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Bioinformatics Advance Access originally published online on May 11, 2007
Bioinformatics 2007 23(11):1394-1400; doi:10.1093/bioinformatics/btm083
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© 2007 The Author(s)This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Data reduction of isotope-resolved LC-MS spectra

Peicheng Du 1,*,{dagger}, Rajagopalan Sudha 1, Michael B. Prystowsky 1 and Ruth Hogue Angeletti 1

1Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA

*To whom correspondence should be addressed.


  Abstract

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.

Contact: pdu{at}us.ibm.com

{dagger}Present Address: IBM Computational Biology Center, P.O. Box 218, Yorktown Heights, NY 10598, USA.

Associate Editor: Alfonso Valencia

Received on November 17, 2006; revised on February 9, 2007; accepted on February 28, 2007

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