PeptideShaker

PeptideShaker: A powerful tool for protein and peptide analysis supporting multiple platforms for interpreting Proteomics results

PeptideShaker is a feature-packed piece of software aimed at chemists, biologists, physicists and other profesionalls that need to analyze proteins and peptides. The program offers advanced algorithms and statistical methods, as well as support for several platforms to interpret Proteomics results, such as MS Amanda, Mascot, X!Tandem, OMSSA, MS-GF+ and others.

The application is very resource-demanding, thus it requires 4GB of RAM or more in order to work properly. Furthermore, you need to latest Java version installed. Should PeptideShaker fail to launch on a 64-bit system, you should uninstall your current version of Java and (re)install the newest 64-bit version.

PeptideShaker offers nine analysis tasks which you can access from the right-side panel in the application’s main window. It offers an impressive amount of descriptive and statistical information like spectrum matches sequences, the number of peptides and gene ontology enrichment analysis.

It can also generate various types of graphics, like bubble plots and bar charts. Depending on the situation, it will highlight individual strings so you can quickly compare different data sets.