MIAPE Extractor Tutorial SHPP meeting, 28 Aug 2012 La Cristalera, Miraflores de la Sierra, Madrid Salvador Martínez de Bartolomé Izquierdo CNB-CSIC / ProteoRed.

Slides:

Advertisements

Similar presentations

This course is designed for system managers/administrators to better understand the SAAZ Desktop and Server Management components Students will learn.

Advertisements

Focus on Your Content, Not on Ingesting Your Content Terry Brady Applications Programmer Analyst Georgetown University Library

1 of 15 Information Access Internal Information © FAO 2005 IMARK Investing in Information for Development Information Access Internal Information.

PSI Mass Spectrometry Standards Working Group Summary HUPO PSI MS Standards Working Group.

For Missouri Commission PLEXOS Q&A for Missouri Commission.

Inclusion List Builder Plug-In. 22 Inclusion List Builder Goal: Create an easy to use lab tool for iterative construction of inclusion lists from MS level.

Usage of the memoQ web service API by LSP – a case study

PSI-Proteome Informatics update Andy Jones PSI 2013 Liverpool.

New tools for MIAPE Generation Emilio Salazar Doñate Bioinformatics Group CNB – CSIC.

For Missouri Commission PLEXOS Q&A for Missouri Commission.

TwtDominator User Guide

Big Data & the CPTAC Data Portal Nathan Edwards, Peter McGarvey Mauricio Oberti, Ratna Thangudu Shuang Cai, Karen Ketchum Georgetown University & ESAC.

MS-Viewer – A Web Based Spectral Viewer For Database Search Results Peter R. Baker 1, Alma L. Burlingame 1 and Robert J. Chalkley 1 1 Mass Spectrometry.

10. Standards in Proteomics MS bioinformatics analysis for proteomics Salvador Martínez de Bartolomé Bioinformatics support – ProteoRed.

EBI is an Outstation of the European Molecular Biology Laboratory. PRIDE associated tools: Practical exercise 1 PRIDE team, Proteomics Services Group PANDA.

SpHPP Bioinformatics. 3 rd CHr-16 Workshop. Miraflores de la Sierra December, 10 th -11 th 2012 Alberto Medina.

1 Introducing Reportnet Miruna Badescu. 2 A linear view of Reportnet process.

SERVO-CCE Tools for GPS Time Series and Earthquake Catalogs.

Overview of Mini-Edit and other Tools Access DB Oracle DB You Need to Send Entries From Your Std To the Registry You Need to Get Back Updated Entries From.

OpenMDR: Generating Semantically Annotated Grid Services Rakesh Dhaval Shannon Hastings.

CLARIN tools for workflows Overview. Objective of this document  Determine which are the responsibilities of the different components of CLARIN workflows.

Proprietary & Confidential The Thread That Ties it All Together Voicethread and Discovery Education Jennifer Dorman denblogs.com/jendorman.

Expert Group Meeting on Price Statistics and National Accounts: ICP Round 2011 Jointly organized by: UN-ECLAC, CARICOM, CARTAC and ECCB 3rd-6th December.

Abuse Testing iCentral 2.8: What’s New?. What’s New in 2.8 Enhanced monitoring capability –Improved Dashboards using Microsoft Silverlight Plugin –PartTracker/Utilization.

Data standards from the Proteomics Standards Initiative Andy Jones University of Liverpool.

MAHI Research Database Data Validation System Software Prototype Demonstration September 18, 2001

Introduction The GPM project (The Global Proteome Machine Organization) Salvador Martínez de Bartolomé Bioinformatics support –

How to assure MIAPE compliance of the data using the ProteoRed MIAPE Extractor tool HUPO-PSI meeting - Liverpool (15th April 2013) Salvador Martínez-Bartolomé.

SWC Spring 2010 Application Version SWC Spring 2010 Select Folder 2.

UCSD: EndNote Essentials. Buy EndNote $

Automation of reporting process. It is required to send weekly management reports based on the received data on bank activities.

E-thesis Service QSpace QSpace Queen’s University Research & Learning Repository.

Class Agenda Excel  PivotTables Excel & Word Integration Try PivotTable tutorial & work on Assignment #1.

Digital Filing A Simple Way to Digitally Centralize and Distribute Documents.

Common parameters At the beginning one need to set up the parameters.

La Cristalera, Miraflores de la Sierra, December 2012 HPPHPP Use of SEQUEST search results with ProteoRed.org MIAPE Extractor.

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

Database System Development Lifecycle 1.  Main components of the Infn System  What is Database System Development Life Cycle (DSDLC)  Phases of the.

1 San Diego’s Regional Planning Agency Regional Metadata Inventory Tool Presented at the San Diego Regional GIS Council meeting.

ATN GIS Support ArcGIS: ArcCatalog.

Patricia HernandezGeneva, 28 th September 2006 Swiss Bio Grid: Proteomics Project (PP)

AL-MAAREFA COLLEGE FOR SCIENCE AND TECHNOLOGY INFO 232: DATABASE SYSTEMS CHAPTER 1 DATABASE SYSTEMS Instructor Ms. Arwa Binsaleh.

