ahupo_vizcaino_remote_presentation_082014

ProteomeXchange: Update for the C-HPP Consortium

Dr. Juan Antonio Vizcaíno PRIDE Group Coordinator

Proteomics Services Team

EMBL-EBI

Hinxton, Cambridge, UK

Juan A. Vizcaíno

[email protected] 10th C-HPP Workshop Bangkok, 9 August 2014

Overview •  The ProteomeXchange (PX) consortium

•  How to submit and access data in PX via PRIDE

•  How to access PX data

•  Miscellaneous

•  Your questions for the discussion

Juan A. Vizcaíno


ProteomeXchange Consortium •  Goal: Development of a framework to allow standard data submission and dissemination pipelines between the main existing proteomics repositories.

•  Includes PeptideAtlas (ISB, Seattle), PRIDE (Cambridge, UK) and (very recently) MassIVE (UCSD, San Diego).

•  EU FP7 CA (01/2011-> 06/2014).

•  Common identifier space (PXD identifiers)

•  Two supported data workflows: MS/MS and SRM.

•  Main objective: Make life easier for researchers

http://www.proteomexchange.org Vizcaíno et al., Nat Biotechnol, 2014

Juan A. Vizcaíno


ProteomeCentral

Metadata / Manuscript

Raw Data*

Results

Journals

UniProt/ neXtProt

Peptide Atlas

Other DBs

Receiving repositories

PASSEL (SRM data)

PRIDE (MS/MS data)

Other DBs

GPMDB

Researcher’s results

Reprocessed results

Raw data*

Metadata

MassIVE (MS/MS data)

Vizcaíno et al., Nat Biotechnol, 2014

ProteomeXchange data workflow

Juan A. Vizcaíno


MassIVE (UCSD)

http://proteomics.ucsd.edu/service/massive/

•  Just joined ProteomeXchange on June 2014 •  Similar role to PRIDE (although not yet formalised).

Juan A. Vizcaíno


ProteomeCentral


Raw Data*

Results

Journals

UniProt/ neXtProt

Peptide Atlas

Other DBs


PASSEL (SRM data)

PRIDE (MS/MS data)

Other DBs

GPMDB


Reprocessed results

Raw data*

Metadata




Juan A. Vizcaíno







Juan A. Vizcaíno


PRIDE (PRoteomics IDEntifications) database

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

• Focused on MS/MS

approaches

Martens et al., Proteomics, 2005 Vizcaíno et al., NAR, 2013

Juan A. Vizcaíno


Manuscript just out detailing the process

Ternent et al., Proteomics, 2014, in press

http://www.proteomexchange.org/submission

Juan A. Vizcaíno


Complete vs Partial submissions

•  The challenge: PRIDE is an archival database, aiming to provide long term access to proteomics data from all workflows

•  Huge variety of proteomics workflows and file formats establishes a data management nightmare

•  Previously, we had to decline submissions since there were in formats we could not handle.

•  Solution: Complete and Partial submissions

•  Metadata, raw data, results are mandatory in both cases, just not parsed for partial submissions

•  Complete submission •  All data in standard formats,

accessible through PRIDE Inspector and web interface (not yet)

•  Results searchable in DB

•  Submission gets DOI

•  Partial submission •  Part of data in non-standard formats

•  Files are made available to download

•  Only metadata searchable

•  No DOI

Juan A. Vizcaíno


PX Data workflow for MS/MS data 1.  Mass spectrometer output files: raw data (binary files) or

peak list spectra in a standardized format (mzML, mzXML).

Raw Files

Juan A. Vizcaíno


1.  Mass spectrometer output files: raw data (binary files) or peak list spectra in a standardized format (mzML, mzXML).

2.  Result files:

a.  Complete submissions: Result files can be converted to PRIDE XML or the mzIdentML data standard.

b.  Partial submissions: For workflows not yet supported by PRIDE, search engine output files will be stored and provided in their original form.

PX Data workflow for MS/MS data

Published

Raw Files

Juan A. Vizcaíno


Complete submissions Search Engine

Results + MS files

Search engines

mzIdentML

-  Mascot -  MSGF+ -  Myrimatch and related tools from D. Tabb’s lab -  OpenMS -  PEAKS -  ProCon (ProteomeDiscoverer, Sequest) -  Scaffold -  TPP via the idConvert tool (ProteoWizard) -  ProteinPilot (planned by the end of 2014) -  Others: library for X!Tandem conversion, lab internal pipelines, …

An increasing number of tools support export to mzIdentML 1.1

-  Referenced spectral files need to be submitted as well

Updated list: http://www.psidev.info/tools-implementing-mzIdentML#.

