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Title: 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:
 [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
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}
}

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Cited by: 17 works
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Works referenced in this record:

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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
  • DOI: 10.1074/mcp.m116.058081

Ancient Regulatory Role of Lysine Acetylation in Central Metabolism
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  • Nakayasu, Ernesto S.; Burnet, Meagan C.; Walukiewicz, Hanna E.
  • mBio, Vol. 8, Issue 6
  • DOI: 10.1128/mbio.01894-17

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
  • DOI: 10.1128/mbio.01894-17