Benchmarking accuracy and precision of intensity-based absolute quantification of protein abundances in Saccharomyces cerevisiae.

摘要: Protein quantification via label-free mass spectrometry (MS) has become an increasingly popular method for predicting genome-wide absolute protein abundances. A known caveat of this approach, however, is the poor technical reproducibility, that is, how consistent predictions are when same sample measured repeatedly. Here, we proteomics data Saccharomyces cerevisiae with both biological and inter-batch triplicates, to analyze accuracy precision MS. Moreover, analyzed these metrics vary applying different methods converting MS intensities We demonstrate our simple normalization rescaling approach can perform as accurately, yet more precisely, than which rely on external standards. Additionally, show reproducibility worse all evaluated methods. These results offer a new benchmark assessing quality quantification, while also underscoring current limitations in approach.