ASAPRatio

ASAPRatio (utomated statistical analysis of protein abundance ratios) is an algorithm designed for the automated statistical analysis of protein abundance ratios between two samples. In this method, proteins are tagged with stable-isotope labels, fragmented, and the resulting tagged peptide fragments are separated using liquid chromatography (LC) and analyzed using electrospray ionization (ESI) tandem mass spectrometry (MS/MS). The algorithm makes use of signals from different isotopic forms of identical peptides and employs various numerical and statistical techniques, including Savitzky-Golay smoothing filters, statistical methods for weighted samples, and Dixon's test for identifying outliers. This approach is used to calculate protein abundance ratios and their associated errors. Additionally, the algorithm offers a statistical evaluation to differentiate proteins with significant changes in abundance from a population of proteins with unchanged abundance. To assess its performance, the ASAPRatio algorithm was applied to two sets of LC-ESI-MS/MS data without human intervention, and the results were compared to expected and manually validated values. The utility of ASAPRatio was highlighted by its efficiency, accurate calculation of protein abundance ratios, and its ability to identify specific core components of the RNA polymerase II transcription complex amid a complex mixture of co-purified proteins.