Massifquant: open-source Kalman filter-based XC-MS isotope trace feature detection
2014 (English)In: Bioinformatics, ISSN 1367-4803, E-ISSN 1367-4811, Vol. 30, no 18, 2636-2643 p.Article in journal (Refereed) Published
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.
Place, publisher, year, edition, pages
2014. Vol. 30, no 18, 2636-2643 p.
IdentifiersURN: urn:nbn:se:su:diva-104503DOI: 10.1093/bioinformatics/btu359ISI: 000342913000013OAI: oai:DiVA.org:su-104503DiVA: diva2:723657