title: Overcoming technical variation and biological variation in quantitative proteomics.
abstract: Quantitative proteomics investigates physiology at the molecular level by measuring relative differences in protein expression between samples under different experimental conditions. A major obstacle to reliably determining quantitative changes in protein expression is to overcome error imposed by technical variation and biological variation. In drug discovery and development the issue of biological variation often rises in concordance with the developmental stage of research, spanning from in vitro assays to clinical trials. In this paper we present case studies to raise awareness to the issues of technical variation and biological variation and the impact this places on applying quantitative proteomics. We defined the degree of technical variation from the process of two-dimensional electrophoresis as 20-30% coefficient of variation. On the other hand, biological variation observed experiment-to-experiment showed a broader degree of variation depending upon the sample type. This was demonstrated with case studies where variation was monitored across experiments with bacteria, established cell lines, primary cultures, and with drug treated human subjects. We discuss technical variation and biological variation as key factors to consider during experimental design, and offer insight into preparing experiments that overcome this challenge to provide statistically significant outcomes for conducting quantitative proteomic research.
authors: Pfizer Global Research & Development, Ann Arbor Laboratories, Ann Arbor, MI 48105, USA. mark.molloy@pfizer.com
authors: Mark P
authors: MP
authors: Molloy
authors: Erin E
authors: EE
authors: Brzezinski
authors: Junqi
authors: J
authors: Hang
authors: Michael T
authors: MT
authors: McDowell
authors: Ruth A
authors: RA
authors: VanBogelen
mesh_terms: D000818:Animals; D001426:Bacterial Proteins / Q000032:analysis; D001798:Blood Proteins / Q000032:analysis / Q000187:drug effects; D001854:Bone Marrow Cells / Q000737:chemistry; D045744:Cell Line, Tumor / Q000737:chemistry; D002478:Cells, Cultured; D003627:Data Interpretation, Statistical; D015180:Electrophoresis, Gel, Two-Dimensional; D004926:Escherichia coli / Q000737:chemistry; D006801:Humans; D007091:Image Processing, Computer-Assisted; D017737:Macrophages, Peritoneal / Q000737:chemistry; D051379:Mice; D008807:Mice, Inbred BALB C; D011506:Proteins / Q000032:analysis; D020543:Proteome / Q000032:analysis*; D040901:Proteomics / Q000379:methods*; D015203:Reproducibility of Results
chemical_list: D001426:Bacterial Proteins; D001798:Blood Proteins; D011506:Proteins; D020543:Proteome