Publication
General Statistical Modeling of Data from Protein Relative Expression Isobaric Tags
Publisher:
American Chemical Society (ACS)
Date:
11-05-2011
DOI:
10.1021/PR1012784
Abstract: Quantitative comparison of the protein content of biological s les is a fundamental tool of research. The TMT and iTRAQ isobaric labeling technologies allow the comparison of 2, 4, 6, or 8 s les in one mass spectrometric analysis. Sound statistical models that scale with the most advanced mass spectrometry (MS) instruments are essential for their efficient use. Through the application of robust statistical methods, we developed models that capture variability from in idual spectra to biological s les. Classical experimental designs with a distinct s le in each channel as well as the use of replicates in multiple channels are integrated into a single statistical framework. We have prepared complex test s les including controlled ratios ranging from 100:1 to 1:100 to characterize the performance of our method. We demonstrate its application to actual biological data sets originating from three different laboratories and MS platforms. Finally, test data and an R package, named isobar, which can read Mascot, Phenyx, and mzIdentML files, are made available. The isobar package can also be used as an independent software that requires very little or no R programming skills.