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Development and evaluation of normalization methods for label-free relative quantification of endogenous peptides
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmaceutical Biosciences. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Clinical Pharmacology. (Medicinsk masspektrometri)
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmaceutical Biosciences. (Medicinsk masspektrometri)
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmaceutical Biosciences. (Toxikologi)
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmaceutical Biosciences.
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2009 (English)In: Molecular & Cellular Proteomics, ISSN 1535-9476, E-ISSN 1535-9484, Vol. 8, no 10, p. 2285-2295Article in journal (Refereed) Published
Abstract [en]

The performances of 10 different normalization methods on data of endogenous brain peptides produced with label-free nano-LC-MS were evaluated. Data sets originating from three different species (mouse, rat, and Japanese quail), each consisting of 35-45 individual LC-MS analyses, were used in the study. Each sample set contained both technical and biological replicates, and the LC-MS analyses were performed in a randomized block fashion. Peptides in all three data sets were found to display LC-MS analysis order-dependent bias. Global normalization methods will only to some extent correct this type of bias. Only the novel normalization procedure RegrRun (linear regression followed by analysis order normalization) corrected for this type of bias. The RegrRun procedure performed the best of the normalization methods tested and decreased the median S.D. by 43% on average compared with raw data. This method also produced the smallest fraction of peptides with interblock differences while producing the largest fraction of differentially expressed peaks between treatment groups in all three data sets. Linear regression normalization (Regr) performed second best and decreased median S.D. by 38% on average compared with raw data. All other examined methods reduced median S.D. by 20-30% on average compared with raw data.

Place, publisher, year, edition, pages
2009. Vol. 8, no 10, p. 2285-2295
Keywords [en]
Bioinformatics, Normalization, endogenous peptide, neuropeptide, LC-MS
National Category
Pharmaceutical Sciences
Identifiers
URN: urn:nbn:se:uu:diva-118338DOI: 10.1074/mcp.M800514-MCP200ISI: 000270492700007PubMedID: 19596695OAI: oai:DiVA.org:uu-118338DiVA, id: diva2:299031
Available from: 2010-02-23 Created: 2010-02-23 Last updated: 2018-01-12Bibliographically approved

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Kultima, KimAndrén, Per E.

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