Probability-based protein identification by searching sequence databases using mass spectrometry data

Perkins, D. N., Pappin, D. J., Creasy, D. M., Cottrell, J. S. (December 1999) Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis, 20 (18). pp. 3551-67. ISSN 0173-0835 (Print)0173-0835 (Linking)

URL: http://www.ncbi.nlm.nih.gov/pubmed/10612281
DOI: 10.1002/(sici)1522-2683(19991201)20:18<3551::aid-elps3551>3.0.co;2-2

Abstract

Several algorithms have been described in the literature for protein identification by searching a sequence database using mass spectrometry data. In some approaches, the experimental data are peptide molecular weights from the digestion of a protein by an enzyme. Other approaches use tandem mass spectrometry (MS/MS) data from one or more peptides. Still others combine mass data with amino acid sequence data. We present results from a new computer program, Mascot, which integrates all three types of search. The scoring algorithm is probability based, which has a number of advantages: (i) A simple rule can be used to judge whether a result is significant or not. This is particularly useful in guarding against false positives. (ii) Scores can be compared with those from other types of search, such as sequence homology. (iii) Search parameters can be readily optimised by iteration. The strengths and limitations of probability-based scoring are discussed, particularly in the context of high throughput, fully automated protein identification.

Item Type: Paper
Additional Information: Perkins, D N Pappin, D J Creasy, D M Cottrell, J S Research Support, Non-U.S. Gov't Germany Electrophoresis Electrophoresis. 1999 Dec;20(18):3551-67.
Uncontrolled Keywords: Amino Acid Sequence Amino Acids/chemistry Databases, Factual Information Storage and Retrieval Mass Spectrometry Molecular Sequence Data Molecular Weight Nucleic Acids/genetics Probability Protein Biosynthesis Proteins/ chemistry
Subjects: bioinformatics > genomics and proteomics > design > amino acid design
bioinformatics
bioinformatics > genomics and proteomics > genetics & nucleic acid processing
Investigative techniques and equipment > spectroscopy > mass spectrometry
CSHL Authors:
Communities: CSHL labs > Pappin lab
Depositing User: Kathleen Darby
Date: December 1999
Date Deposited: 23 Apr 2014 15:28
Last Modified: 23 Apr 2014 15:28
Related URLs:
URI: http://repository.cshl.edu/id/eprint/29856

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