Automated statistical analysis of protein abundance ratios from data generated by stable-isotope dilution and tandem mass spectrometry

TitleAutomated statistical analysis of protein abundance ratios from data generated by stable-isotope dilution and tandem mass spectrometry
Publication TypeJournal Article
Year of Publication2003
AuthorsLi XJ, Zhang H, Ranish J, Aebersold R
JournalAnal Chem
Volume75
Pagination6648-57
Date PublishedDec 1
PMID14640741
KeywordsAnimals, Cattle, Chromatography, Liquid/methods/statistics & numerical data, Isotope Labeling/methods/*statistics & numerical data, numerical data, RNA Polymerase II/*analysis, Serum Albumin, Bovine/*analysis, Spectrometry, Mass, Electrospray Ionization/methods/*statistics &
AbstractWe describe an algorithm for the automated statistical analysis of protein abundance ratios (ASAPRatio) of proteins contained in two samples. Proteins are labeled with distinct stable-isotope tags and fragmented, and the tagged peptide fragments are separated by liquid chromatography (LC) and analyzed by electrospray ionization (ESI) tandem mass spectrometry (MS/MS). The algorithm utilizes the signals recorded for the different isotopic forms of peptides of identical sequence and numerical and statistical methods, such as Savitzky-Golay smoothing filters, statistics for weighted samples, and Dixon's test for outliers, to evaluate protein abundance ratios and their associated errors. The algorithm also provides a statistical assessment to distinguish proteins of significant abundance changes from a population of proteins of unchanged abundance. To evaluate its performance, two sets of LC-ESI-MS/MS data were analyzed by the ASAPRatio algorithm without human intervention, and the data were related to the expected and manually validated values. The utility of the ASAPRatio program was clearly demonstrated by its speed and the accuracy of the generated protein abundance ratios and by its capability to identify specific core components of the RNA polymerase II transcription complex within a high background of copurifying proteins.

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