Correcting systematic bias and instrument measurement drift with mzRefinery

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.