Standardizing Proteomics: Results of a Collaborative Study

The previous installment of this column (1) surveyed the challenges in obtaining high quality results in bottom-up proteomics, the sources of variability in proteomics experiments, and the difficulty in comparing results obtained from different laboratories using different sample preparation procedures, different instrument platforms, and different bioinformatic software. Five organizations were identified that have programs in place for standardizing proteomics workflows. These are the Association of Biomolecular Research Facilities (ABRF), the Biological Reference Material Initiative (BRMI), Clinical Proteomic Technology Assessment for Cancer (CPTAC), the Fixing Proteomics Campaign, and the Human Proteome Organization (HUPO). At the time of writing, the HUPO Test Sample Working Group had completed a collaborative study on protein identification but the results were not published until after the column had gone to press (2). This installment of "Directions in Discovery" will review the results of the study, as they clearly reveal the sources of variability in bottom-up proteomics and point to the road ahead in standardizing proteomics workflows.