Talk during the PSI/ProteomeXchange workshop in HUPO 2014. It summarizes how to submit data to ProteomeXchange via PRIDE.

1. Submitting your data to
ProteomeXchange – A Mini-Tutorial
Dr. Juan Antonio Vizcaíno
PRIDE Group Coordinator
Proteomics Services Team
EMBL-EBI
Hinxton, Cambridge, UK

2. Juan A. Vizcaíno
juan@ebi.ac.uk
13th HUPO World Congress
Madrid, 7 October 2014
Overview
• The ProteomeXchange (PX) consortium
• How to submit and access data in PX via PRIDE
• How to access PX data
• Submitting data triggers data reuse

3. 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).
• Common identifier space (PXD identifiers)
• Two supported data workflows: MS/MS and SRM.
• Main objective: Make life easier for researchers
http://www.proteomexchange.org
Juan A. Vizcaíno
juan@ebi.ac.uk
13th HUPO World Congress
Madrid, 7 October 2014

4. ProteomeXchange data workflow
Results
Raw Data*
Juan A. Vizcaíno
juan@ebi.ac.uk
ProteomeCentral
PRIDE
(MS/MS data)
13th HUPO World Congress
Madrid, 7 October 2014
Metadata /
Manuscript
Journals
UniProt/
neXtProt
Peptide Atlas
Other DBs
Receiving repositories
PASSEL
(SRM data)
Other DBs
GPMDB
Researcher’s results
Reprocessed results
Raw data*
Metadata
MassIVE
(MS/MS data)
Vizcaíno et al., Nat Biotechnol, 2014

5. ProteomeXchange data workflow
Results
Raw Data*
Juan A. Vizcaíno
juan@ebi.ac.uk
ProteomeCentral
PRIDE
(MS/MS data)
13th HUPO World Congress
Madrid, 7 October 2014
Metadata /
Manuscript
Journals
UniProt/
neXtProt
Peptide Atlas
Other DBs
Receiving repositories
PASSEL
(SRM data)
Other DBs
GPMDB
Researcher’s results
Reprocessed results
Raw data*
Metadata
MassIVE
(MS/MS data)
Vizcaíno et al., Nat Biotechnol, 2014

6. Juan A. Vizcaíno
juan@ebi.ac.uk
13th HUPO World Congress
Madrid, 7 October 2014
Overview
• The ProteomeXchange (PX) consortium
• How to submit and access data in PX via PRIDE
• How to access PX data
• Submitting data triggers data reuse

7. PRIDE (PRoteomics IDEntifications) database
http://www.ebi.ac.uk/pride
Juan A. Vizcaíno
juan@ebi.ac.uk
13th HUPO World Congress
Madrid, 7 October 2014
• Focused on MS/MS
approaches
• Other data types can
also be stored as
“Partial submissions”.
Martens et al., Proteomics, 2005
Vizcaíno et al., NAR, 2013

8. Manuscript just out detailing the process
http://www.proteomexchange.org/submission Ternent et al., Proteomics, 2014
Juan A. Vizcaíno
juan@ebi.ac.uk
13th HUPO World Congress
Madrid, 7 October 2014
Example dataset:
PXD000764
- Title: “Discovery of new CSF biomarkers for meningitis in children”
- 12 runs: 4 controls and 8 infected samples
- Identification and quantification data

9. PX Data workflow for MS/MS data
Juan A. Vizcaíno
juan@ebi.ac.uk
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.
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
13th HUPO World Congress
Madrid, 7 October 2014
Published
Raw
Files
Other
files

10. Complete vs Partial submissions: experimental metadata
Complete Partial
General experimental metadata about the projects is similar.
However, at the assay level information in partial submissions is not so detailed
Juan A. Vizcaíno
juan@ebi.ac.uk
13th HUPO World Congress
Madrid, 7 October 2014

11. Complete vs Partial submissions: processed results
For complete submissions, it is possible to connect the spectra with the identification
processed results and they can be visualized.
Juan A. Vizcaíno
juan@ebi.ac.uk
13th HUPO World Congress
Madrid, 7 October 2014
Complete
Partial

