title: Déjà vu in proteomics. A hit parade of repeatedly identified differentially expressed proteins.
abstract: After reading many 2-DE-based articles featuring lists of the differentially expressed proteins, one starts experiencing a disturbing déjà vu. The same proteins seem to predominate regardless of the experiment, tissue or species. To quantify the occurrence of individual differentially expressed proteins in 2-DE experiment reports, we compiled the identities of differentially expressed proteins identified in human, mouse, and rat tissues published in three recent volumes of Proteomics and calculated the appearance of the most predominant proteins in the dataset. The most frequently identified protein is a highly abundant glycolytic enzyme enolase 1, differentially expressed in nearly every third experiment on both human and rodent tissues. Heat-shock protein 27 (HSP27) and heat-shock protein 60 (HSP60) were differentially expressed in about 30 percent of human and rodent samples, respectively. Considering protein families as units, keratins and peroxiredoxins are the most frequently identified molecules, with at least one member of the group being differentially expressed in about 40 percent of all experiments. We suggest that the frequent identification of these proteins must be considered in the interpretation of any 2-DE studies. We consider if these commonly observed changes represent common cellular stress responses or are a reflection of the technical limitations of 2-DE.
authors.affiliation: Institute of Hematology and Blood Transfusion, Prague, Czech Republic. petra@uhkt.cz
authors.forename: Jiri
authors.initials: J
authors.lastname: Petrak
authors.forename: Robert
authors.initials: R
authors.lastname: Ivanek
authors.forename: Ondrej
authors.initials: O
authors.lastname: Toman
authors.forename: Radek
authors.initials: R
authors.lastname: Cmejla
authors.forename: Jana
authors.initials: J
authors.lastname: Cmejlova
authors.forename: Daniel
authors.initials: D
authors.lastname: Vyoral
authors.forename: Jan
authors.initials: J
authors.lastname: Zivny
authors.forename: Christopher D
authors.initials: CD
authors.lastname: Vulpe
mesh_terms: D000818:Animals; D015180:Electrophoresis, Gel, Two-Dimensional; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D024581:Glyceraldehyde-3-Phosphate Dehydrogenase (Phosphorylating) / Q000378:metabolism; D055551:HSP27 Heat-Shock Proteins; D006360:Heat-Shock Proteins / Q000096:biosynthesis*; D006801:Humans; D051379:Mice; D018832:Molecular Chaperones; D005810:Multigene Family; D009363:Neoplasm Proteins / Q000096:biosynthesis*; D054464:Peroxiredoxins / Q000378:metabolism; D010751:Phosphopyruvate Hydratase / Q000096:biosynthesis*; D040901:Proteomics / Q000379:methods*; D051381:Rats; D014158:Transcription, Genetic
chemical_list: D055551:HSP27 Heat-Shock Proteins; C057725:HSPB1 protein, human; D006360:Heat-Shock Proteins; D018832:Molecular Chaperones; D009363:Neoplasm Proteins; D054464:Peroxiredoxins; D024581:Glyceraldehyde-3-Phosphate Dehydrogenase (Phosphorylating); D010751:Phosphopyruvate Hydratase