title: Average peptide score: a useful parameter for identification of proteins derived from database searches of liquid chromatography/tandem mass spectrometry data.
abstract: The quantity and variable quality of data that can be generated from liquid chromatography (LC)/mass spectrometry (MS)-based proteomics analyses creates many challenges in interpreting the spectra in terms of the actual proteins in a complex sample. In spite of improvements in algorithms that match putative peptide sequences to MS/MS spectra, the assembly of these lists of possible or probable peptides into a 'correct' set of proteins is still problematic. We have observed a trend in a simple relationship, derived from standard database search outputs, which can be useful in assessing the quality of a MS/MS-based protein identification. Specifically, the ratio of the protein score and number of non-redundant peptides, or average peptide score (APS), can facilitate initial filtering of database search results in addition to providing a useful measure of confidence for the proteins identified. This parameter has been applied to results from the analysis of multi-protein complexes derived from pull-down experiments analyzed using a two-dimensional LC/MS/MS workflow. In particular, the complex list of protein identifications derived from a drug affinity pull-down with immobilized ampicillin and an E. coli lysate was greatly simplified by applying the APS as a filter, allowing for facile identification of the penicillin-binding proteins known to interact with ampicillin. Furthermore, an APS threshold can be used for any data sets derived from electrospray ionization (ESI)- or matrix-assisted laser desorption/ionization (MALDI)-MS/MS experiments and is also not specific to any database search program.
authors.affiliation: Prolexys Pharmaceuticals, Inc., Salt Lake City, UT 84116, USA.
authors.forename: Cindy Lou
authors.initials: CL
authors.lastname: Chepanoske
authors.forename: Bonnie E
authors.initials: BE
authors.lastname: Richardson
authors.forename: Moritz
authors.initials: M
authors.lastname: von Rechenberg
authors.forename: John M
authors.initials: JM
authors.lastname: Peltier
mesh_terms: D002853:Chromatography, Liquid / Q000379:methods; D030562:Databases, Protein; D004591:Electrophoresis, Polyacrylamide Gel / Q000379:methods; D010455:Peptides / Q000737:chemistry*; D011506:Proteins / Q000737:chemistry*; D021241:Spectrometry, Mass, Electrospray Ionization / Q000379:methods
chemical_list: D010455:Peptides; D011506:Proteins