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Mass spectrometry (MS)-based quantitation of plasma proteomes is challenging due to the extremely wide dynamic range and molecular heterogeneity of plasma samples. However, recent advances in technology, MS instrumentation, and bioinformatics have enabled in-depth quantitative analyses of very complex proteomes, including plasma. Specifically, recent improvements in both label-based and label-free quantitation strategies have allowed highly accurate quantitative comparisons of expansive proteome datasets. Here we present a method for in-depth label-free analysis of human plasma samples using MaxQuant.

Efficient Quantitative Comparisons of Plasma Proteomes Using Label-Free Analysis with MaxQuant