Correcting systematic bias and instrument measurement drift with mzRefinery
Abstract
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/
- Authors:
-
- Pacific Northwest National Lab. (PNNL), Richland, WA (United States). Biological Sciences Division
- Vanderbilt Univ., Nashville, TN (United States). Dept. of Biomedical Informatics
- Publication Date:
- Research Org.:
- Pacific Northwest National Laboratory (PNNL), Richland, WA (United States). Environmental Molecular Sciences Laboratory (EMSL)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER); National Institutes of Health (NIH)
- OSTI Identifier:
- 1241083
- Report Number(s):
- PNNL-SA-108198
Journal ID: ISSN 1367-4803; 48680; KP1601010
- Grant/Contract Number:
- AC05-76RL01830; GM103493; U24 CA159988
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Bioinformatics
- Additional Journal Information:
- Journal Volume: 31; Journal Issue: 23; Journal ID: ISSN 1367-4803
- Publisher:
- Oxford University Press
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 47 OTHER INSTRUMENTATION; Environmental Molecular Sciences Laboratory
Citation Formats
Gibbons, Bryson C., Chambers, Matthew C., Monroe, Matthew E., Tabb, David L., and Payne, Samuel H.. Correcting systematic bias and instrument measurement drift with mzRefinery. United States: N. p., 2015.
Web. doi:10.1093/bioinformatics/btv437.
Gibbons, Bryson C., Chambers, Matthew C., Monroe, Matthew E., Tabb, David L., & Payne, Samuel H.. Correcting systematic bias and instrument measurement drift with mzRefinery. United States. https://doi.org/10.1093/bioinformatics/btv437
Gibbons, Bryson C., Chambers, Matthew C., Monroe, Matthew E., Tabb, David L., and Payne, Samuel H.. Tue .
"Correcting systematic bias and instrument measurement drift with mzRefinery". United States. https://doi.org/10.1093/bioinformatics/btv437. https://www.osti.gov/servlets/purl/1241083.
@article{osti_1241083,
title = {Correcting systematic bias and instrument measurement drift with mzRefinery},
author = {Gibbons, Bryson C. and Chambers, Matthew C. and Monroe, Matthew E. and Tabb, David L. and Payne, Samuel H.},
abstractNote = {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/},
doi = {10.1093/bioinformatics/btv437},
journal = {Bioinformatics},
number = 23,
volume = 31,
place = {United States},
year = {Tue Aug 04 00:00:00 EDT 2015},
month = {Tue Aug 04 00:00:00 EDT 2015}
}
Web of Science
Works referenced in this record:
A cross-platform toolkit for mass spectrometry and proteomics
journal, October 2012
- Chambers, Matthew C.; Maclean, Brendan; Burke, Robert
- Nature Biotechnology, Vol. 30, Issue 10
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
- Charles, Laurence
- Rapid Communications in Mass Spectrometry, Vol. 17, Issue 13
Software Lock Mass by Two-Dimensional Minimization of Peptide Mass Errors
journal, April 2011
- Cox, Jürgen; Michalski, Annette; Mann, Matthias
- Journal of The American Society for Mass Spectrometry, Vol. 22, Issue 8
ProteoWizard: open source software for rapid proteomics tools development
journal, July 2008
- Kessner, Darren; Chambers, Matt; Burke, Robert
- Bioinformatics, Vol. 24, Issue 21
Parts per Million Mass Accuracy on an Orbitrap Mass Spectrometer via Lock Mass Injection into a C-trap
journal, October 2005
- Olsen, Jesper V.; de Godoy, Lyris M. F.; Li, Guoqing
- Molecular & Cellular Proteomics, Vol. 4, Issue 12
Improving Proteomics Mass Accuracy by Dynamic Offline Lock Mass
journal, December 2011
- Zhang, Ying; Wen, Zhihui; Washburn, Michael P.
- Analytical Chemistry, Vol. 83, Issue 24
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
- Charles, Laurence
- Rapid Communications in Mass Spectrometry, Vol. 17, Issue 13
Software Lock Mass by Two-Dimensional Minimization of Peptide Mass Errors
journal, April 2011
- Cox, Jürgen; Michalski, Annette; Mann, Matthias
- Journal of The American Society for Mass Spectrometry, Vol. 22, Issue 8
Improving Proteomics Mass Accuracy by Dynamic Offline Lock Mass
journal, December 2011
- Zhang, Ying; Wen, Zhihui; Washburn, Michael P.
- Analytical Chemistry, Vol. 83, Issue 24
DtaRefinery, a Software Tool for Elimination of Systematic Errors from Parent Ion Mass Measurements in Tandem Mass Spectra Data Sets
journal, December 2009
- Petyuk, Vladislav A.; Mayampurath, Anoop M.; Monroe, Matthew E.
- Molecular & Cellular Proteomics, Vol. 9, Issue 3
ProteoWizard: open source software for rapid proteomics tools development
journal, July 2008
- Kessner, Darren; Chambers, Matt; Burke, Robert
- Bioinformatics, Vol. 24, Issue 21
Works referencing / citing this record:
The Salivary Protein Repertoire of the Polyphagous Spider Mite Tetranychus urticae : A Quest for Effectors
journal, October 2016
- Jonckheere, Wim; Dermauw, Wannes; Zhurov, Vladimir
- Molecular & Cellular Proteomics, Vol. 15, Issue 12
Ancient Regulatory Role of Lysine Acetylation in Central Metabolism
journal, November 2017
- Nakayasu, Ernesto S.; Burnet, Meagan C.; Walukiewicz, Hanna E.
- mBio, Vol. 8, Issue 6
Ancient Regulatory Role of Lysine Acetylation in Central Metabolism
journal, November 2017
- Nakayasu, Ernesto S.; Burnet, Meagan C.; Walukiewicz, Hanna E.
- mBio, Vol. 8, Issue 6