Unlike some protein database search programs, Spectrum Mill for MassHunter Workstation provides multiple options for protein identification and characterization. The Spectrum Mill software can search MS/MS spectra using MS/MS ions search, or search MS spectra using peptide mass fingerprinting (PMF).

Spectrum Mill software s innovative MS/MS database search algorithm uses intelligent parallelization to provide rapid (~200 msec/spectrum) turnaround even for complex queries, without the creation of gigantic index files. It can operate in identity mode to find unmodified peptides, or in variable modifications or homology mode to look for post-translational modifications, mutations, and chemical modifications. The recent Spectrum Mill software release provides support for user-defined post-translational modifications to support a lab s custom work flow or stable isotope-based differential expression studies.

Database matches can be automatically or interactively validated. Unmatched and unvalidated spectra can be re-searched using different parameters or against different databases. Recent database search enhancements further provide confident autovalidation of database search results; these enhancements include the following options:

• Reverse database scoring
• Rank1 Rank2 scoring
• Proton mobility scoring (bonus or penalty for predicted fragmentation tendencies)
• The ability to specify required/disallowed amino acids
• The ability to use fixed and variable modifications on the same site (cross-linking studies)

De novo sequencing is also available for identification of proteins not in a database.