Interpretation of proteome profiling experiments largely relies on comparative analyses. False positive identifications may cause fatal misinterpretation of data. The inadequate missing of proteins in experimental results, as fatal as false positives, is hardly considered for quality control. This may partially be due to the lack of availability of standard analytical assessment tools caused by the overwhelming complexity of cells, tissues and body fluids. Here we suggest making use of cell biology knowledge to generate lists of proteins “to be expected” in the corresponding cell fractions. Following a pragmatic experimental strategy, we compared the cytoplasmic fractions of four largely differing kinds of cells, which were human dendritic cells, endothelial cells, fibroblasts and keratinocytes. Proteome profiling was performed by 2D-PAGE in addition to shotgun analysis. 365 proteins were identified in each of the 2D gels, while 674 proteins were identified by shotgun to occur in each of the cells analyzed. All shotgun analysis data including mass fragmentation spectra of the corresponding peptides are accessible via the PRIDE database. We consider these proteins as good candidates for common proteins. As expected, most of these proteins could be clearly assigned to at least one out of the following functional categories: chaperones, cytoskeleton, energy metabolism, redox regulation, nucleic acid processing , protein turnover, membrane transport, protein synthesis and signalling. We suggest that the present data may proof helpful for data assessment, quality control and interpretation of a large variety of experiments based on proteome profiling.
Slany A, Haudek JV, Gundacker N, Griss J, Mohr T, Wimmer H, Eisenbauer M, Elbling L, Gerner C. Introducing a New Parameter for Quality Control of Proteome Profiles: Consideration of Commonly Expressed Proteins. (2009). Electrophoresis. 30(8): 1306-28.
