Systematic Comparison
of Label-Free, Metabolic Labeling,
and Isobaric Chemical Labeling for Quantitative Proteomics on LTQ
Orbitrap Velos
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Abstract
A variety of quantitative proteomics methods have been
developed,
including label-free, metabolic labeling, and isobaric chemical labeling
using iTRAQ or TMT. Here, these methods were compared in terms of
the depth of proteome coverage, quantification accuracy, precision,
and reproducibility using a high-performance hybrid mass spectrometer,
LTQ Orbitrap Velos. Our results show that (1) the spectral counting
method provides the deepest proteome coverage for identification,
but its quantification performance is worse than labeling-based approaches,
especially the quantification reproducibility; (2) metabolic labeling
and isobaric chemical labeling are capable of accurate, precise, and
reproducible quantification and provide deep proteome coverage for
quantification; isobaric chemical labeling surpasses metabolic labeling
in terms of quantification precision and reproducibility; and (3)
iTRAQ and TMT perform similarly in all aspects compared in the current
study using a CID-HCD dual scan configuration. On the basis of the
unique advantages of each method, we provide guidance for selection
of the appropriate method for a quantitative proteomics study