteomics experiment Provide detailed evidence for the data Allow a researcher to recreate the process which led to the results Be requirements conform (MIAPE, journal guidelines, etc.) In short: be complete in any way

9. Johannes Griss jgriss@ebi.ac.uk PSI Meeting Heidelberg, April 2011 mzTab – Possible Format Specification Three sections (Optional) Metdata section (Required) Protein section (Optional) Peptide section Can report proteomics data at different levels Single experiments Multiple (possibly linked) experiments Data generated as a result to a query (possibly to multiple resources)

10. Johannes Griss jgriss@ebi.ac.uk PSI Meeting Heidelberg, April 2011 mzTab – Metadata Section ----metadata PRIDE_16649-title: The Synaptic Proteome during Development and Plasticity of the Mouse Visual Cortex PRIDE_16649-species: [NEWT, 10090, Mouse,] PRIDE_16649-tissue: [EFO, EFO:0000916, visual cortex,] PRIDE_16649-instrument[1]-type: [MS, MS:1000287, TOF-MS,] PRIDE_16649-search_engine: [MS, MS:1001207, Mascot, ] PRIDE_16649-contact[1]-name: August B Smit PRIDE_16649-contact[1]-email: guus.smit@cncr.vu.nlguus.smit@cncr.vu.nl PRIDE_16649-url: http://www.ebi.ac.uk/pride/q.do?accession=16649 http://www.ebi.ac.uk/pride/q.do?accession=16649 ----END

11. Johannes Griss jgriss@ebi.ac.uk PSI Meeting Heidelberg, April 2011 mzTab – Protein Section ----proteins Accession … reliabilitypeptides … ambiguity_members P12345 4 2 P12346,P123457 … ´----END A Table holding the basic identification information Suggestions of how to include quantitative data multiple search engine scores ambiguous modification positions

12. Johannes Griss jgriss@ebi.ac.uk PSI Meeting Heidelberg, April 2011 mzTab – Peptide Table ----peptides sequence accession unit unique … reliability … DIIL O00160 PRIDE_3381 false 5 … VESVDL O00160 PRIDE_3381 true 4 … ----END A Table holding the basic peptide information Suggestions of how to include quantitative data multiple search engine scores ambiguous modification positions

13. Johannes Griss jgriss@ebi.ac.uk PSI Meeting Heidelberg, April 2011 PRIDE collaborators http://www.ebi.ac.uk/ols http://www.ebi.ac.uk/pride pride-helpdesk@ebi.ac.uk http://www.psidev.info Links, collaborations and funding http://www.ebi.ac.uk/tools/picr Funding http://www.ebi.ac.uk/pride/dod http://www.proteomexchange.org http://www.biodas.orghttp://code.google.com/p/pride-converter