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Analytical model of peptide mass cluster centres with applications

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Item Type:Article
Title:Analytical model of peptide mass cluster centres with applications
Creators Name:Wolski, W.E. and Farrow, M. and Emde, A.K. and Lehrach, H. and Lalowski, M. and Reinert, K.
Abstract:BACKGROUND: The elemental composition of peptides results in formation of distinct, equidistantly spaced clusters across the mass range. The property of peptide mass clustering is used to calibrate peptide mass lists, to identify and remove non-peptide peaks and for the data reduction. RESULTS: We developed an analytical model of the peptide mass cluster centres. Inputs to the model included, the amino acid frequencies in the sequence database, the average length of the proteins in the database, the cleavage specificity of the proteolytic enzyme used and the cleavage probability. We examined the accuracy of our model by comparing it with the model based on a in silico sequence database digest. To identify the crucial parameters we analysed how the cluster centre location depends on the inputs. The distance to the nearest cluster was used to calibrate mass spectrometric peptide peak-lists and to identify non-peptide peaks. CONCLUSIONS: The model introduced here enables to predict the location of the peptide mass cluster centres. It explains how the location of the cluster centres depends on the input parameters. Fast and efficient calibration and filtering of non-peptide peaks is achieved by an distance measure suggested by Wool and Smilansky.
Source:Proteome Science
Publisher:BioMed Central
Page Range:18
Date:23 September 2006
Official Publication:https://doi.org/10.1186/1477-5956-4-18
PubMed:View item in PubMed

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