title: Increasing information from shotgun proteomic data by accounting for misassigned precursor ion masses.
abstract: Although mass spectrometers are capable of providing high mass accuracy data, assignment of true monoisotopic precursor ion mass is complicated during data-dependent ion selection for LC-MS/MS analysis of complex mixtures. The complication arises when chromatographic peak widths for a given analyte exceed the time required to acquire a precursor ion mass spectrum. The result is that many measured monoisotopic masses are misassigned due to calculation from a single mass spectrum with poor ion statistics based on only a fraction of the total available ions for a given analyte. Such data in turn produces errors in automated database searches, where precursor m/z value is one search parameter. We propose here a postacquisition approach to correct misassigned monoisotopic m/z values that involves peak detection over the entire elution profile and correction of the precursor ion monoisotopic mass. As a result of using this approach to reprocess shotgun proteomic data we increased peptide sequence assignments by 10% while reducing the estimated false positive ratio from 1 to 0.2%. We also show that 4% of the salvaged identifications may be accounted for by correction of mixed tandem mass spectra resulting from fragmentation of multiple peptides simultaneously, a situation which we refer to as accidental CID.
authors.affiliation: Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195-7610, USA.
authors.forename: Alexander
authors.initials: A
authors.lastname: Scherl
authors.forename: Yihsuan Shannon
authors.initials: YS
authors.lastname: Tsai
authors.forename: Scott A
authors.initials: SA
authors.lastname: Shaffer
authors.forename: David R
authors.initials: DR
authors.lastname: Goodlett
mesh_terms: D001426:Bacterial Proteins / Q000032:analysis / Q000592:standards; D002853:Chromatography, Liquid / Q000379:methods / Q000592:standards; D019295:Computational Biology / Q000379:methods* / Q000592:standards; D005189:False Positive Reactions; D007477:Ions / Q000032:analysis* / Q000737:chemistry; D008970:Molecular Weight; D040901:Proteomics / Q000379:methods* / Q000592:standards; D011550:Pseudomonas aeruginosa / Q000737:chemistry; D021241:Spectrometry, Mass, Electrospray Ionization / Q000379:methods / Q000592:standards; D053719:Tandem Mass Spectrometry / Q000379:methods / Q000592:standards
chemical_list: D001426:Bacterial Proteins; D007477:Ions