recap. of Heidelberg PSI workshop - Proteomics Informatics (PI) Martin Eisenacher, April 15th, 2011

Overview PSI-PI activities mzIdentML 1.0 for peptide and protein identification (released Aug 2009, not published) mzIdentML 1.1 non-minor changes inspired by implementations MIAPE-Quant Minimum Information about a quantitative Proteomics analysis (incl. SRM) mzQuantML for reporting quant. values of features, peptides, proteins (working draft)

Heidelberg outcome mzIdentML Update to 1.1: review of mzIdentML schema changes: done work over mzIdentML example files and googlecode issues: issues closed, some to be finally agreed in TeleCon TODOs before DocProc submission (approx. 2-4 weeks): assemble final versions of valid example docs check / update the schema documentation prepare spec. doc.

Heidelberg outcome mzQuantML summary OpenMS group presented an alternative schema there are now 3 suggestions, one of which was the most promising at the moment worked intensively on example files for OpenMS schema (SILAC, iTraq, LC/MS label-free) began a list of CV terms (aggregation, layer) include spectral counting: feeling: possible include SRM: feeling: possible include metabolites: feeling: possible later

mzQuantML sketch of version 0.1.2 cvList ProteinList ? value PeptideList QuantitationResult + GroupedQuantitationResult seq., mod., external ref AssayList grouped by … raw file, label, ident. file StudyVariableList replicates, exp. cond. FeatureList mass trace + QuantificationsList QuantMeasurement RatioMeasurement value value DataProcessingList

mzQuantML sketch of OpenMS alternative (version 0.1.2d) cvList ProteinList PeptideList seq., mod., external ref QuantList QuantLayer QuantValue CV : type of data / layer description CV: transformation / aggregation function AssayList raw file, label, ident. file StudyVariableList discussion about optional studyVariableRef attr. in <QuantValue> (could „explain“ the aggregation further) replicates, exp. cond. FeatureList mass trace DataProcessingList

mzQuantML QuantList Self-References from <QuantValue> to <QuantValue> enable description of: „aggregation / transformation“ (CV term in <QuantValue>) „type of data / layer description“ (CV term in <QuantLayer>) If we had studyvariable_ref, there would be finer grained „parallel“ layers (red) corresponding to the experiment structure layer „mutant samples“ „wildtype “ layer „mutant“ layer „protein ratios “ layer „protein values“ layer „peptide values“ layer „raw values“ layer „normalized values“ aggregation: „normalization“ „condense peptides“ / “average“ „condense proteins“ / „sum“ „ratio“ …

mzQuantML references to and from QuantList (proposal for next schema version) Peptide Protein seq., mod., external ref <QuantList> could be the central element of the schema; <FeatureList>, <PeptideList> and <ProteinList> could be optional! QuantList Feature

Acknowledgements MPC / RUB, Bochum, Germany Julian Uszkoreit, Gerhard Mayer, Christian Stephan HUPO PSI and PI group members Andy Jones, David Creasy, et al. EU-FP7 ProteomeXchange ProteoRed Salvador Martinez, Alberto Medina, Juan-Pablo Albar European Bioinformatics Institute Juan-Antonio Vizcaino, Henning Hermjakob, Sandra Orchard Ministerium für Innovation, Wissenschaft und Forschung des Landes Nordrhein-Westfalen