Searching sequence databases via de novo peptide sequencing by tandem mass spectrometry.
There are many computer programs that can match tandem mass spectra of peptides to database-derived sequences; however, situations can arise where mass spectral data cannot be correlated with any database sequence. In such cases, sequences can be automatically deduced de novo, without recourse to sequence databases, and the resulting peptide sequences can be used to perform homologous nonexact searches of sequence databases. This article describes details on how to implement both a de novo sequencing program called "Lutefisk," and a version of FASTA that has been modified to account for sequence ambiguities inherent in tandem mass spectrometry data.
Johnson
Richard S
RS
Immunex Corporation, 51 University Street, Seattle, WA 98101-2936, USA. JohnsonR@immunex.com
Taylor
J Alex
JA
D000465:Algorithms; D000595:Amino Acid Sequence; D000818:Animals; D003628:Database Management Systems; D006801:Humans; D016247:Information Storage and Retrieval / Q000379:methods*; D013058:Mass Spectrometry / Q000379:methods; D051379:Mice; D008969:Molecular Sequence Data; D010455:Peptides / Q000235:genetics; D011381:Programming Languages; D011817:Rabbits; D051381:Rats; D016415:Sequence Alignment / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods*; D012984:Software; D021241:Spectrometry, Mass, Electrospray Ionization / Q000379:methods*
D010455:Peptides