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Enhanced sensitivity in proteomics experiments using FAIMS coupled with a hybrid linear ion trap/Orbitrap mass spectrometer.

Saba J, Bonneil E, Pomiès C, Eng K, Thibault P

Institute for Research in Immunology and Cancer, Université de Montréal, Department of Chemistry, P.O. Box 6128, Station Centre-ville, Montréal, Canada H3C 3J7.

We describe the use and application of high-field asymmetric waveform ion mobility spectrometry combined with nanoscale liquid chromatography mass spectrometry (nanoLC-FAIMS-MS) to improve the sensitivity and dynamic range of proteomics analyses on a hybrid LTQ-Orbitrap mass spectrometer. The ability of FAIMS to enrich multiply protonated peptides against background ions confers a marked advantage in proteomics analyses by decreasing the limits of detection to facilitate the identification of low-abundance peptide ions. These multiply charged ions are recorded into separate acquisition channels to enhance the overall population of detectable peptide ions from a single analysis. NanoLC-FAIMS-MS experiments performed on peptides spiked into complex proteins digests provided more than 10-fold improvement in limits of detection compared to conventional nanoelectrospray mass spectrometry. This enhancement of sensitivity is reflected by a 55% increase in the number of assigned MS/MS spectra contributing to an overall improvement in protein identification and sequence coverage. The application of FAIMS in label-free quantitative proteomics is demonstrated for the identification of differentially abundant proteins from human U937 monocytic cells exposed to phorbol ester.

J. Proteome Res. 2009;8(7):3355-66.

Pubmed ID: 19469569

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