ProRata is a simple application designed to automate the data processing and analysis for quantitative shotgun proteomics. Quantitative shotgun proteomics attempts to estimate the abundance of proteins in the treatment cells relative to their abundance in the reference cells. In such experiments, the reference cells are labeled with stable isotopes via metabolic labeling, enzymatic labeling, or chemical labeling, and are mixed with the treatment cells in equivalent amounts.
After proteolysis, the samples are analyzed with multi-dimensional liquid chromatogram-tandem mass spectrometry. The acquired tandem mass spectra are used to identify the amino acid sequence and post-translational modifications of proteolytic peptides. ProRata takes the peptide identification results and the mass spectral data as input. At this point,
ProRata will only accept the output from the program DTASelect as the identification result and the mass spectral data in the mzXML format. ProRata will perform all steps for estimating protein abundance ratios and their confidence intervals. Those steps include: extraction of selected ion chromatograms, detection of chromatographic peaks, estimation of peptide abundance ratios, and estimation of protein abundance ratios. The results from each of these steps can be manually verified through ProRata graphical user interface.
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