Mascot is a software search engine that uses mass spectrometry data to identify proteins from peptide sequence databases. Mascot is widely used by research facilities around the world. Mascot uses a probabilistic scoring algorithm for protein identification that was adapted from the MOWSE algorithm. Mascot is freely available to use on the website of Matrix Science. A License is required for in-house use where more features can be incorporated.

Identify and quantify proteins in complex biological samples using Thermo Scientific™ Proteome Discoverer™ software. Proteome Discoverer software simplifies a wide range of proteomics workflows, from protein and peptide identification to PTM analysis to isobaric mass tagging and both SILAC and label-free quantitation. It supports multiple database search algorithms (SEQUEST, Z-Core, Mascot, and Byonic) and multiple dissociation techniques (CID, HCD, ETD, and EThcD) for more comprehensive analyses.

MaxQuant is a quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. It is specifically aimed at high-resolution MS data. Several labeling techniques as well as label-free quantification are supported. MaxQuant is freely available and can be downloaded from this site. The download includes the search engine andromeda, which is integrated into MaxQuant as well as the viewer application for inspection of raw data and identification and quantification results. 

Progenesis® QI for proteomics enables you to quantify and identify proteins in your complex samples using the advantages of label-free analysis. 

With support for all common vendor data formats and a guided workflow, Progenesis QI Software helps to overcome your data analysis challenges, enabling you to rapidly, objectively and reliably discover proteins of interest from single or fractionated samples.

Byonic is a software package for peptide and protein identification by tandem mass spectrometry. Byonic allows the user to define an essentially unlimited number of variable modification types. Byonic also allows the user to set a separate limit on the number of occurrences of each modification type, so that a search may consider only one or two chance modifications such as oxidations and deamidations per peptide, yet allow three or four biological modifications such as phosphorylations, which tend to cluster together. Byonic's Glycopeptide Search allows the user to identify glycopeptides without prior knowledge of glycan masses or glycosylation sites.

Spectronaut® is a commercial software package aimed at analyzing data-independent acquisition (DIA) proteomics experiments.

Spectronaut® can quantitatively profile 100s to several 1,000s of proteins in one experiment. Large experiments with several conditions and replicates consisting of up to 10,000s of LC-MS runs can be analyzed.