On the dependence of a characterization of proteomics maps on the number of protein spots considered

Milan Randić, Frank A. Witzmann, Varshna Kodali, Subhash C. Basak

Research output: Contribution to journalArticle

16 Scopus citations

Abstract

We have reexamined the numerical characterization of proteomics maps based on the construction of novel distance matrices associated with the nearest neighbor graph for the protein spots. In particular we consider dependence of a characterization of proteomics map on the number of proteins considered in the analysis. We examined a collection of proteomics maps in which we approximately doubled the number of spots to be used for quantitative analysis, considering cases of maps having 30, 50, 100, 250, 500, and 1054 protein spots. For each case we have compared the similarity-dissimilarity results for five proteomics maps of rat liver cells associated with the control group and four proliferators administrated by intraperitoneal injection. We found that proteins maps based on a set of about the 250 most abundant proteins spots suffice for a satisfactory numerical characterization of such maps.

Original languageEnglish (US)
Pages (from-to)116-122
Number of pages7
JournalJournal of Chemical Information and Modeling
Volume46
Issue number1
DOIs
StatePublished - Jan 1 2006

ASJC Scopus subject areas

  • Chemistry(all)
  • Chemical Engineering(all)
  • Computer Science Applications
  • Library and Information Sciences

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