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Title: Correcting systematic bias and instrument measurement drift with mzRefinery

Journal Article · · Bioinformatics
 [1];  [2];  [1];  [2];  [1]
  1. Pacific Northwest National Lab. (PNNL), Richland, WA (United States). Biological Sciences Division
  2. Vanderbilt Univ., Nashville, TN (United States). Dept. of Biomedical Informatics
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Systematic bias in mass measurement adversely affects data quality and negates the advantages of high precision instruments. We introduce the mzRefinery tool into the ProteoWizard package 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 zero ppm. Because it is part of the ProteoWizard package, mzRefinery can read and write a wide variety of file formats. In conclusion, we report on availability; the mzRefinery tool is part of msConvert, available with the ProteoWizard open source package at http://proteowizard.sourceforge.net/

Research Organization:
Pacific Northwest National Laboratory (PNNL), Richland, WA (United States). Environmental Molecular Sciences Laboratory (EMSL)
Sponsoring Organization:
USDOE Office of Science (SC), Biological and Environmental Research (BER); National Institutes of Health (NIH)
Grant/Contract Number:
AC05-76RL01830; GM103493; U24 CA159988
OSTI ID:
1241083
Report Number(s):
PNNL-SA-108198; 48680; KP1601010
Journal Information:
Bioinformatics, Vol. 31, Issue 23; ISSN 1367-4803
Publisher:
Oxford University PressCopyright Statement
Country of Publication:
United States
Language:
English
Citation Metrics:
Cited by: 17 works
Citation information provided by
Web of Science

References (7)

A cross-platform toolkit for mass spectrometry and proteomics journal October 2012
Flow injection of the lock mass standard for accurate mass measurement in electrospray ionization time-of-flight mass spectrometry coupled with liquid chromatography journal January 2003
Software Lock Mass by Two-Dimensional Minimization of Peptide Mass Errors journal April 2011
ProteoWizard: open source software for rapid proteomics tools development journal July 2008
Parts per Million Mass Accuracy on an Orbitrap Mass Spectrometer via Lock Mass Injection into a C-trap journal October 2005
Improving Proteomics Mass Accuracy by Dynamic Offline Lock Mass journal December 2011
DtaRefinery, a Software Tool for Elimination of Systematic Errors from Parent Ion Mass Measurements in Tandem Mass Spectra Data Sets journal December 2009

Cited By (2)

The Salivary Protein Repertoire of the Polyphagous Spider Mite Tetranychus urticae : A Quest for Effectors journal October 2016
Ancient Regulatory Role of Lysine Acetylation in Central Metabolism journal November 2017

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