From Tech Support with love Susan, Luisa and Nick.

Johannes Griss PSI Meeting Heidelberg, April 2011 EBI is an Outstation of the European Molecular Biology Laboratory. mzTab Proposal for.

XP New Perspectives on Integrating Microsoft Office 2003 Tutorial 2 1 Integrating Microsoft Office 2003 Tutorial 2 – Integrating Word, Excel, and Access.

Dr. David Roldán Martínez Universidad Politécnica de Valencia, Spain & Nuno Fernandes Universidade Fernando Pessoa, Portugal Site Stats, the power of event.

TROI – SPC Database Walkthrough Training Presentation Doc. USTP0213 Rev4.

Creation of PSLID programmatic interface Created URL to return XML file containing list of all proteins in database Created URL to return XML file containing.

SHIWA Desktop Cardiff University, Budapest, 3 rd July 2012.

Microsoft Project – Tutorial 6 Working with Excel as Microsoft Project uses many sheets for entering and working with data, it is fairly easy to import.

May 31 User Interface Design for HTML Pages Updated 4/14/06.

CoLIMS progress Computational Omics and Systems Biology (CompOmics) Group Niels Hulstaert

1 Integration of the LCP Reporting Into the E-PRTR Current status and Technical proposal August 4th.

Democratization of ‘Omics Data Availability and Review Robert Chalkley UCSF Data Management Editor - MCP.

Agenda Welcome from the Skyline team!

Etere Subtitling tool. Advantages Etere subtitle tool simplify the subtitle management It use all the resources of MAM as.

DXL to PST Converter Import from Lotus Domino to Outlook.

Windows Version 3.1

Contract Management in electrical engineering

Algorithms and Computation: Bottom-Up Data Analysis Workflows

IUIE Reporting Basics Workshop

Open source tools for data analysis

Overview PSI-PI activities

denblogs.com/jendorman

Code Analysis, Repository and Modelling for e-Neuroscience

LOANDEX 2 Sneak Peek.

Yating Liu July 2018 G-OnRamp workshop

Code Analysis, Repository and Modelling for e-Neuroscience

Use Cases Simple Machine Translation (using Rainbow)

Lab 8: GUI testing Software Testing LTAT

Presentation transcript:

MIAPE Extractor Tutorial SHPP meeting, 28 Aug 2012 La Cristalera, Miraflores de la Sierra, Madrid Salvador Martínez de Bartolomé Izquierdo CNB-CSIC / ProteoRed

SHPP - Data deposition workflow 1.Convert raw files to mzML or mgf 2.Get search engine results in mzIdentML format 3.Use MIAPE Extractor to generate MIAPE MS and MIAPE MSI (at the same time!!) 4.Inspect your data using the MIAPE Extractor Charts 5.Use MIAPE Extractor to export PRIDE XML file from several MIAPE MS and MSI 6.Upload PRIDE XML file to (PRIDE database / ProteomeXchange consortium)

SHPP - Data deposition workflow 1.Convert raw files to mzML or mgf 2.Get search engine results in mzIdentML format 3.Use MIAPE Extractor to generate MIAPE MS and MIAPE MSI (at the same time!!) 4.Inspect your data using the MIAPE Extractor Charts 5.Use MIAPE Extractor to export PRIDE XML file from several MIAPE MS and MSI 6.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 mgf 2.Get search engine results in mzIdentML format 3.Use MIAPE Extractor to generate MIAPE MS and MIAPE MSI (at the same time!!) 4.Inspect your data using the MIAPE Extractor Charts 5.Use MIAPE Extractor to export PRIDE XML file from several MIAPE MS and MSI 6.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 mgf 2.Get search engine results in mzIdentML format 3.Use MIAPE Extractor to generate MIAPE MS and MIAPE MSI (at the same time!!) 4.Inspect your data using the MIAPE Extractor Charts 5.Use MIAPE Extractor to export PRIDE XML file from several MIAPE MS and MSI 6.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

Metadata from mzML Contained Not 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

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 mgf 2.Get search engine results in mzIdentML format 3.Use MIAPE Extractor to generate MIAPE MS and MIAPE MSI (at the same time!!) 4.Inspect your data using the MIAPE Extractor Charts 5.Use MIAPE Extractor to export PRIDE XML file from several MIAPE MS and MSI 6.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 mgf 2.Get search engine results in mzIdentML format 3.Use MIAPE Extractor to generate MIAPE MS and MIAPE MSI (at the same time!!) 4.Inspect your data using the MIAPE Extractor Charts 5.Use MIAPE Extractor to export PRIDE XML file from several MIAPE MS and MSI 6.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 mgf 2.Get search engine results in mzIdentML format 3.Use MIAPE Extractor to generate MIAPE MS and MIAPE MSI (at the same time!!) 4.Inspect your data using the MIAPE Extractor Charts 5.Use MIAPE Extractor to export PRIDE XML file from several MIAPE MS and MSI 6.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 ( or ProteomeXchange (

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: Pass: miapereport – Use your own account and share MIAPE projects after its creation with