Data Submission Guidelines for the ProteomeXchange Consortium
MS Imaging data in ProteomeXchange (HUPO 2014)
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Transcript of MS Imaging data in ProteomeXchange (HUPO 2014)
Representing Imaging MS Data
Dr. Juan Antonio Vizcaíno PRIDE Group Coordinator
Proteomics Services Team
EMBL-EBI
Hinxton, Cambridge, UK
Juan A. Vizcaíno
[email protected] 13th HUPO World Congress Madrid, 7 October 2014
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
Andreas Roempp Andrea Urbani Bernard Splengler Juan Pablo Albar
Juan A. Vizcaíno
[email protected] 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
Juan A. Vizcaíno
[email protected] 13th HUPO World Congress Madrid, 7 October 2014
General workflow
4
Sample Processing
Sectioning
S454 CV64 76x53 150um E70 OF #1-1960 RT: 0.01-50.08 AV: 1960 NL: 6.14E4T: FTMS + p NSI sid=30.00 Full ms [400.00-1500.00]
400 600 800 1000 1200 1400m/z
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Rel
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e A
bund
ance
443.2324
585.0632
721.0795
545.0709 857.0959
607.0452761.0722 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!
Juan A. Vizcaíno
[email protected] 13th HUPO World Congress Madrid, 7 October 2014
10 µm tissue section (coated with matrix)
Mass spectrum
m/z („mass“)
Inte
nsity
Laser
Mass spectrometer
What is MALDI mass spectrometry imaging ?
Juan A. Vizcaíno
[email protected] 13th HUPO World Congress Madrid, 7 October 2014
Urothel
Myofibroblasts
Blood vessel
Umbrella cells
Adventitial layer
Lamina propria
Basal layer
Detrusor muscle
Histological micrograph (toluidine) MS images
m/z = 741
m/z = 743 m/z = 798
Muscle
Ephithelium Conective tissue
200 µm
Römpp, Guenther, Schober Schulz, Takats, Kummer, Spengler (2010) Angew. Chem. Int. Ed., 9(22): 3834-3838
Raw data! - No interpolation - No normalization
MS Imaging at 10 µm step size:Mouse urinary bladder
Juan A. Vizcaíno
[email protected] 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
Juan A. Vizcaíno
[email protected] 13th HUPO World Congress Madrid, 7 October 2014
D2 Anwendung imzML – common data format for MS imaging
Mirion (JLU) SpectViewer (CEA) DataCube (FOM) BioMap (Novartis)
5000 µm
SIMS
100 µm
MALDI
1000 µm 1000 µm
C)
2000 µm
imzML (imaging mzML)
Juan A. Vizcaíno
[email protected] 13th HUPO World Congress Madrid, 7 October 2014 9
www.imzml.org
Schramm, Hester, Klinkert, Both, Heeren, Brunelle, Laprévote, Desbenoit, Robbe, Stoeckli, Spengler, Römpp (2012). Journal of Proteomics 75: 5106-5110.
Two different files in fact: -* idb: RAW -* imzml: image related metadata
Juan A. Vizcaíno
[email protected] 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
Juan A. Vizcaíno
[email protected] 13th HUPO World Congress Madrid, 7 October 2014
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
[email protected] 13th HUPO World Congress Madrid, 7 October 2014
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
[email protected] 13th HUPO World Congress Madrid, 7 October 2014
Complete
Partial
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
[email protected] 13th HUPO World Congress Madrid, 7 October 2014
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).
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
Published
Raw Files
Other files
Juan A. Vizcaíno
[email protected] 13th HUPO World Congress Madrid, 7 October 2014 15
Schramm, Hester, Klinkert, Both, Heeren, Brunelle, Laprévote, Desbenoit, Robbe, Stoeckli, Spengler, Römpp (2012). Journal of Proteomics 75: 5106-5110.
Two different files in fact: -* idb: RAW -* imzml: MS_IMAGE_DATA
How it works for imzML files
Juan A. Vizcaíno
[email protected] 13th HUPO World Congress Madrid, 7 October 2014
• 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
[email protected] 13th HUPO World Congress Madrid, 7 October 2014
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
not be a problem!!
Juan A. Vizcaíno
[email protected] 13th HUPO World Congress Madrid, 7 October 2014
C
D
From original publication [13] Reconstructed ProteomeXchange data
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
- 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
PRIDE database European
Bioinformatics Institute,
Cambridge, UK
3. Upload
4. Download
Juan A. Vizcaíno
[email protected] 13th HUPO World Congress Madrid, 7 October 2014
ProteomeCentral: Portal for all PX datasets
http://proteomecentral.proteomexchange.org/cgi/GetDataset
Juan A. Vizcaíno
[email protected] 13th HUPO World Congress Madrid, 7 October 2014
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
[email protected] 13th HUPO World Congress Madrid, 7 October 2014
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!