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