Mixed Peptide Sequencing and the FASTF/FASTS Algorithms

The chapter describes two algorithms, FASTF and FASTS that use short peptide sequences to search databases. FASTF uses peptide sequences generated from mixed peptide sequencing Edman degradation, while FASTS uses peptide sequences generated from tandem mass spectrometry (MS/MS) to search protein databases. Both the FASTF and FASTS algorithms are derivations of the heuristic FASTA algorithm for comparison. Based on a process of successive approximations, Heuristic algorithms are much faster than rigorous computational methods. Additionally, both use alignment probability, than similarity score for alignment optimality. The heuristic algorithms employed by these programs quickly identify the protein of interest in a large database with increased sensitivity. For the identification of proteins by mixed peptide sequencing, the chapter presents the use of the ABI Procise cLc Protein Sequencer that utilizes N-terminal Edman degradation chemistry to remove amino acids from the amino terminal of peptide fragments. Mass spectrometry (MS) is a powerful tool in the field of proteomics. The chapter discusses the structural information about proteins obtained in the form of peptide masses or amino acid sequences used to search databases in order to identify the protein. The chapter describes the various steps for MS.