1 research outputs found
Multiplexed Quantification for Data-Independent Acquisition
Data-independent
acquisition (DIA) strategies provide a sensitive
and reproducible alternative to data-dependent acquisition (DDA) methods
for large-scale quantitative proteomic analyses. Unfortunately, DIA
methods suffer from incompatibility with common multiplexed quantification
methods, specifically stable isotope labeling approaches such as isobaric
tags and stable isotope labeling of amino acids in cell culture (SILAC).
Here we expand the use of neutron-encoded (NeuCode) SILAC to DIA applications
(NeuCoDIA), producing a strategy that enables multiplexing within
DIA scans without further convoluting the already complex MS<sup>2</sup> spectra. We demonstrate duplex NeuCoDIA analysis of both mixed-ratio
(1:1 and 10:1) yeast and mouse embryo myogenesis proteomes. Analysis
of the mixed-ratio yeast samples revealed the strong accuracy and
precision of our NeuCoDIA method, both of which were comparable to
our established MS<sup>1</sup>-based quantification approach. NeuCoDIA
also uncovered the dynamic protein changes that occur during myogenic
differentiation, demonstrating the feasibility of this methodology
for biological applications. We consequently establish DIA quantification
of NeuCode SILAC as a useful and practical alternative to DDA-based
approaches