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A Compact Quadrupole-Orbitrap Mass Spectrometer with FAIMS Interface Improves Proteome Coverage in Short LC Gradients

Dorte B. Bekker-Jensen, Ana Martínez del Val, Sophia Steigerwald, Patrick Rüther, Kyle Fort, Tabiwang N. Arrey, Alexander Harder, Alexander Makarov, Jesper V. Olsen
doi: https://doi.org/10.1101/860643
Dorte B. Bekker-Jensen
The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, DENMARK
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Ana Martínez del Val
The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, DENMARK
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Sophia Steigerwald
The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, DENMARK
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Patrick Rüther
The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, DENMARK
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Kyle Fort
Thermo Fisher Scientific, Bremen, GERMANY
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Tabiwang N. Arrey
Thermo Fisher Scientific, Bremen, GERMANY
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Alexander Harder
Thermo Fisher Scientific, Bremen, GERMANY
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Alexander Makarov
Thermo Fisher Scientific, Bremen, GERMANY
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Jesper V. Olsen
The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, DENMARK
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  • For correspondence: jesper.olsen@cpr.ku.dk
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ABSTRACT

State-of-the-art proteomics-grade mass spectrometers can measure peptide precursors and their fragments with ppm mass accuracy at sequencing speeds of tens of peptides per second with attomolar sensitivity. Here we describe a compact and robust quadrupole-orbitrap mass spectrometer equipped with a front-end High Field Asymmetric Waveform Ion Mobility Spectrometry (FAIMS) Interface. The performance of the Orbitrap Exploris 480 mass spectrometer is evaluated in data-dependent acquisition (DDA) and data-independent acquisition (DIA) modes in combination with FAIMS. We demonstrate that different compensation voltages (CVs) for FAIMS are optimal for DDA and DIA, respectively. Combining DIA with FAIMS using single CVs, the instrument surpasses 2500 unique peptides identified per minute. This enables quantification of >5000 proteins with short online LC gradients delivered by the Evosep One LC system allowing acquisition of 60 samples per day. The raw sensitivity of the instrument is evaluated by analyzing 5 ng of a HeLa digest from which >1000 proteins were reproducibly identified with 5 minute LC gradients using DIA-FAIMS. To demonstrate the versatility of the instrument we recorded an organ-wide map of proteome expression across 12 rat tissues quantified by tandem mass tags and label-free quantification using DIA with FAIMS to a depth of >10,000 proteins.

  • ABBREVIATIONS

    ACN
    acetonitrile;
    APD,DDA
    data dependent acquisition;
    DIA
    data independent acquisition;
    FAIMS
    high-field asymmetric waveform ion mobility spectrometry;
    FA
    formic acid;
    HCD
    higher-energy collisional dissociation;
    HCTT
    high capacity transfer tube;
    IT
    maximum injection time;
    LC
    liquid chromatography;
    m/z
    mass-to-charge;
    MS
    mass spectrometry;
    MS/MS
    tandem mass spectrometry;
    PSMs
    peptide spectrum matches;
    PTMs
    post translational modifications;
    TFA
    trifluoroacetic acid;
    TMT
    tandem mass tags.
  • Copyright 
    The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-ND 4.0 International license.
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    Posted November 30, 2019.
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    A Compact Quadrupole-Orbitrap Mass Spectrometer with FAIMS Interface Improves Proteome Coverage in Short LC Gradients
    Dorte B. Bekker-Jensen, Ana Martínez del Val, Sophia Steigerwald, Patrick Rüther, Kyle Fort, Tabiwang N. Arrey, Alexander Harder, Alexander Makarov, Jesper V. Olsen
    bioRxiv 860643; doi: https://doi.org/10.1101/860643
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    A Compact Quadrupole-Orbitrap Mass Spectrometer with FAIMS Interface Improves Proteome Coverage in Short LC Gradients
    Dorte B. Bekker-Jensen, Ana Martínez del Val, Sophia Steigerwald, Patrick Rüther, Kyle Fort, Tabiwang N. Arrey, Alexander Harder, Alexander Makarov, Jesper V. Olsen
    bioRxiv 860643; doi: https://doi.org/10.1101/860643

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