Rapid and Deep Proteomes by Faster Sequencing on a Benchtop Quadrupole Ultra-High-Field Orbitrap Mass Spectrometer

Research output: Contribution to journalJournal articlepeer-review

Standard

Rapid and Deep Proteomes by Faster Sequencing on a Benchtop Quadrupole Ultra-High-Field Orbitrap Mass Spectrometer. / Kelstrup, Christian D; Jersie-Christensen, Rosa R; Batth, Tanveer Singh; Arrey, Tabiwang N; Kuehn, Andreas; Kellmann, Markus; Olsen, Jesper Velgaard.

In: Journal of Proteome Research, Vol. 13, No. 12, 28.10.2014, p. 6187-95.

Research output: Contribution to journalJournal articlepeer-review

Harvard

Kelstrup, CD, Jersie-Christensen, RR, Batth, TS, Arrey, TN, Kuehn, A, Kellmann, M & Olsen, JV 2014, 'Rapid and Deep Proteomes by Faster Sequencing on a Benchtop Quadrupole Ultra-High-Field Orbitrap Mass Spectrometer', Journal of Proteome Research, vol. 13, no. 12, pp. 6187-95. https://doi.org/10.1021/pr500985w

APA

Kelstrup, C. D., Jersie-Christensen, R. R., Batth, T. S., Arrey, T. N., Kuehn, A., Kellmann, M., & Olsen, J. V. (2014). Rapid and Deep Proteomes by Faster Sequencing on a Benchtop Quadrupole Ultra-High-Field Orbitrap Mass Spectrometer. Journal of Proteome Research, 13(12), 6187-95. https://doi.org/10.1021/pr500985w

Vancouver

Kelstrup CD, Jersie-Christensen RR, Batth TS, Arrey TN, Kuehn A, Kellmann M et al. Rapid and Deep Proteomes by Faster Sequencing on a Benchtop Quadrupole Ultra-High-Field Orbitrap Mass Spectrometer. Journal of Proteome Research. 2014 Oct 28;13(12):6187-95. https://doi.org/10.1021/pr500985w

Author

Kelstrup, Christian D ; Jersie-Christensen, Rosa R ; Batth, Tanveer Singh ; Arrey, Tabiwang N ; Kuehn, Andreas ; Kellmann, Markus ; Olsen, Jesper Velgaard. / Rapid and Deep Proteomes by Faster Sequencing on a Benchtop Quadrupole Ultra-High-Field Orbitrap Mass Spectrometer. In: Journal of Proteome Research. 2014 ; Vol. 13, No. 12. pp. 6187-95.

Bibtex

@article{c278af9c8f53467399f8dceaa8c8d45f,
title = "Rapid and Deep Proteomes by Faster Sequencing on a Benchtop Quadrupole Ultra-High-Field Orbitrap Mass Spectrometer",
abstract = "Shotgun proteomics is a powerful technology for global analysis of proteins and their post-translational modifications. Here, we investigate faster sequencing speed of the latest Q Exactive HF mass spectrometer, which features an ultra-high-field Orbitrap mass analyzer. Proteome coverage is evaluated by four different acquisition methods and benchmarked across three generations of Q Exactive instruments (ProteomeXchange dataset PXD001305). We find the ultra-high-field Orbitrap mass analyzer capable of attaining a sequencing speed above 20 Hz and it routinely exceeds 10 peptide spectrum matches per second or up to 600 new peptides sequenced per gradient minute. We identify 4400 proteins from one microgram of HeLa digest using a one hour gradient, which is an approximately 30% improvement compared to previous instrumentation. In addition, we show very deep proteome coverage can be achieved in less than 24 hours of analysis time by offline high pH reversed-phase peptide fractionation from which we identify more than 140,000 unique peptide sequences. This is comparable to state-of-the-art multi-day, multi-enzyme efforts. Finally the acquisition methods are evaluated for single-shot phosphoproteomics, where we identify 7600 unique HeLa phospho-peptides in one gradient hour and find the quality of fragmentation spectra to be more important than quantity for accurate site assignment.",
author = "Kelstrup, {Christian D} and Jersie-Christensen, {Rosa R} and Batth, {Tanveer Singh} and Arrey, {Tabiwang N} and Andreas Kuehn and Markus Kellmann and Olsen, {Jesper Velgaard}",
year = "2014",
month = oct,
day = "28",
doi = "10.1021/pr500985w",
language = "English",
volume = "13",
pages = "6187--95",
journal = "Journal of Proteome Research",
issn = "1535-3893",
publisher = "American Chemical Society",
number = "12",

