title: Improved comparative proteome analysis based on two-dimensional gel electrophoresis.
abstract: The purpose of this study was to test the extent to which differences in spot intensity can be reliably recognized between two groups of two-dimensional electrophoresis gels (pH 4-7, visualized with ruthenium fluorescent stain) each loaded with different amounts of protein from rat brain (power analysis). Initial experiments yielded only unsatisfactory results: 546 spots were matched from two groups of 6 gels each loaded with 200 microg and 250 microg protein, respectively. Only 72 spots were higher (p<0.05), while 58 spots were significantly lower in the 250-microg group. The construction of new apparatuses that allowed the simultaneous processing of 24 gels throughout all steps between rehydration and staining procedure considerably lowered the between-gel variation. This resulted in the detection of significant differences in spot intensities in 77-90% of all matched spots on gel groups with a 25% difference in protein load. This applied both when protein from 24 biological replicates was loaded onto two groups of 12 gels and when two pooled tissue samples were each loaded onto 6 gels. At a difference of 50% in protein load, more than 90% of all spots differed significantly between two experimental groups.
authors.affiliation: Department of Radiology and Nuclear Medicine (Radiochemistry), Charité Universitätsmedizin, Campus Benjamin Franklin, Berlin, Germany.|A+M Proteome Science, Berlin, Germany.
authors.forename: Murat
authors.initials: M
authors.lastname: Eravci
authors.affiliation: Department of Radiology and Nuclear Medicine (Radiochemistry), Charité Universitätsmedizin, Campus Benjamin Franklin, Berlin, Germany.|A+M Proteome Science, Berlin, Germany.
authors.forename: Sandra
authors.initials: S
authors.lastname: Fuxius
authors.affiliation: A+M Proteome Science, Berlin, Germany.
authors.forename: Oliver
authors.initials: O
authors.lastname: Broedel
authors.affiliation: A+M Proteome Science, Berlin, Germany.
authors.forename: Stephanie
authors.initials: S
authors.lastname: Weist
authors.affiliation: A+M Proteome Science, Berlin, Germany.
authors.forename: Selda
authors.initials: S
authors.lastname: Eravci
authors.affiliation: Department of Medical Informatics, Biometry and Epidemiology, University of Munich, Germany.
authors.forename: Ulrich
authors.initials: U
authors.lastname: Mansmann
authors.affiliation: Department of Internal Medicine IV, Charité Universitätsmedizin, Campus Benjamin Franklin, Berlin, Germany.
authors.forename: Hartmut
authors.initials: H
authors.lastname: Schluter
authors.affiliation: Department of Internal Medicine IV, Charité Universitätsmedizin, Campus Benjamin Franklin, Berlin, Germany.
authors.forename: Joachim
authors.initials: J
authors.lastname: Tiemann
authors.affiliation: Department of Radiology and Nuclear Medicine (Radiochemistry), Charité Universitätsmedizin, Campus Benjamin Franklin, Berlin, Germany.|A+M Proteome Science, Berlin, Germany.
authors.forename: Andreas
authors.initials: A
authors.lastname: Baumgartner
mesh_terms: D000818:Animals; D001921:Brain / Q000378:metabolism*; D015180:Electrophoresis, Gel, Two-Dimensional; D008297:Male; D020543:Proteome / Q000032:analysis*; D051381:Rats; D017207:Rats, Sprague-Dawley; D015203:Reproducibility of Results; D012984:Software
chemical_list: D020543:Proteome