The BioWorks data analysis software that we use for protein identification is based on the SEQUEST algorithm. The following papers describe a recent version of SEQUEST and its Windows interface, TurboSEQUEST:
Probability-based validation of protein identifications using a modified SEQUEST algorithm.
MacCoss MJ, Wu CC, Yates JR 3rd. Anal Chem. 2002 Nov 1;74(21):5593-9.
Protein identification using TurboSEQUEST.
Lundgren DH, Han DK, Eng JK. Curr Protoc Bioinformatics. 2005 Jul;Chapter 13:Unit 13.3
For a general review of methods for peptide spectra matching to the protein sequence databases please consult the following paper:
Large-scale database searching using tandem mass spectra: looking up the answer in the back of the book.
Sadygov RG, Cociorva D, Yates JR 3rd. Nat Methods. 2004 Dec;1(3):195-202.