ebi is an outstation of the european molecular biology laboratory. pride associated tools: practical...

EBI is an Outstation of the European Molecular Biology Laboratory.

PRIDE associated tools: Practical exercise 1

PRIDE team, Proteomics Services Group

PANDA group

European Bioinformatics Institute

Hinxton, Cambridge

United Kingdom

Juan Antonio VIZCAINO

EBI RoadshowSofia, 12 June 2012

Juan A. Vizcaí[email protected]

Overview …

• Submission of data: PRIDE Converter

• Visualization of data: PRIDE Inspector:• Review functionality• Charts

• Practical exercise 1



MS Proteomics Typical Workflow

Proteins

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MS/MS spectra

Peptides

SearchEngine

SequenceDatabase

TDMDNQIVVSDYAQMDRLFDQAFGLPR

AKPLMELIERDESTNVDMSLAQRDIVVQET

MEDIDKNGMFFSTYDR

GTAGNALMDGASQL

IPI00302927IPI00025512IPI00002478IPI00185600IPI00014537IPI00298497IPI00329236IPI00002232

PRIDE stores:

1) Peptide Identifications2) Protein Identifications3) Mass spectra4) Valuable additional metadata



DATA SUBMISSION TO PRIDE(Submission-driven resource)



PRIDE Submission Workflow

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SearchEngine

Mascot (.dat),Sequest (.out)

SpectrumMill (.spo)pep.xml, prot.xml

PRIDE XMLPRIDE

Converter



DATA SUBMISSION TO PRIDEUSING PRIDE CONVERTER



PRIDE Converter

• Stand-alone tool for creating PRIDE XML files (the format needed for performing a PRIDE submission)

• It can support a variety of popular proteomics data formats

• Metadata must be provided using CVs/ontologies.

• GUI based tool, easy to use

http://code.google.com/p/pride-converter




Why? Submission made easier: PRIDE Converter


Barsnes et al., Nat. Biotechnology, 2009



PRIDE Converter – interface details



From PRIDE Converter to PRIDE FTP



The need for new toolSearchEngine

Mascot (.dat),Sequest (.out)

SpectrumMill (.spo)pep.xml, prot.xml

• Visualize/Check data• Support for reviewers/ editors• More flexible than the web interface• Initial assessment on data quality

PRIDE Converter



PRIDE Inspector

• Stand-alone GUI based tool for visualising and doing a initial analysis of PRIDE XML files and data already in PRIDE via the PRIDE public DB instance.

• Also private review of data is possible.

• Still under active development (latest version is 1.2.4).

• At present it also supports mzML.

• http://code.google.com/p/pride-toolsuite/wiki/PRIDEInspector

Wang et al., Nat. Biotechnology, 2012

http://code.google.com/p/pride-toolsuite/wiki/PRIDEInspector



How does PRIDE Inspector look like?

Fast loading of large mzML and PRIDE XML files.

Direct access to all PRIDE public database experiments.

Private user download facility.



Experimental Metadata View (1)

General




Sample

Protocol




Instrument

Data processing



Protein Centric View

Selected Protein

Peptides identify the same protein

Spectrum for selected peptide



Protein Centric View (2)

Selected Protein

Peptides identify the same protein

Sequence viewer



Peptide Centric ViewPeptides

Amino Acid Highlighting

PTMs



Spectrum Centric View

Spectrumdetails



Summary Chart View



Summary Chart View (extended)



Who can use PRIDE Inspector?

• Researchers to check their data before they submit it to PRIDE

• Journal’s reviewers and editors in the review process



PRIDE web page: PRIDE Inspector Web Start

http://www/ebi.ac.uk/pride






PRIDE Inspector Web Start

For each submission (private data), a unique URL is generated and it can be included in your manuscript submission:

http://www.ebi.ac.uk:21390/pride/jsp/pages/jnlp/jnlp.jsp?username=review53187&password= - *_3XR8G

http://www.ebi.ac.uk:21390/pride/jsp/pages/jnlp/jnlp.jsp?username=review53187&password=

http://www.ebi.ac.uk:21390/pride/jsp/pages/jnlp/jnlp.jsp?username=review53187&password=



PRIDE tools and search engine exercise



Workflow MS experiment

mgf

omx

PRIDE XML

PRIDE Converter

Search engine

PRIDE Inspector

PRIDE

Your own workflow:

MS/MSdata processing

peak list generation

omssa_results_2780

PRIDEXML



In this exercise…

• You will use the data generated using the OMSSA search engine (imagine that they are the results of your search)

• You will learn how to use PRIDE Converter (tool for performing submissions to PRIDE)

• You will learn how to use PRIDE Inspector (tool for the visualization and analysis of proteomics data)



1) Converting the .omx OMSSA file to PRIDE XML

We need to do this:

• Perform submission of the data to PRIDE• Use PRIDE Inspector to visualize and analyse it

• We will use PRIDE Converter: we need to provide enough metadata to allow the reuse of the data.



DATA SUBMISSION TO PRIDEUSING PRIDE CONVERTER



Why? Submission made easier: PRIDE Converter




1) Converting the .omx OMSSA file to PRIDE XML

We need to do this:

• Perform submission of the data to PRIDE• Use PRIDE Inspector to visualize and analyse it

• We will use PRIDE Converter: we need to provide enough metadata to allow the reuse of the data.



Time to Work on it…



DATA VISUALIZATION AND ANALYSISUSING PRIDE INSPECTOR



2) Visualizing and analysing the data (PRIDE Inspector)

• We will have a look at the new results that have been generated using OMSSA.

• We will browse the metadata, proteins, peptides and spectra.

• We will have a quick look at the quality charts, generated in order to make an initial assessment of data quality at different levels.



How does PRIDE Inspector look like?

Fast loading of large mzML and PRIDE XML files.



Time to Work on it…



Conclusions

• Using PRIDE Converter you are able to annotate the data and get it ready for submission to PRIDE

• Using PRIDE Inspector, you are able to visualize and perform a first analysis of the results.

• You have learnt some of the variables that can affect the final results of a proteomics experiment (list of proteins)



PRIDE Converter 2 (beta available)

http://code.google.com/p/pride-converter-2



The PRIDE Team

Attila CsordasDavid OvelleiroRichard CôtéRui WangDaniel RíosFlorian Reisinger

Gavin O’KellyMelih BirimJoe FosterJohannes GrissSamuel WeinAntonio Fabregat

Juan Antonio VizcaínoHenning Hermjakob



Questions?

ebi is an outstation of the european molecular biology laboratory. pride associated tools: practical...

Documents

pride ftp slide

pride team

ebi roadshow sofia

pride converter http

pride submission workflow

compprideconverter slide

data submission

pride public db instance