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Recognizing Uncertainty Increases Robustness and Reproducibility of Mass Spectrometry-based Protein Inferences
KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.ORCID iD: 0000-0001-5689-9797
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
Abstract [en]

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.
Keyword [en]
probabilistic protein inference, parsimony, protein grouping, Human Du145 prostate cancer cell lines
National Category
Biochemistry and Molecular Biology
Identifiers
URN: urn:nbn:se:kth:diva-109618DOI: 10.1021/pr300426sISI: 000311925900002Scopus ID: 2-s2.0-84870878361OAI: oai:DiVA.org:kth-109618DiVA: diva2:583467
Funder
Swedish Research CouncilScience for Life Laboratory - a national resource center for high-throughput molecular bioscienceSwedish e‐Science Research Center
Note

QC 20130108

Available from: 2013-01-08 Created: 2013-01-08 Last updated: 2017-12-06Bibliographically approved

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Käll, Lukas

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