miape extractor tutorial

MIAPE Extractor Tutorial

SHPP meeting, 28 Aug 2012La Cristalera, Miraflores de la Sierra, Madrid

Salvador Martínez de Bartolomé IzquierdoCNB-CSIC / ProteoRed

smartinez@proteored.org

SHPP - Data deposition workflow

1. Convert raw files to mzML or mgf2. Get search engine results in mzIdentML format3. Use MIAPE Extractor to generate MIAPE MS and

MIAPE MSI (at the same time!!)4. Inspect your data using the MIAPE Extractor Charts5. Use MIAPE Extractor to export PRIDE XML file from

several MIAPE MS and MSI6. Upload PRIDE XML file to (PRIDE database /

ProteomeXchange consortium)

SHPP - Data deposition workflow

1. Convert raw files to mzML or mgf2. Get search engine results in mzIdentML format3. Use MIAPE Extractor to generate MIAPE MS and

MIAPE MSI (at the same time!!)4. Inspect your data using the MIAPE Extractor Charts5. Use MIAPE Extractor to export PRIDE XML file from

several MIAPE MS and MSI6. Upload PRIDE XML file to (PRIDE database /

ProteomeXchange consortium)

Convert raw files to mzML or mgf• Use of available converters but...maybe its not

neccessary to create a mzML

• See afterwards...

SHPP - Data deposition workflow

1. Convert raw files to mzML or mgf2. Get search engine results in mzIdentML format3. Use MIAPE Extractor to generate MIAPE MS and

MIAPE MSI (at the same time!!)4. Inspect your data using the MIAPE Extractor Charts5. Use MIAPE Extractor to export PRIDE XML file from

several MIAPE MS and MSI6. Upload PRIDE XML file to (PRIDE database /

ProteomeXchange consortium)

Get search engine results in mzIdentML format

• MIAPE Extractor works with mzIdentML 1.0 and 1.1

Get search engine results in mzIdentML format

• mzIdentML from MASCOT (v2.3 or later):

Get search engine results in mzIdentML format

• mzIdentML from MASCOT (v2.3 or later):

Get search engine results in mzIdentML format

• mzIdentML from phenyx:

Get search engine results in mzIdentML format

• mzIdentML from phenyx:

Get search engine results in mzIdentML format

• mzIdentML from phenyx:

PROBLEM!!!!The generated mzIdentML has not proteins!!!!!

We are waiting for an update from Genebio

Get search engine results in mzIdentML format

• mzIdentML from Sequest:

• We have used Proteomics Conversion Tool (ProCon) • We experimented some problems. Just worked in Windows XP• Any help from Thermo users? Maybe Oscar Gallardo?

SHPP - Data deposition workflow

1. Convert raw files to mzML or mgf2. Get search engine results in mzIdentML format3. Use MIAPE Extractor to generate MIAPE MS and

MIAPE MSI (at the same time!!)4. Inspect your data using the MIAPE Extractor Charts5. Use MIAPE Extractor to export PRIDE XML file from

several MIAPE MS and MSI6. Upload PRIDE XML file to (PRIDE database /

ProteomeXchange consortium)

Use MIAPE Extractor to generate MIAPE MS and MIAPE MSI(at the same time!!)

• One MIAPE MS per raw file (fraction/band/replicate)• One MIAPE MSI per mzIdentML (per search engine output)

• Create MIAPE MS and MSI (spectra file + mzIdentML) at the same time!

• Otherwise, PRIDE XML cannot be exported correctly!!