12. How to perform a complete PX submission to PRIDE
• Decide between a complete/partial submission.
• File conversion/export to PRIDE XML or mzIdentML
• File check before submission (PRIDE Inspector)
• Experimental annotation and actual file submission (PX
Juan A. Vizcaíno
juan@ebi.ac.uk
13th HUPO World Congress
Madrid, 7 October 2014
submission tool)
• Post-submission steps

13. How to perform a complete PX submission to PRIDE
• Decide between a complete/partial submission.
• File conversion/export to PRIDE XML or mzIdentML
• File check before submission (PRIDE Inspector)
• Experimental annotation and actual file submission (PX
Juan A. Vizcaíno
juan@ebi.ac.uk
13th HUPO World Congress
Madrid, 7 October 2014
submission tool)
• Post-submission steps

14. How to perform a complete PX submission to PRIDE
• Complete submission:
• MS/MS data.
• Processed results can be converted to the PSI standard
mzIdentML or PRIDE XML.
Juan A. Vizcaíno
juan@ebi.ac.uk
13th HUPO World Congress
Madrid, 7 October 2014
• Partial submission:
• Any type of data (not SRM, which goes to PASSEL)
• E.g. top down, data independent acquisition, MS Imaging (to
come), etc.
• Processed results cannot be converted to a data standard.

15. How to perform a complete PX submission to PRIDE
• Decide between a complete/partial submission.
• File conversion/export to mzIdentML or PRIDE XML
• File check before submission (PRIDE Inspector)
• Experimental annotation and actual file submission (PX
Juan A. Vizcaíno
juan@ebi.ac.uk
13th HUPO World Congress
Madrid, 7 October 2014
submission tool)
• Post-submission steps

16. Juan A. Vizcaíno
juan@ebi.ac.uk
Complete submissions
An increasing number of tools support export to mzIdentML
1.1
13th HUPO World Congress
Madrid, 7 October 2014
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, …
- Referenced spectral files need to be submitted as well
(all open formats are supported).
Updated list: http://www.psidev.info/tools-implementing-mzIdentML#.

17. Original data files ‘RESULT’ file generation Final ‘RESULT’ file
Juan A. Vizcaíno
juan@ebi.ac.uk
13th HUPO World Congress
Madrid, 7 October 2014
Search
output
files
Spectra
files
PRIDE
XML
‘RESULT’
Before: file conversion
File conversion
PRIDE
Converter

18. Tools ‘RESULT’ file generation Final ‘RESULT’ file
Juan A. Vizcaíno
juan@ebi.ac.uk
13th HUPO World Congress
Madrid, 7 October 2014
mzIdentML
‘RESULT’
Now: native file export
Spectra
files
Mascot
ProteinPilo
t
Scaffold
PEAKS
MSGF+
Others
Native File export

19. How to perform a complete PX submission to PRIDE
• Decide between a complete/partial submission.
• File conversion/export to PRIDE XML or mzIdentML
• File check before submission (PRIDE Inspector)
• Experimental annotation and actual file submission (PX
Juan A. Vizcaíno
juan@ebi.ac.uk
13th HUPO World Congress
Madrid, 7 October 2014
submission tool)
• Post-submission steps

20. Available for complete submissions
Juan A. Vizcaíno
juan@ebi.ac.uk
13th HUPO World Congress
Madrid, 7 October 2014
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

21. How to perform a complete PX submission to PRIDE
• Decide between a complete/partial submission.
• File conversion/export to PRIDE XML or mzIdentML
• File check before submission (PRIDE Inspector)
• Experimental annotation and actual file submission (PX
Juan A. Vizcaíno
juan@ebi.ac.uk
13th HUPO World Congress
Madrid, 7 October 2014
submission tool)
• Post-submission steps

22. PX submission tool
• 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).
Juan A. Vizcaíno
juan@ebi.ac.uk
13th HUPO World Congress
Madrid, 7 October 2014
Published
Raw
Other
files
http://www.proteomexchange.org/submission
PX
submission
tool
• Command line alternative: some scripting is needed

