Download as PDF, PPTX
![General workflow
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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]
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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!](https://image.slidesharecdn.com/pxmsimaging-141009034715-conversion-gate02/85/MS-Imaging-data-in-ProteomeXchange-HUPO-2014-4-320.jpg)
![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](https://image.slidesharecdn.com/pxmsimaging-141009034715-conversion-gate02/85/MS-Imaging-data-in-ProteomeXchange-HUPO-2014-18-320.jpg)
Uploaded byJuan Antonio Vizcaino
MS Imaging data in ProteomeXchange (HUPO 2014)
The document discusses representing imaging mass spectrometry (MS) data. It describes imzML, a common data standard for MS imaging data. It also outlines how MS imaging data can be submitted to the ProteomeXchange repository via the PRIDE database. MS imaging generates data from tissue sections, and imzML encodes both the raw data files and metadata about the images. Submitting to ProteomeXchange involves uploading raw data files, result files, and metadata descriptions to allow sharing and reuse of MS imaging experiments.
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MS Imaging data in ProteomeXchange (HUPO 2014)
- 1. Representing Imaging MSData 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 MALDImass 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 at10 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 – commondata 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 filesin 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 Partialsubmissions: 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 Partialsubmissions: 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 workflowfor 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 worksfor 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 transferwith 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 Fromoriginal 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 forall 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 aboutnew 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 • Formalmechanism 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?