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How to assure MIAPE compliance of the data using the ProteoRed MIAPE Extractor tool

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

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How to assure MIAPE compliance of the data using the ProteoRed MIAPE Extractor tool

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  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) BioinformaticsSupportWorkingGroup – ProteoRed ISCIII National Center forBiotechnology – CNB - CSIC

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

  3. MIAPE Extraction • Extraction of • MIAPE MassSpectrometry (MS) and • MIAPE MassSpectrometryInformatics (MSI) • fromX!Tandem, mzIdentML, mgf, mzML, PRIDE XML These files are kept in the server and are referenced by the MIAPE documents

  4. MIAPE Extraction

  5. MIAPE Extraction

  6. MIAPE Extraction

  7. MIAPE Extraction Sample Spectrometer Analyzers Acquisition

  8. MIAPE Extraction

  9. MIAPE Extraction

  10. MIAPE Extraction In batchmode

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

  12. Data compilation / aggregation

  13. Data compilation / aggregation 1..n run(s) 1 dataset • 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

  14. Data compilation / aggregation • Level 0: Twobiologicalreplicates Level 0 Level 1 Level 2 • Level 1: Differentrp-HPLC fractions • Level 2: Onesearchforeachfraction

  15. Data compilation / aggregation Prieto G, Aloria K, Osinalde N, Fullaondo A, Arizmendi JM, Matthiesen R: PAnalyzer: A software toolforproteininference in shotgunproteomics.BMC bioinformatics 2012, 13:288. • ImplementsthePAnalyzerproteingroupingalgorithm Gorka Prieto (UPV-EHU)

  16. Data compilation / aggregation Proposal Nesvizhskii & Aebersold PAnalyzer • ImplementsthePAnalyzerproteingroupingalgorithm Conclusive Indistinguishable Distinct Differentiable Indistinguishable Group of proteins identified by shared peptides only Subset Subsumable Non-conclusive Ambiguous group 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 RAW data Data compilation MIAPE Extraction Data submission Data inspection Data curation ProteomeXChange Inspection project definition Data visualization PRIDE XML Export FDR, thresholds, etc… PSI standard MIAPE (MS,MSI) Search engine

