A Comparison of Label-Free Quantitative Technologies: MaxQuant (MS) vs. Skyline (MS) vs. Spectral Counting (MS/MS) vs. Average TIC (MS/MS) vs. Top3 TIC (MS/MS)

摘要

The proteomics community continues to develop strategies for label-free quantification from shotgun LC-MS/MS experiments but no single technique has emerged as universally acceptable. Researchers use a variety of both MS level quantification (Peak Area) and MS/MS level quantification (Total Ion Current and Spectral Counting) and all have shown both advantages and disadvantages depending upon the application. Here, we examined several different methods of label-free quantification from two 48-human protein mixtures, Universal Protein Standards (UPS1 and UPS2) from Sigma. UPS1 contains equal concentrations and UPS2 contains varying concentrations. We compared the quantitative difference in terms of ratio between UPS2 and UPS1 and assesses the methods showing the highest accuracy.