Title: iMOWSE, a scoring scheme bridging in silico and in vitro digestion in PMF

Authors: Ross K.K. Leung; Stephen K.W. Tsui

Addresses: Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong. ' Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong

Abstract: We demonstrated an unexplored issue in Peptide Mass Fingerprinting, 'cleavage site clusters', and formulated iMOWSE to distinguish true positives from false positives. We showed how the cleavage site clusters skew peptide database composition. Concerning the information content of an in silico digestion of a protein, both the number of matches of long peptides and the number of such peptides an entry can generate are taken into account. The resultant iMOWSE allows tolerance of deviation of query mass values from theoretical mass values and fewer matches are needed to identify true positives.

Keywords: PMF; peptide mass fingerprinting; MOWSE; molecular weight search; cleavage site clusters; in silico digestion; proteins; true positives; false positives; bioinformatics; in vitro digestion.

DOI: 10.1504/IJDMB.2012.045543

International Journal of Data Mining and Bioinformatics, 2012 Vol.6 No.1, pp.104 - 113

Received: 20 Feb 2010
Accepted: 20 Oct 2010

Published online: 17 Dec 2014 *

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