  19. Data curation 9 differentfilters

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

  21. Data inspection

  22. Data inspection 36 differentviews/plots

  23. Data inspection

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

  25. Data submission • Filtered data will be prepared for a ProteomeXchange bulk submission • Files attached to the MIAPE reports are downloaded from the MIAPE repository to a local folder: • mzIdentML (attachedtothe MIAPE MSI) • MGF or mzML (attachedtothe 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). MTD name Salvador Martinez-Bartolome MTD email smartinez@proteored.org MTD affiliation CNB-CSIC ProteomicsUnit MTD description Project short description MTD keywords HUPO-PSI,ProteoRed,MIAPE MTD type SUPPORTED MTD commentThisis a commentfromthe test MTD species [NEWT,9606,Human,] MTD instrument [MS, MS:1000447,LTQ,] MTD modification [UNIMOD,UNIMOD:1,Acetyl,] MTD modification [UNIMOD,UNIMOD:4,Carbamidomethyl,] MTD modification [UNIMOD,UNIMOD:35,Oxidation,] MTD pubmed 1234234 MTD pride_loginsmartinez FMH file_idfile_typefile_pathfile_mapping FME 1 result C:\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 FME 2 raw c:\proteomeXchangeExporterTest\RAW_File_1_fake.xml FME 3 raw c:\proteomeXchangeExporterTest\RAW_File_2_fake.xml FME 4 raw c:\proteomeXchangeExporterTest\RAW_File_3_fake.xml FME 5 raw c:\proteomeXchangeExporterTest\RAW_File_4_fake.xml FME 6 raw c:\proteomeXchangeExporterTest\RAW_File_5_fake.xml FME 7 raw c:\proteomeXchangeExporterTest\RAW_File_6_fake.xml FME 8 raw c:\proteomeXchangeExporterTest\RAW_File_7_fake.xml FME 9 raw c:\proteomeXchangeExporterTest\RAW_File_8_fake.xml FME 10 raw c:\proteomeXchangeExporterTest\RAW_File_9_fake.xml FME 11 raw c:\proteomeXchangeExporterTest\RAW_File_10_fake.xml FME 12 peak c:\proteomeXchangeExporterTest\HPP_CHAPS_FR1.mgf.gz 1,2 FME 13 peak c:\proteomeXchangeExporterTest\HPP_CHAPS_FR2.mgf.gz 1,3 FME 14 peak c:\proteomeXchangeExporterTest\HPP_CHAPS_FR3.mgf.gz 1,4 FME 15 peak c:\proteomeXchangeExporterTest\HPP_CHAPS_FR4.mgf.gz 1,5 FME 16 peak c:\proteomeXchangeExporterTest\HPP_CHAPS_FR5.mgf.gz 1,6 FME 17 peak c:\proteomeXchangeExporterTest\HPP_CHAPS_FR6.mgf.gz 1,7 FME 18 peak c:\proteomeXchangeExporterTest\HPP_CHAPS_FR7.mgf.gz 1,8 FME 19 peak c:\proteomeXchangeExporterTest\HPP_CHAPS_FR8.mgf.gz 1,9 FME 20 peak c:\proteomeXchangeExporterTest\HPP_CHAPS_FR9.mgf.gz 1,10 FME 21 peak c:\proteomeXchangeExporterTest\HPP_CHAPS_FR10.mgf.gz 1,11 FME 22 other c:\proteomeXchangeExporterTest\HPP_CHAPS_FR1_MIAPE_MS_report.html 1,2,12 FME 23 other c:\proteomeXchangeExporterTest\HPP_CHAPS_FR2_MIAPE_MS_report.html 1,3,13 FME 24 other c:\proteomeXchangeExporterTest\HPP_CHAPS_FR3_MIAPE_MS_report.html 1,4,14 FME 25 other c:\proteomeXchangeExporterTest\HPP_CHAPS_FR4_MIAPE_MS_report.html 1,5,15 FME 26 other c:\proteomeXchangeExporterTest\HPP_CHAPS_FR5_MIAPE_MS_report.html 1,6,16 FME 27 other c:\proteomeXchangeExporterTest\HPP_CHAPS_FR6_MIAPE_MS_report.html 1,7,17 FME 28 other c:\proteomeXchangeExporterTest\HPP_CHAPS_FR7_MIAPE_MS_report.html 1,8,18 FME 29 other c:\proteomeXchangeExporterTest\HPP_CHAPS_FR8_MIAPE_MS_report.html 1,9,19 FME 30 other c:\proteomeXchangeExporterTest\HPP_CHAPS_FR9_MIAPE_MS_report.html 1,10,20 FME 31 other c:\proteomeXchangeExporterTest\HPP_CHAPS_FR10_MIAPE_MS_report.html 1,11,21 FME 32 other c:\proteomeXchangeExporterTest\HPP_CHAPS_FR1_MIAPE_MSI_report.html 1,2,12 FME 33 other c:\proteomeXchangeExporterTest\HPP_CHAPS_FR2_MIAPE_MSI_report.html 1,3,13 FME 34 other c:\proteomeXchangeExporterTest\HPP_CHAPS_FR3_MIAPE_MSI_report.html 1,4,14 FME 35 other c:\proteomeXchangeExporterTest\HPP_CHAPS_FR4_MIAPE_MSI_report.html 1,5,15 FME 36 other c:\proteomeXchangeExporterTest\HPP_CHAPS_FR5_MIAPE_MSI_report.html 1,6,16 FME 37 other c:\proteomeXchangeExporterTest\HPP_CHAPS_FR6_MIAPE_MSI_report.html 1,7,17 FME 38 other c:\proteomeXchangeExporterTest\HPP_CHAPS_FR7_MIAPE_MSI_report.html 1,8,18 FME 39 other c:\proteomeXchangeExporterTest\HPP_CHAPS_FR8_MIAPE_MSI_report.html 1,9,19 FME 40 other c:\proteomeXchangeExporterTest\HPP_CHAPS_FR9_MIAPE_MSI_report.html 1,10,20 FME 41 other c:\proteomeXchangeExporterTest\HPP_CHAPS_FR10_MIAPE_MSI_report.html 1,11,21 • 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

  27. Data submission

  28. Data submission

  29. Data submission

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

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

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

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