Use MIAPE Extractor to generate MIAPE MS and MIAPE MSI

Use MIAPE Extractor to generate MIAPE MS and MIAPE MSI

Use MIAPE Extractor to generate MIAPE MS and MIAPE MSI

Use MIAPE Extractor to generate MIAPE MS and MIAPE MSI

Use MIAPE Extractor to generate MIAPE MS and MIAPE MSI

Metadata from mzMLProteome Discoverer

1.3.0.0

Compass Xport 3.0.5

Thermo RAW

Waters RAW AB wiff AB t2d

Bruker / Agilent YEP

Thermo RAW

Bruker / Agilent YEP

namemanufacturerversion - S/N

analyserActivation / dissociation componentActivation typenameversionparameters

msConvert 3.0.3643

MIAPE MS section

Ion source

Post-source component

Instrument

Acquisition software

ContainedNot contained

Use MIAPE Extractor to generate MIAPE MS and MIAPE MSI

Two options:• mzML + mzIdentML• mgf + mzIdentML

Poor MS metadata

No MS metadata

Use MIAPE Extractor to generate MIAPE MS and MIAPE MSI

Two options:• mzML + mzIdentML + MS metadata• mgf + mzIdentML + MS metadata

Heavy (GB) and complicated

lighter and easier

Use MIAPE Extractor to generate MIAPE MS and MIAPE MSI

Use MIAPE Extractor to generate MIAPE MS and MIAPE MSI

Use MIAPE Extractor to generate MIAPE MS and MIAPE MSI

Use MIAPE Extractor to generate MIAPE MS and MIAPE MSI

Use MIAPE Extractor to generate MIAPE MS and MIAPE MSI

Use MIAPE Extractor to generate MIAPE MS and MIAPE MSI

Use MIAPE Extractor to generate MIAPE MS and MIAPE MSI

MIAPE projects names consensus:

SHPP + Cell Line + Other exper. feature(s)

“SHPP Lab Jurkat SDSPage RIPA”

Suggestions??????

SHPP - Data deposition workflow

1. Convert raw files to mzML or mgf2. Get search engine results in mzIdentML format3. Use MIAPE Extractor to generate MIAPE MS and

MIAPE MSI (at the same time!!)4. Inspect your data using the MIAPE Extractor Charts5. Use MIAPE Extractor to export PRIDE XML file from

several MIAPE MS and MSI6. Upload PRIDE XML file to (PRIDE database /

ProteomeXchange consortium)

Inspect your data using the MIAPE Extractor Charts

Lets try with examples....

SHPP - Data deposition workflow

1. Convert raw files to mzML or mgf2. Get search engine results in mzIdentML format3. Use MIAPE Extractor to generate MIAPE MS and

MIAPE MSI (at the same time!!)4. Inspect your data using the MIAPE Extractor Charts5. Use MIAPE Extractor to export PRIDE XML file from

several MIAPE MS and MSI6. Upload PRIDE XML file to (PRIDE database /

ProteomeXchange consortium)

Use MIAPE Extractor to export PRIDE XML file from several MIAPE MS and MSI

Now is just possible to create a PRIDE XML file from a MIAPE MS and MSI pair

Shot-gun experiments containing several fractions/bands/replicates

One PRIDE XML file for each fraction/band/replicate

Use MIAPE Extractor to export PRIDE XML file from several MIAPE MS and MSI

The idea is to implement a PRIDE XML exporter from the MIAPE Extractor Charts, creating a PRIDE XML file from each experiment (level 2), and include the FDR filters (or others) that have been applied to the data in the file(s).

TO DO

SHPP - Data deposition workflow

1. Convert raw files to mzML or mgf2. Get search engine results in mzIdentML format3. Use MIAPE Extractor to generate MIAPE MS and

MIAPE MSI (at the same time!!)4. Inspect your data using the MIAPE Extractor Charts5. Use MIAPE Extractor to export PRIDE XML file from

several MIAPE MS and MSI6. Upload PRIDE XML file to (PRIDE database /

ProteomeXchange consortium)

Upload PRIDE XML file to (PRIDE database / ProteomeXchange

consortium)- Once the data is enough curated

- Centralize deposition task?

- Follow EBI PRIDE (http://www.ebi.ac.uk/pride/) or ProteomeXchange (http://www.proteomexchange.org/)

How to share data between us

• How can I see the MIAPE data from other labs?– Use a common account in the MIAPE Extractor:

• Usuario: sphpp-report@proteored.org• Pass: miapereport

– Use your own account and share MIAPE projects after its creation with sphpp-report@proteored.org