title: SPIDER: software for protein identification from sequence tags with de novo sequencing error.
abstract: For the identification of novel proteins using MS/MS, de novo sequencing software computes one or several possible amino acid sequences (called sequence tags) for each MS/MS spectrum. Those tags are then used to match, accounting amino acid mutations, the sequences in a protein database. If the de novo sequencing gives correct tags, the homologs of the proteins can be identified by this approach and software such as MS-BLAST is available for the matching. However, de novo sequencing very often gives only partially correct tags. The most common error is that a segment of amino acids is replaced by another segment with approximately the same masses. We developed a new efficient algorithm to match sequence tags with errors to database sequences for the purpose of protein and peptide identification. A software package, SPIDER, was developed and made available on Internet for free public use. This paper describes the algorithms and features of the SPIDER software.
authors.affiliation: Department of Computer Science, University of Western Ontario, London, Ontario, Canada N6A 5B7, Canada. yhan2@csd.uwo.ca
authors.forename: Yonghua
authors.initials: Y
authors.lastname: Han
authors.forename: Bin
authors.initials: B
authors.lastname: Ma
authors.forename: Kaizhong
authors.initials: K
authors.lastname: Zhang
mesh_terms: D000465:Algorithms; D020224:Expressed Sequence Tags; D013058:Mass Spectrometry / Q000379:methods; D010449:Peptide Mapping / Q000379:methods*; D011506:Proteins / Q000032:analysis / Q000737:chemistry* / Q000145:classification / Q000235:genetics; D016415:Sequence Alignment / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods*; D012984:Software
chemical_list: D011506:Proteins