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

Research output: Contribution to journal › Journal article › Research › peer-review

Standard

A Compact Quadrupole-Orbitrap Mass Spectrometer with FAIMS Interface Improves Proteome Coverage in Short LC Gradients. / Bekker-Jensen, Dorte B.; Martínez-Val, Ana; Steigerwald, Sophia; Rüther, Patrick; Fort, Kyle L; Arrey, Tabiwang N; Harder, Alexander; Makarov, Alexander; Olsen, Jesper V.

In: Molecular and Cellular Proteomics, Vol. 19, No. 4, 2020, p. 716-729.

Research output: Contribution to journal › Journal article › Research › peer-review

Harvard

Bekker-Jensen, DB, Martínez-Val, A, Steigerwald, S, Rüther, P, Fort, KL, Arrey, TN, Harder, A, Makarov, A & Olsen, JV 2020, 'A Compact Quadrupole-Orbitrap Mass Spectrometer with FAIMS Interface Improves Proteome Coverage in Short LC Gradients', Molecular and Cellular Proteomics, vol. 19, no. 4, pp. 716-729. https://doi.org/10.1074/mcp.TIR119.001906

APA

Bekker-Jensen, D. B., Martínez-Val, A., Steigerwald, S., Rüther, P., Fort, K. L., Arrey, T. N., Harder, A., Makarov, A., & Olsen, J. V. (2020). A Compact Quadrupole-Orbitrap Mass Spectrometer with FAIMS Interface Improves Proteome Coverage in Short LC Gradients. Molecular and Cellular Proteomics, 19(4), 716-729. https://doi.org/10.1074/mcp.TIR119.001906

Vancouver

Bekker-Jensen DB, Martínez-Val A, Steigerwald S, Rüther P, Fort KL, Arrey TN et al. A Compact Quadrupole-Orbitrap Mass Spectrometer with FAIMS Interface Improves Proteome Coverage in Short LC Gradients. Molecular and Cellular Proteomics. 2020;19(4):716-729. https://doi.org/10.1074/mcp.TIR119.001906

Author

Bekker-Jensen, Dorte B. ; Martínez-Val, Ana ; Steigerwald, Sophia ; Rüther, Patrick ; Fort, Kyle L ; Arrey, Tabiwang N ; Harder, Alexander ; Makarov, Alexander ; Olsen, Jesper V. / A Compact Quadrupole-Orbitrap Mass Spectrometer with FAIMS Interface Improves Proteome Coverage in Short LC Gradients. In: Molecular and Cellular Proteomics. 2020 ; Vol. 19, No. 4. pp. 716-729.

Bibtex

@article{8b747fa69ec7404cbdca2fbe69fc45ca,
title = "A Compact Quadrupole-Orbitrap Mass Spectrometer with FAIMS Interface Improves Proteome Coverage in Short LC Gradients",
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 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 min 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.",
author = "Bekker-Jensen, {Dorte B.} and Ana Mart{\'i}nez-Val and Sophia Steigerwald and Patrick R{\"u}ther and Fort, {Kyle L} and Arrey, {Tabiwang N} and Alexander Harder and Alexander Makarov and Olsen, {Jesper V}",
year = "2020",
doi = "10.1074/mcp.TIR119.001906",
language = "English",
volume = "19",
pages = "716--729",
journal = "Molecular and Cellular Proteomics",
issn = "1535-9476",
publisher = "American Society for Biochemistry and Molecular Biology",
number = "4",

}

RIS

TY - JOUR

T1 - A Compact Quadrupole-Orbitrap Mass Spectrometer with FAIMS Interface Improves Proteome Coverage in Short LC Gradients

AU - Bekker-Jensen, Dorte B.

AU - Martínez-Val, Ana

AU - Steigerwald, Sophia

AU - Rüther, Patrick

AU - Fort, Kyle L

AU - Arrey, Tabiwang N

AU - Harder, Alexander

AU - Makarov, Alexander

AU - Olsen, Jesper V

PY - 2020

Y1 - 2020

N2 - 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 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 min 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.

AB - 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 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 min 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.

U2 - 10.1074/mcp.TIR119.001906

DO - 10.1074/mcp.TIR119.001906

M3 - Journal article

C2 - 32051234

VL - 19

SP - 716

EP - 729

JO - Molecular and Cellular Proteomics

JF - Molecular and Cellular Proteomics

SN - 1535-9476

IS - 4

ER -

ID: 239209124