title: Integrated post-experiment monoisotopic mass refinement: an integrated approach to accurately assign monoisotopic precursor masses to tandem mass spectrometric data.
abstract: Accurate assignment of monoisotopic precursor masses to tandem mass spectrometric (MS/MS) data is a fundamental and critically important step for successful peptide identifications in mass spectrometry based proteomics. Here we describe an integrated approach that combines three previously reported methods of treating MS/MS data for precursor mass refinement. This combined method, "integrated post-experiment monoisotopic mass refinement" (iPE-MMR), integrates steps (1) generation of refined MS/MS data by DeconMSn; (2) additional refinement of the resultant MS/MS data by a modified version of PE-MMR; and (3) elimination of systematic errors of precursor masses using DtaRefinery. iPE-MMR is the first method that utilizes all MS information from multiple MS scans of a precursor ion including multiple charge states, in an MS scan, to determine precursor mass. With the combination of these methods, iPE-MMR increases sensitivity in peptide identification and provides increased accuracy when applied to complex high-throughput proteomics data.
authors.affiliation: Department of Chemistry, Korea University, 1, 5-ka, Anam-dong, Seongbuk-gu, Seoul 136-701, Republic of Korea.
authors.forename: Hee-Jung
authors.initials: HJ
authors.lastname: Jung
authors.forename: Samuel O
authors.initials: SO
authors.lastname: Purvine
authors.forename: Hokeun
authors.initials: H
authors.lastname: Kim
authors.forename: Vladislav A
authors.initials: VA
authors.lastname: Petyuk
authors.forename: Seok-Won
authors.initials: SW
authors.lastname: Hyung
authors.forename: Matthew E
authors.initials: ME
authors.lastname: Monroe
authors.forename: Dong-Gi
authors.initials: DG
authors.lastname: Mun
authors.forename: Kyong-Chul
authors.initials: KC
authors.lastname: Kim
authors.forename: Jong-Moon
authors.initials: JM
authors.lastname: Park
authors.forename: Su-Jin
authors.initials: SJ
authors.lastname: Kim
authors.forename: Nikola
authors.initials: N
authors.lastname: Tolic
authors.forename: Gordon W
authors.initials: GW
authors.lastname: Slysz
authors.forename: Ronald J
authors.initials: RJ
authors.lastname: Moore
authors.forename: Rui
authors.initials: R
authors.lastname: Zhao
authors.forename: Joshua N
authors.initials: JN
authors.lastname: Adkins
authors.forename: Gordon A
authors.initials: GA
authors.lastname: Anderson
authors.forename: Hookeun
authors.initials: H
authors.lastname: Lee
authors.forename: David G
authors.initials: DG
authors.lastname: Camp
authors.forename: Myeong-Hee
authors.initials: MH
authors.lastname: Yu
authors.forename: Richard D
authors.initials: RD
authors.lastname: Smith
authors.forename: Sang-Won
authors.initials: SW
authors.lastname: Lee
mesh_terms: D010455:Peptides / Q000032:analysis; D020543:Proteome / Q000032:analysis; D040901:Proteomics; D012441:Saccharomyces cerevisiae / Q000737:chemistry; D053719:Tandem Mass Spectrometry / Q000379:methods*
chemical_list: D010455:Peptides; D020543:Proteome