Quantitation Analysis using OpenMS of iPRG2015: Detection of Differentially Abundant Proteins in Label-Free Quantitative LC–MS/MS Experiments

ABSTRACT: The 2015 study of the Proteome Informatics Research Group (iPRG) of the Association of Biomolecular Resource Facilities (ABRF) aimed to evaluate the effects of the statistical analysis on the accuracy of the results. The study used LC–tandem mass spectra acquired from a controlled mixture, and made the data available to anonymous volunteer participants. The participants used methods of their choice to detect differentially abundant proteins, estimate the associated fold changes, and characterize the uncertainty of the results. The study found that multiple strategies (including the use of spectral counts versus peak intensities, and various software tools) could lead to accurate results, and that the performance was primarily determined by the analysts’ expertise. This manuscript summarizes the outcome of the study, and provides representative examples of good computational and statistical practice. The data set generated as part of this study is publicly available. This project contains the analysis performed with OpenMS framework and exported to mztab. This is the first official submission of mzTab (PRIDE Complete Submission) and should used as reference by software providers as example of How to export Quantitative results into PRIDE database as Complete submission.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Saccharomyces Cerevisiae (baker's Yeast)

SUBMITTER: Yasset Perez-Riverol  

LAB HEAD: Timo Sachsenberg

PROVIDER: PXD010981 | Pride | 2018-09-10

REPOSITORIES: Pride