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10. Standards in Proteomics
MS bioinformatics analysis for proteomics
Salvador Martínez de Bartolomé[email protected] support – ProteoRedProteomics Facility, National Center for Biotechnology, Madrid
Index
• Need of standards in Proteomics• HUPO-PSI
– Organization– Standard data formats– MIAPEs
• PEFF: A Common Sequence Database Format in Proteomics
• PRIDE• Standard data format converters
Index
• Need of standards in Proteomics• HUPO-PSI
– Organization– Standard data formats– MIAPEs
• PEFF: A Common Sequence Database Format in Proteomics
• PRIDE• Standard data format converters
Proteomics data is often only made available as arbitrarily formatted PDF tables, carrying important limitations:
• Source data (mass spectra) are not made available• No peer review validation possible• Very little raw materials for testing innovative in silico techniques are available
• Automated (re-)processing of the identifications is impossible (eliminating objective technique comparison)
Need of standards in Proteomics
Thoughts in Standards•Bradshaw RA, Burlingame AL, Carr S, Aebersold R.Reporting protein identification data: the next generation of guidelines.Mol Cell Proteomics. 2006 May;5(5):787-8.
•Wilkins et al. Guidelines for the next 10 years of proteomics.Proteomics. 2006 Jan;6(1):4-8.
•Nature Biotechnology 2006, Nov:
•Editorial: Standards Operating Procedures
•Burgoon LD. The need for standards, not guidelines, in biological data reporting and sharing.
•Ball C. Are we stuck in standards?
•Nature Biotechnology: Planned focus issue and Community Consultation on Standards: http://www.nature.com/nbt/consult/index.html
Need of standards in Proteomics
• Proteomics: No standardized reporting, not standard database submission
• Proteomics data is generated at a high rate, and lost at a high rate
• Experiments are repeated unnecessarily, the field advances slower than necessary
Need of standards in Proteomics
• Standards for:
• Exchange data
• Compare data
• Review data
• Reproduce results
• Store data
Index
• Need of standards in Proteomics• HUPO-PSI
– Organization– Standard data formats– CVs– MIAPEs
• PEFF: A Common Sequence Database Format in Proteomics
• PRIDE• Standard data format converters
Index
• Need of standards in Proteomics• HUPO-PSI
– Organization– Standard data formats– CVs– MIAPEs
• PEFF: A Common Sequence Database Format in Proteomics
• PRIDE• Standard data format converters
HUPO PSIProtein Standard Initiative
http://www.psidev.info
HUPO PSIProtein Standard Initiative
Meetings http://www.psidev.info
HUPO PSI
• Open community initiative
• Develop data format standards
• Data representation and annotation standards
• Involve data producers, database providers, software producers, publishers
Protein Standard Initiativehttp://psidev.info
The Proteomics Standards Initiative (PSI) aims to define community standards for data representation in proteomics and to facilitate data comparison, exchange and verification
Proteomics 2003, 3 (7): The proteomics standards initiative.Orchard,S. , Hermjakob,H. , Apweiler,R.
HUPO PSI structure
Main unit is workgroup• Gel Electrophoresis• Molecular Interactions• Sample Processing• Mass spectrometry• Proteomic Informatics (MS oriented)• Protein Modifications
Transversal activities• One Steering Group• Controlled vocabulary• MIAPE guidelines
HUPO PSI structure
• Annual workshop, reporting activity at annual HUPO, conference calls, dedicated workshops
• No permanent funding, active members work on their “spare time”
• Website (http://psidev.info) and mailing-lists
• PSI Document process•Vizcaino, J.A., Martens, L., Hermjakob, H., Julian, R.K. and Paton, N.W. (2007) The PSI formal document process and its implementation on the PSI website. Proteomics 7: 2355-2357.