Juan A. Vizcaíno


Available for complete submissions

Wang et al., Nat. Biotechnology, 2012

PRIDE Inspector 2.0

PRIDE Inspector 2.0 supports: -  PRIDE XML -  mzIdentML + all types of spectra files -  mzML -  mzTab Ident (work in progress)

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

Juan A. Vizcaíno




2.  Result files:



3.  Metadata: Sufficiently detailed description of sample origin, workflow, instrumentation, submitter.

Published

Raw Files

Juan A. Vizcaíno




2.  Result files:



3.  Metadata: Sufficiently detailed description of sample origin, workflow, instrumentation, submitter.

4.  Other files: Optional files: a.  QUANT: Quantification related results e. FASTA b.  PEAK: Peak list files f. SP_LIBRARY c.  GEL: Gel images d.  OTHER: Any other file type

Published

Raw Files

Other files

Juan A. Vizcaíno


•  Capture the mappings between the different types of files.

•  Make the file upload process straightforward to the submitter (It transfers all the files using Aspera or FTP).

PX submission tool

Published

Raw

Other files

http://www.proteomexchange.org/submission

PX submission

tool

•  Command line alternative: some scripting is needed

Juan A. Vizcaíno


Fast file transfer with Aspera

- Aspera is the default file transfer protocol to PRIDE: - PX Submission tool - Command line

- Up to 50X faster than FTP

Part C: Difficulties in Connections: Q1. How to make the connections between local server and central DBs much faster and accessible (e.g. local server and ProteomeXchange)?

File transfer speed should not be a problem!!

Juan A. Vizcaíno


PX submission tool

Juan A. Vizcaíno


PX submission tool: HPP tags

Juan A. Vizcaíno


Complete vs Partial submissions

•  The challenge: PRIDE is an archival database, aiming to provide long term access to proteomics data from all workflows

•  Huge variety of proteomics workflows and file formats establishes a data management nightmare

•  Previously, we had to decline submissions since there were in formats we could not handle.

•  Solution: Complete and Partial submissions

•  Metadata, raw data, results are mandatory in both cases, just not parsed for partial submissions

•  Complete submission •  All data in standard formats,

accessible through PRIDE Inspector and web interface (not yet)

•  Results searchable in DB

•  Submission gets DOI

•  Partial submission •  Part of data in non-standard formats

•  Files are made available to download

•  Only metadata searchable

•  No DOI

Juan A. Vizcaíno


Partial submissions •  Everything can be stored, not only MS/MS data: very flexible

mechanism to be able to capture all types of datasets

•  Top down proteomics datasets

•  Mass Spectrometry Imaging datasets

•  Data independent acquisition techniques: e.g. SWATH-MS datasets, among other DIA approaches

Juan A. Vizcaíno


Origin: 235 USA 142 Germany 97 United Kingdom 67 Switzerland 64 Netherlands 62 China 60 France 48 Canada 43 Spain 36 Belgium 32 Sweden 29 Australia 26 Denmark 23 Japan 18 Taiwan 17 India 16 Ireland 14 Norway 14 Italy 12 Finland 11 Republic of Korea 10 Brazil 8 Austria 7 Israel 7 Singapore …

ProteomeXchange: 1,148 datasets up until August 2014

Type: 386 PRIDE complete 687 PRIDE partial 51 PeptideAtlas/PASSEL complete 1 MassIVE 23 reprocessed

Publicly Accessible: 544 datasets, 50% of all 90% PRIDE 10% PASSEL

Data volume: Total: ~51 TB Number of all files: ~130,000 PXD000320-324: ~ 5 TB PXD000065: ~ 1.4TB

Top Species studied by at least 10 datasets: 510 Homo sapiens 142 Mus musculus 46 Saccharomyces cerevisiae 45 Arabidopsis thaliana 23 Rattus norvegicus 16 Escherichia coli 15 Bos taurus 15 Mycobacterium tuberculosis 13 Oryza sativa 12 Drosophila melanogaster 12 Glycine max ~ 265 species in total

Datasets/year: 2012: 102 2013: 527 2014: 519

Juan A. Vizcaíno







Juan A. Vizcaíno


ProteomeCentral


Raw Data*

Results

Journals

UniProt/ neXtProt

Peptide Atlas

Other DBs


PASSEL (SRM data)

PRIDE (MS/MS data)

Other DBs

GPMDB


Reprocessed results

Raw data*

Metadata




Juan A. Vizcaíno


ProteomeCentral: Portal for all PX datasets

http://proteomecentral.proteomexchange.org/cgi/GetDataset

Juan A. Vizcaíno


Get notified about new PX datasets

- Subscribe to the RSS Feed to receive information about the new datasets:

http://groups.google.com/group/proteomexchange/feed/rss_v2_0_msgs.xml

Proteome Central Researchers

Juan A. Vizcaíno


Reuse of datasets in PeptideAtlas can be tracked

Juan A. Vizcaíno







Juan A. Vizcaíno


HPP datasets are now tagged The Projects are now tagged and can be browsed as a group of data sets.""

