Mascot Server

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https://www.matrixscience.com/server.html
Mascot Server is a powerful search engine which uses mass spectrometry data to identify proteins from DNA, RNA and protein sequence databases as well as spectral libraries. While a number of similar programs are available, Mascot is unique in that it integrates all of the proven methods of database searching: peptide mass fingerprinting, sequence query and MS/MS ions search.

Mascot’s capabilities increase with every major version. Below is an overview of functionality, and full descriptions can be found in the online documentation.

Very fast, parallel execution on any number of processors
Probabilistic scoring universally applicable to any instrument type
Novel protein inference
Standard and custom chemical and post-translational modifications
Robust false discovery rate (FDR) estimation, optionally followed by semi-supervised machine learning using Percolator
Identify unsuspected modifications, amino acid substitutions and semi-specific cleavage
Top-down protein identification
Quantitation using isobaric labeling (e.g. iTRAQ, TMT)
Create and search spectral libraries
Identify intact crosslinks