SpectraST (short for "Spectra Search Tool" and rhymes with "contrast") is a spectral library building and searching tool designed primarily for shotgun proteomics applications.
BiblioSpec is a suite of software tools for creating and searching MS/MS peptide spectrum libraries. BiblioSpec is available free of charge for noncommercial use through an interactive web-site
MSSA Parser is a Java based parser for OMSSA (Open Mass Spectrometry Search Algorithm) omx files. Initially created by Steffen Huber for Prof. Dr. Albert Sickmann under the guidance of Dr. Lennart Martens, and further developed by Harald Barsnes, including the addition of a simple, ligh...
MassSieve is a free tool for parsing MS/MS search engine results. It allows you to combine the results of several searches into a single experiment and parsimoniously separate the results. Many different experiments can be loaded and the results can be compared and contrasted.
MSQuant is a tool for quantitative proteomics/mass spectrometry and processes spectra and LC runs to find quantitative information about proteins and peptides. Though automated it also allows manual inspection and change. MSQuant’s main purpose is to make quantitation of proteins and pe...
A quantitative analysis software tool for mass spectrometry-based proteomics. Sung Kyu Park, John D Venable, Tao Xu, John R Yates III, Nature Methods, 2008, 5, 319-322.