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Bioinformatics. 2015 Dec 1;31(23):3838-40. doi: 10.1093/bioinformatics/btv437. Epub 2015 Aug 4.

Correcting systematic bias and instrument measurement drift with mzRefinery.

Author information

1
Biological Sciences Division, Pacific Northwest National Laboratory, Richland WA 99354 and.
2
Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.

Abstract

MOTIVATION:

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.

AVAILABILITY AND IMPLEMENTATION:

The mzRefinery tool is part of msConvert, available with the ProteoWizard open source package at http://proteowizard.sourceforge.net/

CONTACT:

samuel.payne@pnnl.gov.

SUPPLEMENTARY INFORMATION:

Supplementary data are available at Bioinformatics online.

PMID:
26243018
PMCID:
PMC4653383
DOI:
10.1093/bioinformatics/btv437
[Indexed for MEDLINE]
Free PMC Article

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