- Supports top-down and middle-down experiments.
- Includes five different search modes–Accurate Mass, BioMarker, Sequence Tag, Single Protein, and Gene Restricted search–to determine exact protein sequence including modifications and alternative splicing.
- Supports ECD, IRMPD or CID fragmentation (with UVPD and EThcD coming in v3.1).
- Delta-m Mode for identifying unexpected modifications.
- Includes the proprietary ProSight Warehouse containing all known post-translational modifications (PTMs), alternative splicing events and single nucleotide polymorphisms (SNPs).
- Support for high-throughput LC-MS/MS experiments.
- Imports UniProt databases and shotgun annotates them with all possible proteoforms, or import simple FASTA sequence data.
- Includes Sequence Gazer, which allows users to review search results and add, remove, or change modifications to find better fits.
New to Version 3.1:
- Support for two new fragmentation methods; EThcD and UVPD
- Multithreading for faster processing
- True 64 bit support
- One click to transfer a result to ProSight Lite
- Support for direct infusion experiments