Data reduction of isotope-resolved LC-MS spectra.
BACKGROUND
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.


BACKGROUND
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.
Du
Peicheng
P
Albert Einstein College of Medicine, Bronx, NY 10461, USA. pdu@us.ibm.com
Sudha
Rajagopalan
R
Prystowsky
Michael B
MB
Angeletti
Ruth Hogue
RH
D000465:Algorithms; D016477:Artifacts; D002853:Chromatography, Liquid / Q000379:methods*; D044962:Data Compression / Q000379:methods; D030562:Databases, Protein; D007553:Isotope Labeling / Q000379:methods; D013058:Mass Spectrometry / Q000379:methods*; D010449:Peptide Mapping / Q000379:methods*; D020543:Proteome / Q000737:chemistry*; D020539:Sequence Analysis, Protein / Q000379:methods*; D012984:Software
D020543:Proteome