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Correcting systematic bias and instrument measurement drift with mzRefinery.


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.

SUBMITTER: Gibbons BC 

PROVIDER: S-EPMC4653383 | biostudies-literature | 2015 Dec

REPOSITORIES: biostudies-literature

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Publications

Correcting systematic bias and instrument measurement drift with mzRefinery.

Gibbons Bryson C BC   Chambers Matthew C MC   Monroe Matthew E ME   Tabb David L DL   Payne Samuel H SH  

Bioinformatics (Oxford, England) 20150804 23


<h4>Motivation</h4>Systematic bias in mass measurement adversely affects data quality and negates the advantages of high precision instruments.<h4>Results</h4>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  ...[more]

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