Overcoming technical variation and biological variation in quantitative proteomics

Mark P. Molloy*, Erin E. Brzezinski, Junqi Hang, Michael T. McDowell, Ruth A. VanBogelen

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

238 Citations (Scopus)


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.

Original languageEnglish
Pages (from-to)1912-1919
Number of pages8
Issue number10
Publication statusPublished - Oct 2003
Externally publishedYes


  • Reproducibility
  • Sample size
  • Two-dimensional gel electrophoresis
  • Variation


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