X!TandemPipeline

Development from the higher education and research community

Creation or important update: 24/04/13
Minor correction: 24/04/13

Index card author: Olivier Langella (UMR de Génétique Végétale)
Theme leader : Christelle Dantec (CRBM)

Keywords

Laboratories : Vegetable genetics
Head institution : Agro ParisTech, CNRS, INRA, Univ Paris 11
System : UNIX-like, Windows, MacOS X
Profession-activity : biology, scientific computing
IT sector : profession
Use : personal
Main features : data processing
Various other keywords : Java

X!TandemPipeline : edit, filter, merge and group your peptide/protein identifications from MS/MS mass spectra

This software was developed (or is under development) within the higher education and research community. Its stability can vary (see fields below) and its working state is not guaranteed.

Web site
System: UNIX-like, Windows, MacOS X
Current version: 3.3.0 - 7 juillet 2012
License(s): GPL - v3
Status: stable release
Support: maintained, ongoing development
Designer(s): Benoit Valot, Olivier Langella
Contact designer(s): olivier.langella@moulon.inra.fr
Laboratory, service: Vegetable genetics

General software features

X!TandemPipeline is a free software (GPL v3) that helps you to filter and group your peptide/protein identifications from MS/MS mass spectra.

Main features :

easy to install and run (Windows 32 or 64bits, Linux, MacOsX)

reads X!Tandem xml results files
read MASCOT dat results files
offer a graphical user interface (gui) to run X!Tandem analyses
various filters based on statistical values at peptide and protein levels
powerfull original grouping algorithm to filter redundancy
"phosphopeptide" mode to handle phosphoproteomic datasets
edit, search and sort your data graphically
export your data directly to Microsoft Office 2010, OpenOffice and LibreOffice (ods export)
handle huge datasets very quickly
peptide quantification throught MassChroQml export
online support throught the pappso-tools mailing list

Context in which the software is used

X!TandemPipeline is designed for a day use by biologists. It performs MS identifications, filters and groups huge data very quickly.

Publications related to the software

Ludovic Bonhomme, Benoit Valot, Francois Tardieu, Michel Zivy. “Phosphoproteome Dynamics Upon Changes in Plant Water Status Reveal Early Events Associated with Rapid Growth Adjustment in Maize Leaves.” Molecular & Cellular Proteomics: MCP (July 10, 2012). http://www.ncbi.nlm.nih.gov/pubmed/22787273.

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