How to assure MIAPE compliance of the data using the
ProteoRed MIAPE Extractor tool
HUPO-PSI meeting - Liverpool(15th April 2013)
Salvador Martínez-Bartolomé ([email protected])Bioinformatics Support Working Group – ProteoRed ISCIII
National Center for Biotechnology – CNB - CSIC
ProteoRed MIAPE ExtractorComplete workflow
Data submission
PRIDE XML
Export
RAW data
PSI standard
MIAPE (MS,MSI)
Inspection project
definition
MIAPE Extraction Data compilation
ProteomeXChange
Data inspection
Data visualization
Search engine
FDR, thresholds,
etc…
Data curation
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
MIAPE Extraction
MIAPE Extraction
MIAPE Extraction
MIAPE Extraction
Sample
Spectrometer
Analyzers
Acquisition
MIAPE Extraction
MIAPE Extraction
MIAPE ExtractionIn batch mode
ProteoRed MIAPE ExtractorComplete workflow
Data submission
PRIDE XML
Export
RAW data
PSI standard
MIAPE (MS,MSI)
Inspection project
definition
MIAPE Extraction Data compilation
ProteomeXChange
Data inspection
Data visualization
Search engine
FDR, thresholds,
etc…
Data curation
Data compilation / aggregation
Data compilation / aggregation
• 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
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
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)
Data compilation / aggregation
Proposal Nesvizhskii & Aebersold PAnalyzer
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
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
ProteoRed MIAPE ExtractorComplete workflow
Data submission
PRIDE XML
Export
RAW data
PSI standard
MIAPE (MS,MSI)
Inspection project
definition
MIAPE Extraction Data compilation
ProteomeXChange
Data inspection
Data visualization
Search engine
FDR, thresholds,
etc…
Data curation
Data curation
9 different filters
ProteoRed MIAPE ExtractorComplete workflow
Data submission
PRIDE XML
Export
RAW data
PSI standard
MIAPE (MS,MSI)
Inspection project
definition
MIAPE Extraction Data compilation
ProteomeXChange
Data inspection
Data visualization
Search engine
FDR, thresholds,
etc…
Data curation
Data inspection
36 different views/plots
Data inspection
Data inspection
ProteoRed MIAPE ExtractorComplete workflow
Data submission
PRIDE XML
Export
RAW data
PSI standard
MIAPE (MS,MSI)
Inspection project
definition
MIAPE Extraction Data compilation
ProteomeXChange
Data inspection
Data visualization
Search engine
FDR, thresholds,
etc…
Data curation
• 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
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
MTD name Salvador Martinez-BartolomeMTD email [email protected] affiliation CNB-CSIC Proteomics UnitMTD description Project short descriptionMTD keywords HUPO-PSI,ProteoRed,MIAPEMTD type SUPPORTEDMTD comment This is a comment from the testMTD 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 1234234MTD pride_login smartinez
