ms imaging data in proteomexchange (hupo 2014)
DESCRIPTION
Short presentation in HUPO 2014 about the support for MS imaging data in ProteomeXchange via PRIDETRANSCRIPT
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Representing Imaging MS Data
Dr. Juan Antonio Vizcaíno PRIDE Group Coordinator
Proteomics Services Team
EMBL-EBI
Hinxton, Cambridge, UK
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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
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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
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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
0
10
20
30
40
50
60
70
80
90
100
Rel
ativ
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!
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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 ?
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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
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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
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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)
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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
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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
![Page 11: MS Imaging data in ProteomeXchange (HUPO 2014)](https://reader033.vdocument.in/reader033/viewer/2022052900/55617205d8b42aac268b474c/html5/thumbnails/11.jpg)
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
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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
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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.
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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
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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
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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
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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!!
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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
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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
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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
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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!