title: Correcting systematic bias and instrument measurement drift with mzRefinery.
abstract: BACKGROUND
  Systematic bias in mass measurement adversely affects data quality and negates the advantages of high precision instruments.
  
  
  RESULTS
  We introduce the mzRefinery tool for calibration of mass spectrometry data files. Using confident peptide spectrum matches, three different calibration methods are explored and the optimal transform function is chosen. After calibration, systematic bias is removed and the mass measurement errors are centered at 0 ppm. Because it is part of the ProteoWizard package, mzRefinery can read and write a wide variety of file formats.
  
  
  METHODS
  The mzRefinery tool is part of msConvert, available with the ProteoWizard open source package at http://proteowizard.sourceforge.net/
  
  
  BACKGROUND
  samuel.payne@pnnl.gov.
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Biological Sciences Division, Pacific Northwest National Laboratory, Richland WA 99354 and.
authors.forename: Bryson C
authors.initials: BC
authors.lastname: Gibbons
authors.affiliation: Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.
authors.forename: Matthew C
authors.initials: MC
authors.lastname: Chambers
authors.affiliation: Biological Sciences Division, Pacific Northwest National Laboratory, Richland WA 99354 and.
authors.forename: Matthew E
authors.initials: ME
authors.lastname: Monroe
authors.affiliation: Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.
authors.forename: David L
authors.initials: DL
authors.lastname: Tabb
authors.affiliation: Biological Sciences Division, Pacific Northwest National Laboratory, Richland WA 99354 and.
authors.forename: Samuel H
authors.initials: SH
authors.lastname: Payne
mesh_terms: D000465:Algorithms; D002138:Calibration; D002853:Chromatography, Liquid / Q000379:methods; D016000:Cluster Analysis; D006801:Humans; D016247:Information Storage and Retrieval; D013058:Mass Spectrometry / Q000295:instrumentation* / Q000379:methods*; D010446:Peptide Fragments / Q000032:analysis*; D011506:Proteins / Q000032:analysis*; D020543:Proteome / Q000032:analysis*; D040901:Proteomics / Q000379:methods; D012984:Software
chemical_list: D010446:Peptide Fragments; D011506:Proteins; D020543:Proteome