FMH file_id file_type file_path file_mappingFME 1 result C:\proteomeXchangeExporterTest\964-HPLC-RF CNB Jurkat_PRIDE.xml2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41FME 2 raw c:\proteomeXchangeExporterTest\RAW_File_1_fake.xmlFME 3 raw c:\proteomeXchangeExporterTest\RAW_File_2_fake.xmlFME 4 raw c:\proteomeXchangeExporterTest\RAW_File_3_fake.xmlFME 5 raw c:\proteomeXchangeExporterTest\RAW_File_4_fake.xmlFME 6 raw c:\proteomeXchangeExporterTest\RAW_File_5_fake.xmlFME 7 raw c:\proteomeXchangeExporterTest\RAW_File_6_fake.xmlFME 8 raw c:\proteomeXchangeExporterTest\RAW_File_7_fake.xmlFME 9 raw c:\proteomeXchangeExporterTest\RAW_File_8_fake.xmlFME 10 raw c:\proteomeXchangeExporterTest\RAW_File_9_fake.xmlFME 11 raw c:\proteomeXchangeExporterTest\RAW_File_10_fake.xmlFME 12 peak c:\proteomeXchangeExporterTest\HPP_CHAPS_FR1.mgf.gz 1,2FME 13 peak c:\proteomeXchangeExporterTest\HPP_CHAPS_FR2.mgf.gz 1,3FME 14 peak c:\proteomeXchangeExporterTest\HPP_CHAPS_FR3.mgf.gz 1,4FME 15 peak c:\proteomeXchangeExporterTest\HPP_CHAPS_FR4.mgf.gz 1,5FME 16 peak c:\proteomeXchangeExporterTest\HPP_CHAPS_FR5.mgf.gz 1,6FME 17 peak c:\proteomeXchangeExporterTest\HPP_CHAPS_FR6.mgf.gz 1,7FME 18 peak c:\proteomeXchangeExporterTest\HPP_CHAPS_FR7.mgf.gz 1,8FME 19 peak c:\proteomeXchangeExporterTest\HPP_CHAPS_FR8.mgf.gz 1,9FME 20 peak c:\proteomeXchangeExporterTest\HPP_CHAPS_FR9.mgf.gz 1,10FME 21 peak c:\proteomeXchangeExporterTest\HPP_CHAPS_FR10.mgf.gz 1,11FME 22 other c:\proteomeXchangeExporterTest\HPP_CHAPS_FR1_MIAPE_MS_report.html 1,2,12FME 23 other c:\proteomeXchangeExporterTest\HPP_CHAPS_FR2_MIAPE_MS_report.html 1,3,13FME 24 other c:\proteomeXchangeExporterTest\HPP_CHAPS_FR3_MIAPE_MS_report.html 1,4,14FME 25 other c:\proteomeXchangeExporterTest\HPP_CHAPS_FR4_MIAPE_MS_report.html 1,5,15FME 26 other c:\proteomeXchangeExporterTest\HPP_CHAPS_FR5_MIAPE_MS_report.html 1,6,16FME 27 other c:\proteomeXchangeExporterTest\HPP_CHAPS_FR6_MIAPE_MS_report.html 1,7,17FME 28 other c:\proteomeXchangeExporterTest\HPP_CHAPS_FR7_MIAPE_MS_report.html 1,8,18FME 29 other c:\proteomeXchangeExporterTest\HPP_CHAPS_FR8_MIAPE_MS_report.html 1,9,19FME 30 other c:\proteomeXchangeExporterTest\HPP_CHAPS_FR9_MIAPE_MS_report.html 1,10,20FME 31 other c:\proteomeXchangeExporterTest\HPP_CHAPS_FR10_MIAPE_MS_report.html 1,11,21FME 32 other c:\proteomeXchangeExporterTest\HPP_CHAPS_FR1_MIAPE_MSI_report.html 1,2,12FME 33 other c:\proteomeXchangeExporterTest\HPP_CHAPS_FR2_MIAPE_MSI_report.html 1,3,13FME 34 other c:\proteomeXchangeExporterTest\HPP_CHAPS_FR3_MIAPE_MSI_report.html 1,4,14FME 35 other c:\proteomeXchangeExporterTest\HPP_CHAPS_FR4_MIAPE_MSI_report.html 1,5,15FME 36 other c:\proteomeXchangeExporterTest\HPP_CHAPS_FR5_MIAPE_MSI_report.html 1,6,16FME 37 other c:\proteomeXchangeExporterTest\HPP_CHAPS_FR6_MIAPE_MSI_report.html 1,7,17FME 38 other c:\proteomeXchangeExporterTest\HPP_CHAPS_FR7_MIAPE_MSI_report.html 1,8,18FME 39 other c:\proteomeXchangeExporterTest\HPP_CHAPS_FR8_MIAPE_MSI_report.html 1,9,19FME 40 other c:\proteomeXchangeExporterTest\HPP_CHAPS_FR9_MIAPE_MSI_report.html 1,10,20FME 41 other c:\proteomeXchangeExporterTest\HPP_CHAPS_FR10_MIAPE_MSI_report.html 1,11,21
Data submission
Data submission
Data submission
Data submission
ProteomeXchange submission toolhttp://www.proteomexchange.org/submission
1.640.782 proteins (35.351 distinct)
The ProteoRed MIAPE repository
10.063.199 peptides (784.276 distinct)
ProteoRed MIAPE Extractor
Data submission
PRIDE XML
Export
RAW data
PSI standard
MIAPE (MS,MSI)
Inspection project
definition
MIAPE Extraction Data compilation
ProteomeXChange
Data inspection
Data visualization
Search engine
FDR, thresholds,
etc…
Data curation
Its possible and easy to reach the MIAPE compliance of the submitted data