23. PX submission tool: step by step
Juan A. Vizcaíno
juan@ebi.ac.uk
13th HUPO World Congress
Madrid, 7 October 2014
Step 1
Step 2

24. PX submission tool: step by step
Juan A. Vizcaíno
juan@ebi.ac.uk
13th HUPO World Congress
Madrid, 7 October 2014
Step 3
Step 4

25. PX submission tool: step by step
Juan A. Vizcaíno
juan@ebi.ac.uk
Step 5 Step 6
13th HUPO World Congress
Madrid, 7 October 2014

26. PX submission tool: step by step
Juan A. Vizcaíno
juan@ebi.ac.uk
13th HUPO World Congress
Madrid, 7 October 2014
Step 7
Step 8

27. PX submission tool: step by step
Juan A. Vizcaíno
juan@ebi.ac.uk
Step 9
13th HUPO World Congress
Madrid, 7 October 2014

28. Fast file transfer with Aspera
- Aspera is the default file transfer protocol to PRIDE:
- Up to 50X faster than FTP
Juan A. Vizcaíno
juan@ebi.ac.uk
- PX Submission tool
- Command line
File transfer speed should
not be a problem!!
13th HUPO World Congress
Madrid, 7 October 2014

29. PX submission tool: HPP tags
Juan A. Vizcaíno
juan@ebi.ac.uk
13th HUPO World Congress
Madrid, 7 October 2014

30. Batch submissions on the command line
• Generate on your own the PX summary file (generated
by default by the PX submission tool).
MTD first_name John Arthur
MTD last_name Smith
MTD email john.smith@cam.edu
MTD affiliation University of Cambridge
MTD title Human proteome
MTD description An experiment about human proteome
MTD keyword human, proteome
MTD pubmed 12345
MTD px 10.1000/182
MTD pride_login pride-user
FMH file_id file_type file_path file_mapping
FME 1 result /path/to/pride/xml/files/pride-1.xml7,8,9
FME 2 result /path/to/pride/xml/files/pride-2.xml4
FME 3 result /path/to/mzidentml/files/mzidentml-1.xml 5,10
FME 4 raw /path/to/raw/files/raw-1.bin
FME 5 raw /path/to/raw/files/raw-2.bin
FME 6 raw /path/to/raw/files/raw-3.bin
FME 7 raw ftp://some.url/at/some/place/raw-4.bin
FME 8 search/path/to/search/engine/output/search-1.out
FME 9 other /path/to/other/file/other-1.e
FME 10 peak /path/to/peak/list/mzml-1.xml
Juan A. Vizcaíno
juan@ebi.ac.uk
13th HUPO World Congress
Madrid, 7 October 2014

31. Batch submissions on the command line
• Generate on your own the PX summary file (generated
by default by the PX submission tool).
Juan A. Vizcaíno
juan@ebi.ac.uk
13th HUPO World Congress
Madrid, 7 October 2014

32. Batch submissions on the command line (2)
• Generate on your own the PX summary file (generated
by default by the PX submission tool).
• Put together all the files plus the PX summary file.
• Ask PRIDE team for a specific upload directory (pride-support@
Juan A. Vizcaíno
juan@ebi.ac.uk
ebi.ac.uk)
13th HUPO World Congress
Madrid, 7 October 2014

33. How to perform a complete PX submission to PRIDE
• Decide between a complete/partial submission.
• File conversion/export to PRIDE XML or mzIdentML
• File check before submission (PRIDE Inspector)
• Experimental annotation and actual file submission (PX
Juan A. Vizcaíno
juan@ebi.ac.uk
13th HUPO World Congress
Madrid, 7 October 2014
submission tool)
• Post-submission steps

34. Post-processing steps
• PRIDE curators will check the files
• Files must be valid to the schema
• All the required annotations must be there
• Basic QC check (e.g. detect errors in PTM annotation)
• If everything is correct, submission to PRIDE is done
• The author receives a PXD identifier, a reviewer username
and a password, and a DOI (for complete submissions).
Juan A. Vizcaíno
juan@ebi.ac.uk
13th HUPO World Congress
Madrid, 7 October 2014

