Characterization and Optimization of Multiplexed Quantitative Analyses Using High-Field Asymmetric-Waveform Ion Mobility Mass Spectrometry.

Autor:	Schweppe DK; Department of Cell Biology , Harvard Medical School , Cambridge , Massachusetts 02115 , United States., Prasad S; Thermo Scientific LSMS, San Jose , California 95134 , United States., Belford MW; Thermo Scientific LSMS, San Jose , California 95134 , United States., Navarrete-Perea J; Department of Cell Biology , Harvard Medical School , Cambridge , Massachusetts 02115 , United States., Bailey DJ; Thermo Scientific LSMS, San Jose , California 95134 , United States., Huguet R; Thermo Scientific LSMS, San Jose , California 95134 , United States., Jedrychowski MP; Department of Cell Biology , Harvard Medical School , Cambridge , Massachusetts 02115 , United States., Rad R; Department of Cell Biology , Harvard Medical School , Cambridge , Massachusetts 02115 , United States., McAlister G; Thermo Scientific LSMS, San Jose , California 95134 , United States., Abbatiello SE; Thermo Scientific LSMS, San Jose , California 95134 , United States., Woulters ER; Thermo Scientific LSMS, San Jose , California 95134 , United States., Zabrouskov V; Thermo Scientific LSMS, San Jose , California 95134 , United States., Dunyach JJ; Thermo Scientific LSMS, San Jose , California 95134 , United States., Paulo JA; Department of Cell Biology , Harvard Medical School , Cambridge , Massachusetts 02115 , United States., Gygi SP; Department of Cell Biology , Harvard Medical School , Cambridge , Massachusetts 02115 , United States.
Jazyk:	angličtina
Zdroj:	Analytical chemistry [Anal Chem] 2019 Mar 19; Vol. 91 (6), pp. 4010-4016. Date of Electronic Publication: 2019 Feb 26.
DOI:	10.1021/acs.analchem.8b05399
Abstrakt:	Multiplexed, isobaric tagging methods are powerful techniques to increase throughput, precision, and accuracy in quantitative proteomics. The dynamic range and accuracy of quantitation, however, can be limited by coisolation of tag-containing peptides that release reporter ions and conflate quantitative measurements across precursors. Methods to alleviate these effects often lead to the loss of protein and peptide identifications through online or offline filtering of interference containing spectra. To alleviate this effect, high-Field Asymmetric-waveform Ion Mobility Spectroscopy (FAIMS) has been proposed as a method to reduce precursor coisolation and improve the accuracy and dynamic range of multiplex quantitation. Here we tested the use of FAIMS to improve quantitative accuracy using previously established TMT-based interference standards (triple-knockout [TKO] and Human-Yeast Proteomics Resource [HYPER]). We observed that FAIMS robustly improved the quantitative accuracy of both high-resolution MS 2 (HRMS 2 ) and synchronous precursor selection MS 3 (SPS-MS 3 )-based methods without sacrificing protein identifications. We further optimized and characterized the main factors that enable robust use of FAIMS for multiplexed quantitation. We highlight these factors and provide method recommendations to take advantage of FAIMS technology to improve isobaric-tag-quantification moving forward.
Databáze:	MEDLINE
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