PeptideShaker

Analyzing proteins and peptides involves highly complex algorithms and statistical methods. Fortunately, the exponential increase in digital tools has also meant that biologists, chemists, physicists and all other professionals interested in the field of Proteomics now have powerful analysis tools at their disposal.

PeptideShaker is one such tool that goes about the problem in a different method. With it, users can query nine platforms for the interpretation of Proteomics results: X!Tandem, MS-GF+, MS Amanda, OMSSA, MyriMatch, Comet, Tide, Mascot, and mzIdentML. This diminishes the risk of errors and ensures data is properly analyzed.

However, before any proteins are processed, users should know that the application is highly resource-intensive and requires at least 4 GB of RAM. Also, the latest version of Java should be installed (if one cannot launch the program, users should try the x64 bit version).

These technical specs left to the side, the application provides users with a comprehensive protein analysis environment. There are nine analysis tasks supported, ranging from overviews to 3D structures and QC plots. These can be accessed from the right-side panel.

PeptideShaker provides users with a wealth of statistical and descriptive data, including the number of peptides, spectrum matches sequences and gene ontology enrichment analyzes. Where applicable, the application generates data-rich graphics in multiple forms, including bar charts and bubble plots. When cases allow it, individual strings are highlighted in different colors, allowing for quick comparisons between data sets.

PeptideShaker is a great tool for scientists and other professionals involved in studying proteins and peptides.