35. Juan A. Vizcaíno
juan@ebi.ac.uk
13th HUPO World Congress
Madrid, 7 October 2014
Overview
• The ProteomeXchange (PX) consortium
• How to submit and access data in PX via PRIDE
• How to access PX data
• Submitting data triggers data reuse

36. ProteomeXchange data workflow
Results
Raw Data*
Juan A. Vizcaíno
juan@ebi.ac.uk
ProteomeCentral
PRIDE
(MS/MS data)
13th HUPO World Congress
Madrid, 7 October 2014
Metadata /
Manuscript
Journals
UniProt/
neXtProt
Peptide Atlas
Other DBs
Receiving repositories
PASSEL
(SRM data)
Other DBs
GPMDB
Researcher’s results
Reprocessed results
Raw data*
Metadata
MassIVE
(MS/MS data)
Vizcaíno et al., Nat Biotechnol, 2014

37. ProteomeCentral: Portal for all PX datasets
http://proteomecentral.proteomexchange.org/cgi/GetDataset
Juan A. Vizcaíno
juan@ebi.ac.uk
13th HUPO World Congress
Madrid, 7 October 2014

38. ProteomeXchange: 1,148 datasets up until August 2014
Juan A. Vizcaíno
juan@ebi.ac.uk
13th HUPO World Congress
Madrid, 7 October 2014
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 …
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
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
Data volume:
Total: ~51 TB
Number of all files: ~130,000
PXD000320-324: ~ 5 TB
PXD000065: ~ 1.4TB
Datasets/year:
2012: 102
2013: 527
2014: 519

39. Juan A. Vizcaíno
juan@ebi.ac.uk
13th HUPO World Congress
Madrid, 7 October 2014
Overview
• The ProteomeXchange (PX) consortium
• How to submit and access data in PX via PRIDE
• How to access PX data
• Submitting data triggers data reuse

40. Which are the most accessed datasets?
PXD Identifier Hits Dataset title Publication
PXD000561 153512 A draft map of the human proteome
Juan A. Vizcaíno
juan@ebi.ac.uk
13th HUPO World Congress
Madrid, 7 October 2014
Kim et al.,
Nature,2014.
PMID: 24870542
PXD000851 111587
Membrane proteomic analysis of
colorectal cancer tissue
Kume et al., MCP,
2014.
PMID:24687888
PXD000865 51639
Mass spectrometry based draft of
the human proteome
Wilhelm et al., 2014,
Nature,
PMID:24870543

41. Which are the most accessed datasets?
Juan A. Vizcaíno
juan@ebi.ac.uk
13th HUPO World Congress
Madrid, 7 October 2014
Total Numbers

42. CompOmics Open Source Analysis Pipeline
Juan A. Vizcaíno
juan@ebi.ac.uk
Vaudel M, Burkhart J, Zahedi RP, Berven FS, Sickmann A, Martens L,
Barsnes H:
Nature Biotechnology (in press)
13th HUPO World Congress
Madrid, 7 October 2014
Vaudel M, Barsnes H, Berven FS, Sickmann A,
Martens L:
Proteomics 2011;11(5):996-9.
http://searchgui.googlecode.com http://peptide-shaker.googlecode.com

43. Juan A. Vizcaíno
juan@ebi.ac.uk
13th HUPO World Congress
Madrid, 7 October 2014
Find the desired PRIDE project …
… inspect the project details ….
… and start re-analyzing the data!
Reshake PRIDE data!

44. Juan A. Vizcaíno
juan@ebi.ac.uk
13th HUPO World Congress
Madrid, 7 October 2014
Conclusions
• Submission to ProteomeXchange via PRIDE is easy.
• Decide between complete and partial submissions.
• Different open source tools available to facilitate the process.
• File transfer speed should not be a problem (Aspera support)

45. Acknowledgements
Juan A. Vizcaíno
juan@ebi.ac.uk
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
13th HUPO World Congress
Madrid, 7 October 2014
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

46. Juan A. Vizcaíno
juan@ebi.ac.uk
13th HUPO World Congress
Madrid, 7 October 2014
Questions?