title: SQID: an intensity-incorporated protein identification algorithm for tandem mass spectrometry.
abstract: To interpret LC-MS/MS data in proteomics, most popular protein identification algorithms primarily use predicted fragment m/z values to assign peptide sequences to fragmentation spectra. The intensity information is often undervalued, because it is not as easy to predict and incorporate into algorithms. Nevertheless, the use of intensity to assist peptide identification is an attractive prospect and can potentially improve the confidence of matches and generate more identifications. On the basis of our previously reported study of fragmentation intensity patterns, we developed a protein identification algorithm, SeQuence IDentfication (SQID), that makes use of the coarse intensity from a statistical analysis. The scoring scheme was validated by comparing with Sequest and X!Tandem using three data sets, and the results indicate an improvement in the number of identified peptides, including unique peptides that are not identified by Sequest or X!Tandem. The software and source code are available under the GNU GPL license at http://quiz2.chem.arizona.edu/wysocki/bioinformatics.htm.
authors.affiliation: Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721, United States.
authors.forename: Wenzhou
authors.initials: W
authors.lastname: Li
authors.forename: Li
authors.initials: L
authors.lastname: Ji
authors.forename: Jonathan
authors.initials: J
authors.lastname: Goya
authors.forename: Guanhong
authors.initials: G
authors.lastname: Tan
authors.forename: Vicki H
authors.initials: VH
authors.lastname: Wysocki
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D000596:Amino Acids / Q000032:analysis; D002853:Chromatography, Liquid / Q000295:instrumentation / Q000379:methods; D029721:Drosophila Proteins / Q000032:analysis; D008969:Molecular Sequence Data; D010455:Peptides / Q000032:analysis*; D040901:Proteomics / Q000295:instrumentation / Q000379:methods; D029701:Saccharomyces cerevisiae Proteins / Q000032:analysis; D012984:Software; D053719:Tandem Mass Spectrometry / Q000295:instrumentation* / Q000379:methods
chemical_list: D000596:Amino Acids; D029721:Drosophila Proteins; D010455:Peptides; D029701:Saccharomyces cerevisiae Proteins