MOTIVATION: Data reduction of liquid chromatography-mass spectrometry (LC-MS) spectra can be a challenge due to the inherent complexity of biological samples, noise and non-flat baseline. We present a new algorithm, LCMS-2D, for reliable data reduction of LC-MS proteomics data. RESULTS: LCMS-2D can reliably reduce LC-MS spectra with multiple scans to a list of elution peaks, and subsequently to a list of peptide masses. It is capable of noise removal, and deconvoluting peaks that overlap in m/z, in retention time, or both, by using a novel iterative peak-picking step, a 'rescue' step, and a modified variable selection method. LCMS-2D performs well with three sets of annotated LC-MS spectra, yielding results that are better than those from PepList, msInspect and the vendor software BioAnalyst. AVAILABILITY: The software LCMS-2D is available under the GNU general public license from http://www.bioc.aecom.yu.edu/labs/angellab/as a standalone C program running on LINUX.
MOTIVATION: Data reduction of liquid chromatography-mass spectrometry (LC-MS) spectra can be a challenge due to the inherent complexity of biological samples, noise and non-flat baseline. We present a new algorithm, LCMS-2D, for reliable data reduction of LC-MS proteomics data. RESULTS: LCMS-2D can reliably reduce LC-MS spectra with multiple scans to a list of elution peaks, and subsequently to a list of peptide masses. It is capable of noise removal, and deconvoluting peaks that overlap in m/z, in retention time, or both, by using a novel iterative peak-picking step, a 'rescue' step, and a modified variable selection method. LCMS-2D performs well with three sets of annotated LC-MS spectra, yielding results that are better than those from PepList, msInspect and the vendor software BioAnalyst. AVAILABILITY: The software LCMS-2D is available under the GNU general public license from http://www.bioc.aecom.yu.edu/labs/angellab/as a standalone C program running on LINUX.
Authors: Thomas M Harris; Peicheng Du; Nicole Kawachi; Thomas J Belbin; Yanhua Wang; Nicolas F Schlecht; Thomas J Ow; Christian E Keller; Geoffrey J Childs; Richard V Smith; Ruth Hogue Angeletti; Michael B Prystowsky; Jihyeon Lim Journal: Arch Pathol Lab Med Date: 2014-10-08 Impact factor: 5.534
Authors: Mi-Youn Brusniak; Bernd Bodenmiller; David Campbell; Kelly Cooke; James Eddes; Andrew Garbutt; Hollis Lau; Simon Letarte; Lukas N Mueller; Vagisha Sharma; Olga Vitek; Ning Zhang; Ruedi Aebersold; Julian D Watts Journal: BMC Bioinformatics Date: 2008-12-16 Impact factor: 3.169