pr8b00016_si_003.xlsx (67.72 MB)
Proteome-Wide Evaluation of Two Common Protein Quantification Methods
dataset
posted on 2018-04-10, 00:00 authored by Jeremy
D. O’Connell, Joao A. Paulo, Jonathon J. O’Brien, Steven P. GygiProteomics
experiments commonly aim to estimate and detect differential
abundance across all expressed proteins. Within this experimental
design, some of the most challenging measurements are small fold changes
for lower abundance proteins. While bottom-up proteomics methods are
approaching comprehensive coverage of even complex eukaryotic proteomes,
failing to reliably quantify lower abundance proteins can limit the
precision and reach of experiments to much less than the identifiedlet
alone totalproteome. Here we test the ability of two common
methods, a tandem mass tagging (TMT) method and a label-free quantitation
method (LFQ), to achieve comprehensive quantitative coverage by benchmarking
their capacity to measure 3 different levels of change (3-, 2-, and
1.5-fold) across an entire data set. Both methods achieved comparably
accurate estimates for all 3-fold-changes. However, the TMT method
detected changes that reached statistical significance three times
more often due to higher precision and fewer missing values. These
findings highlight the importance of refining proteome quantitation
methods to bring the number of usefully quantified proteins into closer
agreement with the number of total quantified proteins.