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


Overview •  MS Imaging Data

•  imzML: Data standard for MS Imaging data

•  Way to submit MS Imaging data to ProteomeXchange via PRIDE

Juan A. Vizcaíno


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!

Juan A. Vizcaíno


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


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





Juan A. Vizcaíno


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





Juan A. Vizcaíno


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


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


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


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


•  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


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


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


ProteomeCentral: Portal for all PX datasets

http://proteomecentral.proteomexchange.org/cgi/GetDataset

Juan A. Vizcaíno


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


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


Questions?

MS Imaging data in ProteomeXchange (HUPO 2014)

Science

ms imaging data way

overview ms imaging

mraw data

imaging ms datadr

mzidentml data standard

px data workflow

imzml common data format

result files