}

RIS

TY - JOUR

T1 - Rapid and Deep Proteomes by Faster Sequencing on a Benchtop Quadrupole Ultra-High-Field Orbitrap Mass Spectrometer

AU - Kelstrup, Christian D

AU - Jersie-Christensen, Rosa R

AU - Batth, Tanveer Singh

AU - Arrey, Tabiwang N

AU - Kuehn, Andreas

AU - Kellmann, Markus

AU - Olsen, Jesper Velgaard

PY - 2014/10/28

Y1 - 2014/10/28

N2 - Shotgun proteomics is a powerful technology for global analysis of proteins and their post-translational modifications. Here, we investigate faster sequencing speed of the latest Q Exactive HF mass spectrometer, which features an ultra-high-field Orbitrap mass analyzer. Proteome coverage is evaluated by four different acquisition methods and benchmarked across three generations of Q Exactive instruments (ProteomeXchange dataset PXD001305). We find the ultra-high-field Orbitrap mass analyzer capable of attaining a sequencing speed above 20 Hz and it routinely exceeds 10 peptide spectrum matches per second or up to 600 new peptides sequenced per gradient minute. We identify 4400 proteins from one microgram of HeLa digest using a one hour gradient, which is an approximately 30% improvement compared to previous instrumentation. In addition, we show very deep proteome coverage can be achieved in less than 24 hours of analysis time by offline high pH reversed-phase peptide fractionation from which we identify more than 140,000 unique peptide sequences. This is comparable to state-of-the-art multi-day, multi-enzyme efforts. Finally the acquisition methods are evaluated for single-shot phosphoproteomics, where we identify 7600 unique HeLa phospho-peptides in one gradient hour and find the quality of fragmentation spectra to be more important than quantity for accurate site assignment.

AB - Shotgun proteomics is a powerful technology for global analysis of proteins and their post-translational modifications. Here, we investigate faster sequencing speed of the latest Q Exactive HF mass spectrometer, which features an ultra-high-field Orbitrap mass analyzer. Proteome coverage is evaluated by four different acquisition methods and benchmarked across three generations of Q Exactive instruments (ProteomeXchange dataset PXD001305). We find the ultra-high-field Orbitrap mass analyzer capable of attaining a sequencing speed above 20 Hz and it routinely exceeds 10 peptide spectrum matches per second or up to 600 new peptides sequenced per gradient minute. We identify 4400 proteins from one microgram of HeLa digest using a one hour gradient, which is an approximately 30% improvement compared to previous instrumentation. In addition, we show very deep proteome coverage can be achieved in less than 24 hours of analysis time by offline high pH reversed-phase peptide fractionation from which we identify more than 140,000 unique peptide sequences. This is comparable to state-of-the-art multi-day, multi-enzyme efforts. Finally the acquisition methods are evaluated for single-shot phosphoproteomics, where we identify 7600 unique HeLa phospho-peptides in one gradient hour and find the quality of fragmentation spectra to be more important than quantity for accurate site assignment.

U2 - 10.1021/pr500985w

DO - 10.1021/pr500985w

M3 - Journal article

C2 - 25349961

VL - 13

SP - 6187

EP - 6195

JO - Journal of Proteome Research

JF - Journal of Proteome Research

SN - 1535-3893

IS - 12

ER -

ID: 127245954