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Comparative analysis to guide quality improvements in proteomics

Nature Methods volume 6, pages 717–719 (2009)Cite this article

The potential of mass spectrometry–based proteomics to advance biology and biomedicine is nearly unlimited but so is its potential for generating bad data. Apart from the pursuit of technological progress in protocols and instruments, stringent comparative analyses of different approaches are critical for fully developing the discipline.

Systems-wide analysis of any biological entity is hard. For proteins it is particularly daunting because proteomics lacks an equivalent to hybridization assays based on Watson-Crick base pairing or amplification reactions based on PCR. Fortunately, we do have the wonderful tool of mass spectrometry (MS) at our disposal. MS is one of the most versatile technologies used in biology, and continuing radical improvements in the technology amaze even the most seasoned observers. 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. Purely technological improvements in proteomics will go a long way to overcome these difficulties1, but they need to be accompanied by rigorous analysis. Three 'analysis' papers published in the last five years in Nature Methods have broken new ground in investigating crucial data quality issues in the proteomics field. One of them deals with protein identification, another with the enrichment of phosphorylated peptides, and the third with the evaluation of proteomics researchers themselves!

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  1. Matthias Mann is at the Max Planck Institute for Biochemistry, Matrinsried, Germany. mmann@biochem.mpg.de,

    Matthias Mann

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Mann, M. Comparative analysis to guide quality improvements in proteomics. Nat Methods 6, 717–719 (2009). https://doi.org/10.1038/nmeth1009-717

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