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J Proteome Res. 2012 Dec 7;11(12):5586-91. doi: 10.1021/pr300426s. Epub 2012 Nov 19.

Recognizing uncertainty increases robustness and reproducibility of mass spectrometry-based protein inferences.

Author information

  • 1Department of Neurobiology, Harvard Medical School Children's Hospital Boston, Boston, Massachusetts, United States. Oliver.Serang@Childrens.Harvard.edu

Abstract

Parsimony and protein grouping are widely employed to enforce economy in the number of identified proteins, with the goal of increasing the quality and reliability of protein identifications; however, in a counterintuitive manner, parsimony and protein grouping may actually decrease the reproducibility and interpretability of protein identifications. We present a simple illustration demonstrating ways in which parsimony and protein grouping may lower the reproducibility or interpretability of results. We then provide an example of a data set where a probabilistic method increases the reproducibility and interpretability of identifications made on replicate analyses of Human Du145 prostate cancer cell lines.

PMID:
23148905
[PubMed - indexed for MEDLINE]
PMCID:
PMC3534833
Free PMC Article
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