HUPO PSI document process
Candidate Recommendation
submitted to PSI Editor
PSI Editor reviews draft
PSI Editor submits draft to PSI-SG
PSI Editor returns Draft Revise
Pass
15 Day PSI-SG Comment
PSI Editor reviews
comments
PSI Editor posts & announces
PSI Working Draft Proposal
(PWD-R.P)
Revise
Pass
30-day Public Comment
PSI Editor reviews
comments
PSI Editor returns Draft, remove
PWD from indexRevise
PSI Editor posts & announces PSI Final
Document Proposal(PFD-R.P)
Pass
PSI-WG submits PFD-R.P with supporting documents (tutorials,etc)
To PSI-SG requestingPFD-R status
PSI-SG reviews request
PSI-SG Provide Feedback to WG
Chairs
PSI-SG and PSI Editor conduct
Formal External Review
Pass
Revise
60 day Formal Review and Public
Comment
PSI-SG Examines Reviews Revise
PSI Editor posts & announces PSI Final
Document(PFD-R)
Pass
Community consultation at:http://www.nature.com/nbt/consult/
HUPO PSI structure
HUPO-PSI
• Project status
HUPO-PSIPSI deliverables• Data formats
• MIML
• mzML
• AnalysisXML
• gelML
• giML
• spML
•MIAPE minimal reporting requirements
• One parent document - The minimum information about a proteomics experiment (MIAPE), Nature Biotechnology 25, 887-893 (2007)
• MIAPE MI, MS, MSI, GE, GI, CC, CE, SP
• Formats (XML schema, instance docs, specification docs)
• Controlled Vocabularies• MIAPE docs (representation and annotation standards)
Index
• Need of standards in Proteomics• HUPO-PSI
– Organization– Standard data formats– CVs– MIAPEs
• PEFF: A Common Sequence Database Format in Proteomics
• PRIDE• Standard data format converters
Standard data formats for
Experimental data: spectra, acquisition parameters, acquisition equipment, ...
Analyzed data: identifications, quantitations, data analysis software ...
Standard data formatsExperimental data: spectra, acquisition parameters, acquisition equipment, ...
mzXML 2.0
mzXML 1.05
mzXML 3.0 mzXML 4.0
mzXML 2.0
mzML 1.0
mzML: Released on June 1st, 2008
Seattle Proteome Center at the Institute for Systems Biology
HUPO-PSI
• data format capturing peak list information. • Its aim is to unite the large number of current formats (pkl's, dta's, mgf's, .....) into one • It is NOT a substitute for the rawfile formats of the instrument vendors. Some vendors, if not all, will provide software transforming their raw files to that standards
Sample instance document mzML 1.0
Standard data formats for
Experimental data: spectra, acquisition parameters, acquisition equipment, ...
Analyzed data: identifications, quantitations, data analysis software ...
Standard data formatsAnalyzed data: identifications, quantitations, data analysis software ...
• describes the results of identification and quantitation processes for proteins, peptides and protein modifications from mass spectrometry
protXML
pepXML
AnalysisXML
AnalysisXML: v1.0 – candidate (Dic 08)
Seattle Proteome Center at the Institute for Systems Biology
HUPO-PSI
Sample instance document AnalysisXML (beta)
Standard data formatsOther data:
XML data format
MIAPE
GelML MIAPE GE
GelInfoML MIAPE GI
miXML MIAPE MIMIX
spML MIAPE SP
proprie-tary format
mass spectrometer B
mass spectrometer A
converter
mzML
search engine A
search engine B
analysisXML
Public repository
Standard data formats
Index
• Need of standards in Proteomics• HUPO-PSI
– Organization– Standard data formats– CVs– MIAPEs
• PEFF: A Common Sequence Database Format in Proteomics
• PRIDE• Standard data format converters
Controlled VocabulariesThe Controlled Vocabularies (CVs) of the Proteomic Standard Initiative (PSI) provide a consensus annotation system to standardize the meaning, syntax and formalism of terms used across proteomics, as required by the PSI Working Groups.
Each PSI working group develop the CVs required by the technology or data type it aims to standardize, following common recommendations for development and maintenance.
At the PSI meeting in Washington (Sept 06), it was decided that all PSI working groups should adopt the same CVs standardizing some overlapping concepts (units and resources).
