Targeted data extraction of the MS/MS spectra generated by data-independent acquisition: a new concept for consistent and accurate proteome analysis

LC Gillet, P Navarro, S Tate, H Röst, N Selevsek… - Molecular & Cellular …, 2012 - ASBMB
Most proteomic studies use liquid chromatography coupled to tandem mass spectrometry to
identify and quantify the peptides generated by the proteolysis of a biological sample.
However, with the current methods it remains challenging to rapidly, consistently,
reproducibly, accurately, and sensitively detect and quantify large fractions of proteomes
across multiple samples. Here we present a new strategy that systematically queries sample
sets for the presence and quantity of essentially any protein of interest. It consists of using …