Recognizing Uncertainty Increases Robustness and Reproducibility of Mass Spectrometry-based Protein Inferences
2012 (English)In: Journal of Proteome Research, ISSN 1535-3893, E-ISSN 1535-3907, Vol. 11, no 12, 5586-5591 p.Article in journal (Refereed) Published
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.
Place, publisher, year, edition, pages
2012. Vol. 11, no 12, 5586-5591 p.
probabilistic protein inference, parsimony, protein grouping, Human Du145 prostate cancer cell lines
Biochemistry and Molecular Biology
IdentifiersURN: urn:nbn:se:su:diva-85531DOI: 10.1021/pr300426sISI: 000311925900002OAI: oai:DiVA.org:su-85531DiVA: diva2:585973