Challenges of Using Isobaric Labeling for In-Depth Analysis of Large Numbers of Plasma Samples in a Cardiotoxicity Biomarker Discovery Study

摘要

Using extensive multiplexing with isobaric reagents such as the TMT-10plex can greatly reduce instrument time when analyzing large numbers of plasma samples in depth, but limitation of reliably quantification of low level signals reduces depth of analysis to some extent. Specifically, applying data filters may enhance accuracy of quantification, but the total quantified protein and peptide numbers are reduced. Previous reports showed filtering out MS/MS spectra involving co-isolation of >25% unrelated ions could minimize ratio suppression. However, the tradeoff in large scale plasma experiments is the further loss of quantified peptides and proteins.