Short presentation in HUPO 2014 about the support for MS imaging data in ProteomeXchange via PRIDE

1. Representing Imaging MS Data
Dr. Juan Antonio Vizcaíno
PRIDE Group Coordinator
Proteomics Services Team
EMBL-EBI
Hinxton, Cambridge, UK

2. Acknowledgements
PRIDE Team
Attila Csordas
Rui Wang
Florian Reisinger
Jose A. Dianes
Tobias Ternent
Yasset Perez-Riverol
Noemi del Toro
Henning Hermjakob
Juan A. Vizcaíno
juan@ebi.ac.uk
Andreas Roempp
Andrea Urbani
Bernard Splengler
Juan Pablo Albar
EU FP7 grant number 260558
13th HUPO World Congress
Madrid, 7 October 2014

3. Juan A. Vizcaíno
juan@ebi.ac.uk
13th HUPO World Congress
Madrid, 7 October 2014
Overview
• MS Imaging Data
• imzML: Data standard for MS Imaging data
• Way to submit MS Imaging data to ProteomeXchange via
PRIDE

4. General workflow
100
90
80
70
60
50
40
30
20
10
Juan A. Vizcaíno
juan@ebi.ac.uk
13th HUPO World Congress
Madrid, 7 October 2014
4
Sample
Processing
Sectioning
S454 CV64 76x53 150um E70 OF #1-1960 RT: 0.01-50.08 AV: 1960 NL: 6.14E4
T: FTMS + p NSI sid=30.00 Full ms [400.00-1500.00]
400 600 800 1000 1200 1400
m/z
0
Relative Abundance
443.2324
585.0632
721.0795
545.0709 857.0959
607.0452
761.0722 897.0885 988.1571 1124.1739 1265.1445 1401.1600
MS Imaging
(Data acquisition)
Data analysis
and identification
Matrix
application
Sample
(selection)
Storage Storage
(Biological) interpretation!

5. What is MALDI mass spectrometry imaging ?
Juan A. Vizcaíno
juan@ebi.ac.uk
13th HUPO World Congress
Madrid, 7 October 2014
10 μm tissue section
(coated with matrix)
Mass spectrum
m/z
(„mass“)
Intensity
Laser
Mass spectrometer

6. MS Imaging at 10 μm step size:Mouse urinary bladder
Histological MS images micrograph (toluidine)
m/z = 741
Conective
tissue
Juan A. Vizcaíno
juan@ebi.ac.uk
Ephithelium
200 μm
Raw data!
- No interpolation
- No normalization
13th HUPO World Congress
Madrid, 7 October 2014
Myofibroblasts
Blood vessel
Urothel
Umbrella cells
Adventitial layer
Lamina propria
Basal layer
Detrusor muscle
Muscle
m/z = 798 m/z = 743
Römpp, Guenther, Schober Schulz, Takats, Kummer, Spengler (2010) Angew. Chem. Int. Ed., 9(22): 3834-3838

7. Juan A. Vizcaíno
juan@ebi.ac.uk
13th HUPO World Congress
Madrid, 7 October 2014
Overview
• MS Imaging Data
• imzML: Data standard for MS Imaging data
• Way to submit MS Imaging data to ProteomeXchange via
PRIDE

8. imzML – common data format for MS imaging D2 Anwendung
Mirion (JLU) DataCube (FOM) BioMap (Novartis) SpectViewer (CEA)
Juan A. Vizcaíno
juan@ebi.ac.uk
13th HUPO World Congress
Madrid, 7 October 2014
5000 μm
SIMS
100 μm
MALDI
1000 μm 1000 μm
C)
2000 μm
imzML (imaging mzML)

9. Two different files in fact:
-* idb: RAW
-* imzml: image related
metadata
Schramm, Hester, Klinkert, Both, Heeren, Brunelle, Laprévote, Desbenoit, Robbe, Stoeckli, Spengler, Römpp
(2012). Journal of Proteomics 75: 5106-5110.
Juan A. Vizcaíno
juan@ebi.ac.uk
www.imzml.org
13th HUPO World Congress
Madrid, 7 October 2014 9

10. Juan A. Vizcaíno
juan@ebi.ac.uk
13th HUPO World Congress
Madrid, 7 October 2014
Overview
• MS Imaging Data
• imzML: Data standard for MS Imaging data
• Way to submit MS Imaging data to ProteomeXchange
via PRIDE

11. 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 r e positories
PASSEL
(SRM data)
Other DBs
GPMDB
Researcher’s results
Reprocessed results
Raw data*
Metadata
MassIVE
(MS/MS data)
Vizcaíno et al., Nat Biotechnol, 2014

12. 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

13. 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

14. 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. MS_IMAGE_DATA: Metadata information about images
b. OPTICAL: Optical image
13th HUPO World Congress
Madrid, 7 October 2014
Published
Raw
Files
Other
files

15. How it works for imzML files
Two different files in fact:
-* idb: RAW
-* imzml: MS_IMAGE_DATA
Schramm, Hester, Klinkert, Both, Heeren, Brunelle, Laprévote, Desbenoit, Robbe, Stoeckli, Spengler, Römpp
(2012). Journal of Proteomics 75: 5106-5110.
Juan A. Vizcaíno
juan@ebi.ac.uk
13th HUPO World Congress
Madrid, 7 October 2014 15

16. 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

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

18. 4. Download
From original publication [13] Reconstructed ProteomeXchange data
Juan A. Vizcaíno
juan@ebi.ac.uk
C
D
13th HUPO World Congress
Madrid, 7 October 2014
1. Thermo RAW data / UDP
2. Mirion Software (JLU)
1. Thermo RAW data / UDP
2. Convert to imzML
3. Upload to PRIDE
(EBI, Cambridge, UK)
4. Download from PRIDE
5. Display in MSiReader
3. Upload
PRIDE
database
European
Bioinformatics
Institute,
Cambridge, UK
- Vendor-independent data format
- Freely available software (open source)
- ‘open data‘ – free to reuse
- Anybody can do this!
è A public repository for mass spectrometry imaging data
Römpp, Wang, Albar, Urbani, Hermjakob, Spengler, Vizcaino, submitted

19. 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

20. 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
Juan A. Vizcaíno
juan@ebi.ac.uk
Proteome Central Researchers
13th HUPO World Congress
Madrid, 7 October 2014

21. Conclusions
• Formal mechanism to submit MS Imaging data to
ProteomeXchange via PRIDE
• Partial PX submission mechanism.
• Proof of concept data submission done (PXD001283, still
private).
• MS Imaging data is welcome in PRIDE/PX!
Juan A. Vizcaíno
juan@ebi.ac.uk
13th HUPO World Congress
Madrid, 7 October 2014

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