title: MRCQuant- an accurate LC-MS relative isotopic quantification algorithm on TOF instruments.
abstract: BACKGROUND
  Relative isotope abundance quantification, which can be used for peptide identification and differential peptide quantification, plays an important role in liquid chromatography-mass spectrometry (LC-MS)-based proteomics. However, several major issues exist in the relative isotopic quantification of peptides on time-of-flight (TOF) instruments: LC peak boundary detection, thermal noise suppression, interference removal and mass drift correction. We propose to use the Maximum Ratio Combining (MRC) method to extract MS signal templates for interference detection/removal and LC peak boundary detection. In our method, MRCQuant, MS templates are extracted directly from experimental values, and the mass drift in each LC-MS run is automatically captured and compensated. We compared the quantification accuracy of MRCQuant to that of another representative LC-MS quantification algorithm (msInspect) using datasets downloaded from a public data repository.
  
  
  RESULTS
  MRCQuant showed significant improvement in the number of accurately quantified peptides.
  
  
  CONCLUSIONS
  MRCQuant effectively addresses major issues in the relative quantification of LC-MS-based proteomics data, and it provides improved performance in the quantification of low abundance peptides.
authors.affiliation: Pediatric Biochemistry Laboratory, University of Texas at San Antonio, 78249, USA.
authors.forename: William E
authors.initials: WE
authors.lastname: Haskins
authors.forename: Konstantinos
authors.initials: K
authors.lastname: Petritis
authors.forename: Jianqiu
authors.initials: J
authors.lastname: Zhang
mesh_terms: D000465:Algorithms; D002853:Chromatography, Liquid; D007554:Isotopes / Q000737:chemistry; D013058:Mass Spectrometry; D010455:Peptides / Q000032:analysis / Q000737:chemistry; D040901:Proteomics / Q000379:methods*
chemical_list: D007554:Isotopes; D010455:Peptides