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A Triple Knockout Isobaric-Labeling Quality Control Platform with an Integrated Online Database Search
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posted on 2020-03-26, 20:45 authored by Jeremy
P. Gygi, Ramin Rad, Jose Navarrete-Perea, Simon Younesi, Steven P. Gygi, Joao A. PauloSample
multiplexing using isobaric tagging is a powerful strategy
for proteome-wide protein quantification. One major caveat of isobaric
tagging is ratio compression that results from the isolation, fragmentation,
and quantification of coeluting, near-isobaric peptides, a phenomenon
typically referred to as “ion interference”. A robust
platform to ensure quality control, optimize parameters, and enable
comparisons across samples is essential as new instrumentation and
analytical methods evolve. Here, we introduce TKO-iQC, an integrated
platform consisting of the Triple Knockout (TKO) yeast digest standard
and an automated web-based database search and protein profile visualization
application. We highlight two new TKO standards based on the TMTpro
reagent (TKOpro9 and TKOpro16) as well as an updated TKO Viewing Tool,
TVT2.0. TKO-iQC greatly facilitates the comparison of instrument performance
with a straightforward and streamlined workflow.
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near-isobaric peptidesTMTpro reagentTKOpro 9quality controlinstrument performanceTriple Knockoutproteome-wide protein quantificationplatformIntegrated Online Databaseratio compressionSample multiplexingprotein profile visualization applicationTriple Knockout Isobaric-Labeling Quality Control Platformweb-based database searchTVT 2.0. TKO-iQCTKO standards
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