1. How to assure MIAPE compliance of the data using the ProteoRed MIAPE Extractor tool HUPO-PSI meeting - Liverpool (15th April 2013) Salvador Martínez-Bartolomé (smartinez@proteored.org) Bioinformatics Support Working Group – ProteoRed ISCIII National Center for Biotechnology – CNB - CSIC

2. ProteoRed MIAPE Extractor Complete workflow Data submission PRIDE XML Export RAW data PSI standard MIAPE (MS,MSI) Inspection project definition MIAPE Extraction Data compilation Proteome XChange Data inspection Data visualization Search engine FDR, thresholds, etc… Data curation

3. MIAPE Extraction Extraction of MIAPE Mass Spectrometry (MS) and MIAPE Mass Spectrometry Informatics (MSI) from X!Tandem, mzIdentML, mgf, mzML, PRIDE XML These files are kept in the server and are referenced by the MIAPE documents

4. MIAPE Extraction

7. Sample Spectrometer Analyzers Acquisition

8. MIAPE Extraction

10. In batch mode

11. ProteoRed MIAPE Extractor Complete workflow Data submission PRIDE XML Export RAW data PSI standard MIAPE (MS,MSI) Inspection project definition MIAPE Extraction Data compilation Proteome XChange Data inspection Data visualization Search engine FDR, thresholds, etc… Data curation

12. Data compilation / aggregation

13. Define which data is going to be inspected / compared User can organize datasets in three different levels: – Level 2: data sets that can be composed by 1..n runs – Level 1: experiment: fractions, bands – Level 0: experiment list: different experiments, replicates 1..n run(s)1 dataset

14. Data compilation / aggregation Level 0 Level 1 Level 2 Level 0: Two biological replicates Level 1: Different rp-HPLC fractions Level 2: One search for each fraction

15. Data compilation / aggregation Implements the PAnalyzer protein grouping algorithm Prieto G, Aloria K, Osinalde N, Fullaondo A, Arizmendi JM, Matthiesen R: PAnalyzer: A software tool for protein inference in shotgun proteomics. BMC bioinformatics 2012, 13:288. Gorka Prieto (UPV-EHU)

16. Data compilation / aggregation Proposal Nesvizhskii & AebersoldPAnalyzer Distinct Differentiable Indistinguishable Subset Subsumable Group of proteins identified by shared peptides only Conclusive Indistinguishable Non-conclusive Ambiguous group Implements the PAnalyzer protein grouping algorithm Prieto G et al. BMC bioinformatics 2012, 13:288.Nesvizhskii A, Aebersold R: Mol Cell Proteomics 2005, 4(10):1419-1440

17. Data compilation / aggregation At experiment level (level 1), protein grouping is made from proteins and peptides coming from all fractions: Proteins and peptides are collected from fractions Then, PAnalyzer algorithm is run over them

18. ProteoRed MIAPE Extractor Complete workflow Data submission PRIDE XML Export RAW data PSI standard MIAPE (MS,MSI) Inspection project definition MIAPE Extraction Data compilation Proteome XChange Data inspection Data visualization Search engine FDR, thresholds, etc… Data curation

19. 9 different filters

20. ProteoRed MIAPE Extractor Complete workflow Data submission PRIDE XML Export RAW data PSI standard MIAPE (MS,MSI) Inspection project definition MIAPE Extraction Data compilation Proteome XChange Data inspection Data visualization Search engine FDR, thresholds, etc… Data curation

21. Data inspection

22. 36 different views/plots Data inspection

24. ProteoRed MIAPE Extractor Complete workflow Data submission PRIDE XML Export RAW data PSI standard MIAPE (MS,MSI) Inspection project definition MIAPE Extraction Data compilation Proteome XChange Data inspection Data visualization Search engine FDR, thresholds, etc… Data curation

25. Filtered data will be prepared for a ProteomeXchange bulk submission Data submission Files attached to the MIAPE reports are downloaded from the MIAPE repository to a local folder: – mzIdentML (attached to the MIAPE MSI) – MGF or mzML (attached to the MIAPE MS) Human readable reports are also generated and downloaded to the local folder