Tags for: HPP, C-HPP and B/D-HPP

Juan A. Vizcaíno


HPP PX datasets

Juan A. Vizcaíno


HPP PX datasets: some numbers Since January 2014, we started capturing the PI information -  25 HPP datasets: 22 C-HPP and 3 B/D-HPP

-  Countries represented in C-HPP: -  5 Spain -  4 South Korea -  3 Brazil, China Only a small proportion of the datasets have been made publicly available, at least through ProteomeXchange

Juan A. Vizcaíno


For the near future in PRIDE…

•  Complete data workflow for data visualization in PRIDE Archive web

•  Improvement of existing PRIDE REST API

•  Incorporation of reprocessed data in PRIDE (in collaboration with Prof. L. Martens (VIB/Ghent) and Dr. A. Jones (U. Liverpool)

•  Integration of the data in the EBI Molecular Atlas

Juan A. Vizcaíno


Conclusions •  ProteomeXchange is widely used. It has now a new

consortium member: MassIVE (UCSD).

•  PRIDE is getting a lot of data via ProteomeXchange. Pipeline in production since summer 2012. More than 1,100 datasets have been already submitted.

•  Half of them already public.

•  Different open source tools available to facilitate the process: •  File transfer speed should not be a problem (Aspera support)

Juan A. Vizcaíno


Acknowledgements PRIDE Team Attila Csordas Rui Wang Florian Reisinger Jose A. Dianes Tobias Ternent Yasset Perez-Riverol Noemi del Toro Henning Hermjakob

EU FP7 grant number 260558

PeptideAtlas Team (ISB, Seattle) Eric Deutsch Terry Farrah Zhi Sun Andrew R. Jones Lennart Martens Juan Pablo Albar Martin Eisenacher Gil Omenn And many other PX partners and stakeholders

Juan A. Vizcaíno


Questions?

Juan A. Vizcaíno







Juan A. Vizcaíno


Questions for discussion Part A: Proteomic Dataset with PXD:

Q1. How to make deposited through ProteomeXchange or published data available for the consortium members as well as public DB managers (GPMDB, neXtProt, PeptideAtlas and ProteinAtlas)?

•  There is plenty of documentation available:

•  http://www.proteomexchange.com/submission

•  PRIDE documentation

•  Original paper (PMID: 24727771) and submission tutorial paper (PMID: 25047258).

•  Resources need to be devoted to this…

Juan A. Vizcaíno



Q2. What can we do for such inaccessible datasets in the public DB?

•  Contact the author directly and convince him/her to make a

submission to ProteomeXchange.

Juan A. Vizcaíno



Q3. Do we need to ask people to place a link with PXD identifier on the Wiki in order to see which chromosome team placed which datasets online (for sharing)?

•  NO, in the PX submission tool it is possible to specify the tags for

HPP and/or C-HPP or B/D-HPP.

•  Visit ‘ProteomeCentral’ and look for them.

•  Visit PRIDE and look for them there (specific tags)

Juan A. Vizcaíno


HPP datasets are now tagged The Projects are now tagged and can be browsed as a group of data sets.""

Tags for: HPP, C-HPP and B/D-HPP

Juan A. Vizcaíno


Questions for discussion Part B: Proteogenomic Dataset:

Q1. How to make easy access to or deposit proteogenomic dataset including RNAseq and other types of genetic data?

•  Not easy to do at present. •  NCBI and EBI have created “BioSamples databases” to be able to

link different studies performed using the same sample.

•  Proteomics data could be submitted to PRIDE/ProteomeXchange and RNAseq data to e.g. ArrayExpress (EBI), linked by the same sample number.

•  Sample IDs coming from the BioSamples DB to be integrated in the PX submission tool and in PRIDE (expected before the end of the year).

Juan A. Vizcaíno


Biosamples DB

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

Juan A. Vizcaíno


Fast file transfer with Aspera

- Aspera is the default file transfer protocol to PRIDE: - PX Submission tool - Command line

- Up to 50X faster than FTP

Part C: Difficulties in Connections: Q1. How to make the connections between local server and central DBs much faster and accessible (e.g. local server and ProteomeXchange)?

File transfer speed should not be a problem!!

ahupo_vizcaino_remote_presentation_082014

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