期刊
BIOINFORMATICS
卷 30, 期 18, 页码 2636-2643出版社
OXFORD UNIV PRESS
DOI: 10.1093/bioinformatics/btu359
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资金
- National Science Foundation [0639328]
- Brigham Young University
- NSF GRF [DGE-0750759]
- Division Of Mathematical Sciences
- Direct For Mathematical & Physical Scien [0639328] Funding Source: National Science Foundation
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.
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