News: The first version of PRIDE Inspector 2.0 is now available

PRIDE Inspector 2.0 is an integrated desktop application for MS Proteomics data analysis and visualization. 

- The current version support PRIDE XML, mzIdentML, as well as providing direct access to PRIDE public database. 

- The new version also support of Mass Spectra Formats such as mzxml, mgf, pkl, ms2, dta.

- Some of the new features are: Fragmentation Visualization.

- Protein and Peptide Group Visualization.

- Visualization of Peptide and Protein Properties (Scores, pI, etc)

- New Chart Options.

- Others ...

Links:

 - Publication: http://www.nature.com/nbt/journal/v30/n2/pdf/nbt.2112.pdf

 - Release: http://ftp.pride.ebi.ac.uk/pride/resources/tools/inspector/latest/desktop/pride-inspector.zip

 - Source Code: http://code.google.com/p/pride-toolsuite/wiki/PRIDEInspector

 

Creating an Open Source Revolution in Computational Proteomics

First of all, I don’t want to discuss in this post about Open-Source, its strengths & strengths. This post is about the most useful Open-Source packages, frameworks or libraries in the field of computational proteomics (a short version of our manuscript “Open source libraries and frameworks for Mass Spectrometry based Proteomics: A developer’s perspective”). 

Schema of the possible computational processing steps of a proteomics data set.

In proteomics like other Omics, the bioinformatics efforts can be divided in three major fields: data processing, storage and visualization. From MS/MS preprocessing to post-processing of the identifications results, even though the objectives of these libraries and packages can vary significantly, they usually share a number of features. Common use cases include the handling of protein and peptide sequences, the parsing of results from various proteomics search engines output files, and the visualization of MS-related information (including mass spectra and chromatograms).