TY - JOUR
T1 - Data reduction of isotope-resolved LC-MS spectra
AU - Du, Peicheng
AU - Sudha, Rajagopalan
AU - Prystowsky, Michael B.
AU - Angeletti, Ruth Hogue
N1 - Funding Information:
We acknowledge NIH for financial support: CA101150 (RHA) and CA103547 (MBP). Thanks to Dr. Frank Suits for helpful discussions and careful review of the manuscript. Funding for open-access will be provided by ‘‘CA101150 (RHA)’’ from NIH.
PY - 2007/6
Y1 - 2007/6
N2 - 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.
AB - 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.
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U2 - 10.1093/bioinformatics/btm083
DO - 10.1093/bioinformatics/btm083
M3 - Article
C2 - 17496000
AN - SCOPUS:34447321056
SN - 1367-4803
VL - 23
SP - 1394
EP - 1400
JO - Bioinformatics
JF - Bioinformatics
IS - 11
ER -