title: On the dependence of a characterization of proteomics maps on the number of protein spots considered.
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.
authors.affiliation: National Institute of Chemistry, Ljubljana, Slovenia. mrandic@msn.com
authors.forename: Milan
authors.initials: M
authors.lastname: Randić
authors.forename: Frank A
authors.initials: FA
authors.lastname: Witzmann
authors.forename: Varshna
authors.initials: V
authors.lastname: Kodali
authors.forename: Subhash C
authors.initials: SC
authors.lastname: Basak
mesh_terms: D000818:Animals; D002210:Caprylates; D002994:Clofibrate; D003652:Decanoic Acids; D004051:Diethylhexyl Phthalate; D004305:Dose-Response Relationship, Drug; D005466:Fluorocarbons; D005786:Gene Expression Regulation / Q000187:drug effects; D000960:Hypolipidemic Agents; D008099:Liver / Q000166:cytology / Q000187:drug effects / Q000378:metabolism; D008297:Male; D010449:Peptide Mapping / Q000379:methods*; D040901:Proteomics / Q000379:methods*; D051381:Rats; D011916:Rats, Inbred F344
chemical_list: D002210:Caprylates; D003652:Decanoic Acids; D005466:Fluorocarbons; D000960:Hypolipidemic Agents; C036567:perfluorodecanoic acid; C023036:perfluorooctanoic acid; D004051:Diethylhexyl Phthalate; D002994:Clofibrate