26. Data submission A fully MIAPE compliant PRIDE XML file is generated at local folder from each level 1 (normally an experiment/several runs). RAW data files can be added and related to the existing files A ProteomeXchange summary file is generated containing the list of files to submit and their relationships MTDnameSalvador Martinez-Bartolome MTDemailsmartinez@proteored.org MTDaffiliationCNB-CSIC Proteomics Unit MTDdescriptionProject short description MTDkeywordsHUPO-PSI,ProteoRed,MIAPE MTDtypeSUPPORTED MTDcommentThis is a comment from the test MTDspecies[NEWT,9606,Human,] MTDinstrument[MS, MS:1000447,LTQ,] MTDmodification[UNIMOD,UNIMOD:1,Acetyl,] MTDmodification[UNIMOD,UNIMOD:4,Carbamidomethyl,] MTDmodification[UNIMOD,UNIMOD:35,Oxidation,] MTDpubmed1234234 MTDpride_loginsmartinez FMHfile_idfile_typefile_pathfile_mapping FME1resultC:\proteomeXchangeExporterTest\964-HPLC-RF CNB Jurkat_PRIDE.xml 2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41 FME2rawc:\proteomeXchangeExporterTest\RAW_File_1_fake.xml FME3rawc:\proteomeXchangeExporterTest\RAW_File_2_fake.xml FME4rawc:\proteomeXchangeExporterTest\RAW_File_3_fake.xml FME5rawc:\proteomeXchangeExporterTest\RAW_File_4_fake.xml FME6rawc:\proteomeXchangeExporterTest\RAW_File_5_fake.xml FME7rawc:\proteomeXchangeExporterTest\RAW_File_6_fake.xml FME8rawc:\proteomeXchangeExporterTest\RAW_File_7_fake.xml FME9rawc:\proteomeXchangeExporterTest\RAW_File_8_fake.xml FME10rawc:\proteomeXchangeExporterTest\RAW_File_9_fake.xml FME11rawc:\proteomeXchangeExporterTest\RAW_File_10_fake.xml FME12peakc:\proteomeXchangeExporterTest\HPP_CHAPS_FR1.mgf.gz1,2 FME13peakc:\proteomeXchangeExporterTest\HPP_CHAPS_FR2.mgf.gz1,3 FME14peakc:\proteomeXchangeExporterTest\HPP_CHAPS_FR3.mgf.gz1,4 FME15peakc:\proteomeXchangeExporterTest\HPP_CHAPS_FR4.mgf.gz1,5 FME16peakc:\proteomeXchangeExporterTest\HPP_CHAPS_FR5.mgf.gz1,6 FME17peakc:\proteomeXchangeExporterTest\HPP_CHAPS_FR6.mgf.gz1,7 FME18peakc:\proteomeXchangeExporterTest\HPP_CHAPS_FR7.mgf.gz1,8 FME19peakc:\proteomeXchangeExporterTest\HPP_CHAPS_FR8.mgf.gz1,9 FME20peakc:\proteomeXchangeExporterTest\HPP_CHAPS_FR9.mgf.gz1,10 FME21peakc:\proteomeXchangeExporterTest\HPP_CHAPS_FR10.mgf.gz1,11 FME22otherc:\proteomeXchangeExporterTest\HPP_CHAPS_FR1_MIAPE_MS_report.html1,2,12 FME23otherc:\proteomeXchangeExporterTest\HPP_CHAPS_FR2_MIAPE_MS_report.html1,3,13 FME24otherc:\proteomeXchangeExporterTest\HPP_CHAPS_FR3_MIAPE_MS_report.html1,4,14 FME25otherc:\proteomeXchangeExporterTest\HPP_CHAPS_FR4_MIAPE_MS_report.html1,5,15 FME26otherc:\proteomeXchangeExporterTest\HPP_CHAPS_FR5_MIAPE_MS_report.html1,6,16 FME27otherc:\proteomeXchangeExporterTest\HPP_CHAPS_FR6_MIAPE_MS_report.html1,7,17 FME28otherc:\proteomeXchangeExporterTest\HPP_CHAPS_FR7_MIAPE_MS_report.html1,8,18 FME29otherc:\proteomeXchangeExporterTest\HPP_CHAPS_FR8_MIAPE_MS_report.html1,9,19 FME30otherc:\proteomeXchangeExporterTest\HPP_CHAPS_FR9_MIAPE_MS_report.html1,10,20 FME31otherc:\proteomeXchangeExporterTest\HPP_CHAPS_FR10_MIAPE_MS_report.html1,11,21 FME32otherc:\proteomeXchangeExporterTest\HPP_CHAPS_FR1_MIAPE_MSI_report.html1,2,12 FME33otherc:\proteomeXchangeExporterTest\HPP_CHAPS_FR2_MIAPE_MSI_report.html1,3,13 FME34otherc:\proteomeXchangeExporterTest\HPP_CHAPS_FR3_MIAPE_MSI_report.html1,4,14 FME35otherc:\proteomeXchangeExporterTest\HPP_CHAPS_FR4_MIAPE_MSI_report.html1,5,15 FME36otherc:\proteomeXchangeExporterTest\HPP_CHAPS_FR5_MIAPE_MSI_report.html1,6,16 FME37otherc:\proteomeXchangeExporterTest\HPP_CHAPS_FR6_MIAPE_MSI_report.html1,7,17 FME38otherc:\proteomeXchangeExporterTest\HPP_CHAPS_FR7_MIAPE_MSI_report.html1,8,18 FME39otherc:\proteomeXchangeExporterTest\HPP_CHAPS_FR8_MIAPE_MSI_report.html1,9,19 FME40otherc:\proteomeXchangeExporterTest\HPP_CHAPS_FR9_MIAPE_MSI_report.html1,10,20 FME41otherc:\proteomeXchangeExporterTest\HPP_CHAPS_FR10_MIAPE_MSI_report.html1,11,21

27. Data submission

30. ProteomeXchange submission tool http://www.proteomexchange.org/submission

31. 1.640.782 proteins (35.351 distinct) The ProteoRed MIAPE repository 10.063.199 peptides (784.276 distinct)

32. ProteoRed MIAPE Extractor Data submission PRIDE XML Export RAW data PSI standard MIAPE (MS,MSI) Inspection project definition MIAPE Extraction Data compilation Proteome XChange Data inspection Data visualization Search engine FDR, thresholds, etc… Data curation Its possible and easy to reach the MIAPE compliance of the submitted data