100173
TOF T.O.F.
time of flight
time-of-flight
What is a CV?TermSynonyms
Controlled Vocabularies
Controlled Vocabularies• PSI CVs are composed of two documents:
• a design principle description• the implementation of the CVs in OBO (Open Biomedical Ontologies)
•Developing CVs is a process of collecting, and if necessary defining terms.
• Every effort must be made to adopt and re-use existing ontologies or CVs where they exist, to avoid “re-inventing the wheel”.
Ontology Lookup Servicehttp://www.ebi.ac.uk/ontology-lookup/
• The OLS provides a web service interface to query multiple ontologies from a single location with a unified output format.
Ontology Lookup Servicehttp://www.ebi.ac.uk/ontology-lookup/
Index
• Need of standards in Proteomics• HUPO-PSI
– Organization– Standard data formats– CVs– MIAPEs
• PEFF: A Common Sequence Database Format in Proteomics
• PRIDE• Standard data format converters
Sufficiency and practicability
• Unambiguous description of the experimental context• Allow understanding of the results and their interpretation• Sufficient to permit a critical evaluation• In principle allow recreation of the work
MIAPE: Minimum Information About a Proteomics ExperimentTaylor, C.F., Paton, N.W., Lilley, K.S., Binz, P.A., Julian, R.K., Jr., Jones, A.R., Zhu, W., Apweiler, R., Aebersold, R., Deutsch, E.W., Dunn, M.J., Heck, A.J., Leitner, A., Macht, M., Mann, M., Martens, L., Neubert, T.A., Patterson, S.D., Ping, P., Seymour, S.L., Souda, P., Tsugita, A., Vandekerckhove, J., Vondriska, T.M., Whitelegge, J.P., Wilkins, M.R., Xenarios, I., Yates, J.R., 3rd and Hermjakob, H. (2007)
The minimum information about a proteomics experiment (MIAPE). Nat Biotechnol 25: 887-893.
• It is:– Describing a list of information and data to provide when an experiment is reported (it is a content descriptor)
• Peptide sequence, scores, modifications, mass errors, etc.
– Helping to assess quality control• Number of replicates, expected error rate
MIAPE guidelines
• It is not:– Describing the way to run an experiment
• does not specify the use of a search engine in particular• does not force the use of one protocol
– Describing the data representation• Use excel to create a table with these five following columns:…
– Including any quality judgment• need 30% sequence coverage to identify a protein• “The absence of thorough validation of both analytical and biological results, including error analysis should result in rejection”• “Authors should justify the use of a very small database or database that excludes common contaminants, since this may generate misleading assignments”
MIAPE guidelines
• MIAPE Gel Electrophoresis (GE) v1.4• MIAPE Gel Informatics (GI) v0.5• MIAPE Mass Spectrometry (MS) v2.22• MIAPE Mass Spectrometry Informatics (MSI) v0.8• MIAPE Column Chromatography (CC) v1.0• MIAPE Capillary Electrophoresis (CE) v0.7• MIAPE Sample Preparation and handling (SP) v0.2• MIAPE Molecular Interactions (MI) v1.1.2
MIAPE guidelines
Online tool to generate and store MIAPE documentshttp://www.proteored.org
A MIAPE generator tool
Fill all minimal informationby hand
Fill only some changes or new items by hand, and add automatically static informationfrom previous MIAPE documents
ProteoRedserver
A MIAPE generator toolhttp://www.proteored.org
A MIAPE generator tool
A MIAPE generator tool
A MIAPE generator tool
A MIAPE generator tool
HUPO-PSI: MIAPE Gel Electrophoresis v1.2
Generate XML
Generate report
Delete document
Edit document
MIAPE Reports
Generate report
MIAPE Reports
MIAPE Reports
MIAPE Reports
MIAPE Reports
MIAPE Reports
MIAPE Reports
MIAPE Reports
Index
• Need of standards in Proteomics• HUPO-PSI
– Organization– Standard data formats– MIAPEs
• PEFF: A Common Sequence Database Format in Proteomics
• PRIDE• Standard data format converters
A Common Sequence Database Format in Proteomics
•P-A Binz, S Seymour, J Shofsthal, D Creasy, E Kapp
•Problem: interpretation of current fasta format by search engines:• Protein identifiers• Description• Taxonomy• Other annotation (PTMs, sequence variants, etc)
•Propose an alternative to the heterogeneous fasta format, ideally generated by the database providers, or alternatively via an accepted converter, to submit one single source sequence database to various search engines
• SwissProt and EBI already agreed on the principle
•Format proposal reached (not only for MS, flexible, extensible)
PEFF: PSI Extended FASTA Format
• A unified format for protein and nucleotide sequence databases to be used by sequence search engines and other associated tools (spectra library search tools, sequence alignment software, data repositories, etc).
