Data Standards Submission 1st CHr-16 Workshop.Miraflores de la SierraAugust, 28th-29th 2012 Alberto Medina

Summary

1. Data standards (just a quick view)2. Trusted pipeline3. Starting!4. Other search engines

Summary

1. Data standards (just a quick view)2. Trusted pipeline3. Starting!4. Other search engines

Data Standards – PSI fram

ework

Spanish Consortium Bioinformatics pipeline

Mass Spectra

Raw data MzMl/TraML

Protein/Peptides

Search Engines MzIdentml

Quantitation

Vendor/Free software MzQuantml

Data Reporting – ProteoRed M

IAPE W

eb toolkit

MIAPE MS/MSI

PRIDE

Data Reporting –

with stable release

MIAPEQuant

PRIDEQuan¿?

Data validation and subm

ission

ProteomeXchange

External repositories

Development of bioinformatic environment:Spanish HPP will join the different resources to provide an unique enquiring system

PAtlasNProt

GPMDB

PRIDE

UProtUpcoming

Proteomics results

Data standards submission

(ProteomeXchange)+ +Emsembl

Summary

1. Data standards (just a quick view)2. Trusted pipeline3. Starting!4. Other search engines

Trusted pipeline

Mass Spectra

.mgf

Identification

Mascot

Output file

mzIdentML

MIAPE Generation

MIAPE MS MIAPE MSI

Trusted pipeline

MIAPE MS MIAPE MSI

PRIDE Generation

PRIDE XML

Stats (MIAPE Extractor)

Charts and Reports

Check and View PRIDE

Summary

1. Data standards (just a quick view)2. Trusted pipeline3. Starting!4. Other search engines

Starting (1)• Step 1)• Element to achieve: Peak lists (acquired data).• Issues:

• Several data formats (mgf, wiff, pkl, etc).• Different Software packets.• Translators.

• Goal: • MGF file or mzML.

• Translators• MSConvert, OpenMS, ABSciex MS Data Converter, CompassXport,

ProCon.

Starting (2)• Step 2)• Element to achieve: Identification of Proteins and Peptides.• Issues:

• Have your own Mascot Server.• Release 2.3 in advance• Other search engines (check section 4).

• Goal: • Submit to Mascot peak list obtained in step 1.

Starting (3)• Step 3)• Element to achieve: Mascot results formatted as mzIdentML• Issues:

• Version 2.3 is rather slow. • It is not possible to do using batch mode.

• Goal: • mzIdentML.

Starting (3)

MIAPE Generation

1. GO to ProteoRed MIAPE web toolkit site.www.proteored.org/MIAPE

2. Click on Create MIAPE Automatic

3. Download the application (Java application).

4. Run the application

MIAPE Generation

PRIDE Generation

PRIDE Generation

PRIDE Visualizationhttp://proteo.cnb.csic.es/prideviewer

PRIDE Submissionhttp://www.ebi.ac.uk/pride/easySubmitData.do?

Exchanging through the cloud

MIAPE Extractor

A hopefully universe

• ProteoRed MIAP

E repository

• MPWTK

• mzML

• mzIdentML

• MPWTK

• MIAPE

Extractor

• PRIDE XML

• A

• B

• C

Summary

1. Data standards (just a quick view)2. Trusted pipeline3. Starting!4. Other search engines

Other Search Engines• Phenyx:

• Waiting new patch to save the results in a straighforward manner. Similar to Mascot export.

• X!Tandem:• Full integrated thorugh X!Tandem results files.

• Sequest:• It is possible to save the results formatted as mzIdentML through

ProCon tool (runnable from Windows XP OS).http://www.medizinisches-proteom-center.de/ProConWe need some feedback from Sequest users.

• OMSSA:• Not integrated, but it is possible to use mzIdentML-Parsershttp://code.google.com/p/mzidentml-parsers/

Questions