MassIVE MSV000082293

Partial Public PXD009547

A novel differential ion mobility interface expands the depth of proteome coverage and the sensitivity of multiplex proteomic measurements

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Description

We present a new high field asymmetric waveform ion mobility spectrometry (FAIMS) interface that can be coupled to the Orbitrap Tribrid mass spectrometers. The interface provides several advantages over previous generations of FAIMS devices including ease of operation, robustness, and high ion transmission. Replicate LC-FAIMS-MS/MS analyses (N=100) of protein digests showed stable ion current over extended time periods with uniform peptide identification on more than 10,000 distinct peptides. For complex tryptic digest analyses, the coupling of FAIMS to LC-MS/MS enabled a 30% gain in unique peptide identification compared to non FAIMS experiments. Improvement in sensitivity facilitated the identification of low abundance peptides, and extended the limit of detection by almost an order of magnitude. The reduction in chimeric MS/MS spectra using FAIMS also improved the precision and the number of quantifiable peptides when using isobaric labeling with tandem mass tag (TMT) 10-plex reagent. We compared quantitative proteomic measurements for LC-MS/MS analyses performed using synchronous precursor selection (SPS) and LC-FAIMS-MS/MS to profile the temporal changes in protein abundance of HEK293 cells following heat shock for periods up to 9h. FAIMS provided 2.5-fold increase in the number of quantifiable peptides compared to non-FAIMS. Altogether, the enhancement in ion transmission and duty cycle of the new FAIMS interface extended the depth and comprehensiveness of proteomic analyses and improved the precision of quantitative measurements. [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: High field asymmetric waveform ion mobility spectrometry (FAIMS) ; quantitative proteomics ; isobaric peptide labeling ; tandem mass tag (TMT) ; heat shock

Contact

Principal Investigators:
(in alphabetical order) 		Pierre Thibault, University of Montreal, Canada
Submitting User: francis_mcmanus

Publications

Pfammatter S, Bonneil E, McManus FP, Prasad S, Bailey DJ, Belford M, Dunyach JJ, Thibault P.
A novel differential ion mobility device expands the depth of proteome coverage and the sensitivity of multiplex proteomic measurements.
Mol. Cell Proteomics. Epub 2018 Jul 14.

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