Fixing Proteomics Campaign

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The challenge of reproducible MS analysis

Aligned chromatograms of three repeated LC-MS/MS analyses

"MS is one of the most versatile technologies used in biology... However, not all is well in the discipline of proteomics, and much fuzzy thinking and bad data have unfortunately found their way into the literature" 2

"Determining significant differences between mass spectrometry datasets from biological samples is one of the major challenges for proteome informatics. Accurate and reproducible protein quantitation in complex samples in the face of biological and technical variability has long been a desired goal for proteomics." 5

Mass Spectrometry is well known for the potential it offers for discovery and validation within proteomics research1-3. But it's also recognised1-9 that MS is a technically challenging technique; not a black-box solution to delivering reproducible quantitative proteomics results each time you run the same experiment. This was highlighted in the results of a 3-year HUPO quality control study4 using test samples in order to assess issues of reproducibility and sampling in proteomics. Only seven of the 27 participating labs were 100% successful in the first part of the study, which dealt with protein identification. The labs were also subjected to a subsequent sampling and reporting exercise with peptide of very similar molecular weights. Only one of the 27 labs was successful in this attempt.

The 4-step approach to Fixing Proteomics applies to any technique so it helps deliver cross-lab reproducibility for MS. It allows you to create experiments that incrementally increase the level of reliability and reproducibility of your proteomics data, controlling the technical variation with rigorous, standardised approaches in each case.

See also: Protocols for reproducible Mass Spec proteomics


  1. Clinical Proteomic Technologies for Cancer initiative Annual Report, September 2007.
  2. Comparative analysis to guide quality improvements in proteomics. Nature Methods 6 (Oct 2009), pages 717 - 719
  3. Multi-site assessment of the precision and reproducibility of multiple reaction monitoring–based measurements of proteins in plasma. Nature Biotechnology 27 (28 June 2009), pages 633 - 641  
  4. A HUPO test sample study reveals common problems in mass spectrometry–based proteomics. Nature Methods 6 (2009), 423 - 430
  5. ABRF iPRG2009 Study Announcement, Association of Biomolecular Resource Facilities, 1 October 2008
  6. Proteomics Ponders Time. Science 26 September 2008: Vol. 321. no. 5897, pp. 1758 - 1761
  7. Comments on Standards in Proteomics and the Concept of Fitness-for-Purpose. Mark W. Duncan, Stephen W. Hunsucker. Proteomics 2006, 6, No. S2, 45-47.
  8. BioMarket Trends: Mass Spec Finds a Niche in Biomarkers, Genetic Engineering News, Mar 1, 2007. Vol 27, No. 5
  9. Proteome analysis by two-dimensional gel electrophoresis and mass spectrometry: strengths and limitations. Sarka Bernova-Giorgianni. Trends in Analytical Chemistry, Vol 22, No 5, 2003.