Massifquant: Open-source Kalman filter-based XC-MS isotope trace feature detection

Abstract

Motivation: Isotope trace (IT) detection is a fundamental step for liquid or gas chromatography mass spectrometry (XC-MS) data analysis that faces a multitude of technical challenges on complex samples. The Kalman filter (KF) application to IT detection addresses some of these challenges; it discriminates closely eluting ITs in the m/z dimension, flexibly handles heteroscedastic m/z variances and does not bin the m/z axis. Yet, the behavior of this KF application has not been fully characterized, as no cost-free open-source implementation exists and incomplete evaluation standards for IT detection persist. Results: Massifquant is an open-source solution for KF IT detection that has been subjected to novel and rigorous methods of performance evaluation. The presented evaluation with accompanying annotations and optimization guide sets a new standard for comparative IT detection. Compared with centWave, matchedFilter and MZMine2-alternative IT detection engines-Massifquant detected more true ITs in a real LC-MS complex sample, especially low-intensity ITs. It also offers competitive specificity and equally effective quantitation accuracy. Availability and implementation: Massifquant is integrated into XCMS with GPL license ≥2.0 and hosted by Bioconductor: http://bioconductor.org. Annotation data are archived at http://hdl.lib.byu.edu/1877/3232. Parameter optimization code and documentation is hosted at https://github.com/topherconley/optimize-it.