PEFF: PSI Extended FASTA Format
• Enables consistent extraction, display and processing of information such as protein/nucleotide sequence database entry identifier, description, taxonomy, etc. across software platforms.• Allows the representation of structural annotations such as post-translational modifications, mutations and other processing events.• Flat file that includes a header of meta data to describe relevant information about the database(s) from which the sequence has been obtained (i.e., name, version, etc).• Sequence database providers are encouraged to generate this format as part of their release policy or to provide appropriate converters that can be incorporated into processing tools.
Index
• Need of standards in Proteomics• HUPO-PSI
– Organization– Standard data formats– MIAPEs
• PEFF: A Common Sequence Database Format in Proteomics
• PRIDE• Standard data format converters
PRIDE – Protein Identification Database
• Turns publicly available data into publicly accessible data
• Protein identifications
• Experimental detail
• Peak lists
• Linkout to raw data
• Fully open source
• Fully open data
• Implementation of PSI standards as they are released
proprie-tary format
mass spectrometer B
mass spectrometer A
converter
mzML
search engine A
search engine B
analysisXML
Public repository
PRIDE
PRIDE
PRIDE – Protein Identification Database
...Tomorrow with Alberto Medina
Index
• Need of standards in Proteomics• HUPO-PSI
– Organization– Standard data formats– MIAPEs
• PEFF: A Common Sequence Database Format in Proteomics
• PRIDE• Standard data format converters
Standard data format converters
• msconvert (ProteoWizard):– From: mzML, mzXML, Thermo RAW, MGF – To: mzML, mzXML – Vendor format reading restrictions: Thermo
RAW: Windows with XCalibur XDK installed
Standard data format converters
• ReAdW version 4.0.2:– From:
• Thermo RAW
– Exports to: • mzXML• mzML (not yet updated to final mzML 1.0 standard; try
msconvert)
– Requires a valid installation of the Thermo XCalibur software system, as it relies on the XCalibur libraries.
Standard data format converters
• CompassXport 1.3.6 :– From:
• analysis.baf (instrument families: APEX, micrOTOF, micOTOF-Q, ...)
• analysis.yep (esquire/HCT instrument family)• AutoXecute run for LCMaldi (instrument family: autoFlex,
ultraFlex, ...)• fid files (flex instrument family)
– Exports to: • mzXML version 2.1 • mzData, version 1.05• mzML in progress
– Do not requires to install Bruker propietary software
– Replace to mzBruker
Standard data format converters
• massWolf 4.0.2 (1st july 08):– From:
• MassLynx native acquisition files
– Exports to: • mzXML
– Requires installation of MassLynx software on the same computer
– You must select the appropriate massWolf download to match the version of your MassLynx software (4.0 or 4.1).
Standard data format converters
• mzWiff 4.0.2 (1st July 08):– From:
• Analyst native acquisition (.wiff) files
– Exports to: • mzXML
– Requires installation of Analyst software
Standard data format converters
• T2DExtractor (Dec 07):– From:
• data from a SCIEX/ABI 4000 series MALDI TOFTOF instruments
– Exports to: • mzXML
Standard data format converters
• Trapper 4.1.0 (17 th july 08):– From:
• Agilent MassHunter format (.d directories)
– Exports to: • mzXML
– Requires Agilent's MHDAC software installed– This software will be included in the
upcoming 4.1.0 TPP distribution