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The One Hour Yeast Proteome
Open accessAbstract
We describe the comprehensive analysis of the yeast proteome in just over one hour of optimized analysis. We achieve this expedited proteome characterization with improved sample preparation, chromatographic separations, and by using a new Orbitrap hybrid mass spectrometer equipped with a mass filter, a collision cell, a high-field Orbitrap analyzer, and, finally, a dual cell linear ion trap analyzer (Q-OT-qIT, Orbitrap Fusion). This system offers high MS(2) acquisition speed of 20 Hz and detects up to 19 peptide sequences within a single second of operation. Over a 1.3 h chromatographic method, the Q-OT-qIT hybrid collected an average of 13,447 MS(1) and 80,460 MS(2) scans (per run) to produce 43,400 (x) peptide spectral matches and 34,255 (x) peptides with unique amino acid sequences (1% false discovery rate (FDR)). On average, each one hour analysis achieved detection of 3,977 proteins (1% FDR). We conclude that further improvements in mass spectrometer scan rate could render comprehensive analysis of the human proteome within a few hours.
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“Currently, benchtop Orbitrap mass spectrometers are the most common instrument for proteomics as they bypass the need for cryogenic cooling (which is needed for the magnets of FTICR instruments) while still offering high-resolution and faster acquisition speeds [98,99].”
From Top-down proteomics: challenges, innovations, and applications in basic and clinical research (2020) · cites this paper as [99]
In the citing paper
“intact protein MS cannot match the analysis throughput typically obtainable through BUP (i.e., thousands of protein families identified in a single experiment).15”
From Proton Transfer Charge Reduction Enables High-Throughput Top-Down Analysis of Large Proteoforms (2019) · cites this paper as [15]
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OMICS – Mass Spectrometry-Based Proteomics in Systems Biology Research
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Quantitative physiology and biomass composition of Cyberlindnera jadinii in ethanol-grown culturesPreprint
Vieira‐Lara, M. A., Warmerdam, M., de Hulster, E. A. F., van den Broek, M. A., Daran, J.-M. G., & Pronk, J. T. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.08.31.610600 · Cited by 1
Kulej, K., Steinberg, A. P., Zhang, J., Casalena, G., Havasov, E., Shah, S. P., McPherson, A., & Kentsis, A. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.08.23.671943 · Cited by 1
The accuracy of statistical confidence estimates in shotgun proteomics
Granholm, V. (2014) · KTH Publication Database DiVA (KTH Royal Institute of Technology)
Kawamura, T. (2016) · Journal of the Mass Spectrometry Society of Japan · doi:10.5702/massspec.s16-16
Development and application of novel proteomics methods in proteomics research
Hao, P. (2015) · DR-NTU (Nanyang Technological University) · doi:10.32657/10356/62181
“The collected fractions were then dried with vacuum centrifuge, pooled into 5 fractions by combining (1-4); (5-6); (7-8); (9-11); (12-18), and redissolved in 3% ACN/0.”
BackgroundMethodgrowing and stationary phase marine bacteria
Muthusamy, S., Lundin, D., Miguel, R., Branca, M., Baltar, F., Lehtiö, J., & Pinhassi, J. (2016)
Characterizing the Termini of Recombinant Proteins
Solis, N., & Overall, C. M. (2017) · Wiley eBooks · doi:10.1002/9781119384434.ch3
A path to the powerhouse: systems‐to‐structure approaches for studying mitochondrial proteins
Pagliarini, D. J. (2018) · Protein Science · doi:10.1002/pro.3430
“As an orthogonal approach, we took advantage of a broader range of MS-based profiling strategies being optimized by our collaborators in the Coon Lab.(12,13) We began with the yeast S.”
MethodGao, Z., Chang, C., Zhu, Y., & Fu, Y. (2018) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/399436
Production of Synthetic Spider Silk
Hekman, R. M. (2018) · Scholarly Commons (University of the Pacific)
Suttapitugsakul, S., Xiao, H., & Wu, R. (2019) · Mass Spectrometry‐Based Chemical Proteomics · doi:10.1002/9781118970195.ch8
Haseeb, M., & Saeed, F. (2021) · arXiv (Cornell University) · doi:10.48550/arxiv.2102.02286
“Millions of raw, noisy spectra can be produced, in a span of few hours, using modern mass spectrometry technologies producing several gigabytes of data [18] (Supplementary Fig.”
BackgroundMICOS and F 1 F O -ATP synthase crosstalk is a fundamental property of mitochondrial cristaePreprint
Cadena, L. R., Gahura, O., Panicucci, B., Zı́ková, A., & Hashimi, H. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.04.01.438160
“Protein preparation and Mass Spectroscopy 420 Triplicate eluates of co-IP proteins were processed for mass spectroscopy analysis as 421 described elsewhere (57, 58).”
MethodDiving into cellular signalling
Leijten, N. M. (2021) · Utrecht University Repository (Utrecht University) · doi:10.33540/622
Gao, A. W., Alam, G. E., Lalou, A., Li, T. Y., Molenaars, M., Zhu, Y., Overmyer, K. A., Shishkova, E., Hof, K., Sleiman, M. S. B., et al. (2021) · SSRN Electronic Journal · doi:10.2139/ssrn.3917209
Self-citationAdvances and Challenges in Bacterial Phosphoproteomics
Prust, N. (2022) · Utrecht University Repository (Utrecht University) · doi:10.33540/878
High‐Performance Liquid Chromatography–Mass Spectrometry in Peptide and Protein Analysis
Shen, T. (2021) · Wiley eBooks · doi:10.1002/9780470027318.a1618.pub4
Kumar, A. (2019) · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature · doi:10.3410/f.735304940.793558138
Hermann, J. (2022) · Research Publications (Maastricht University) · doi:10.26481/dis.20220425jh
“Mass spectrometry analysis detects biological protein processing steps such as post-translational modifications [10-13].”
Background
Metadata
- Authors
- Hebert, A. S., Richards, A. L., Bailey, D. J., Ulbrich, A., Coughlin, E. E., Westphall, M. S., & Coon, J. J.
- Affiliations
- University of Wisconsin–Madison (US)
- Corresponding author
- Coon, Joshua J.
- Venue
- Molecular & Cellular Proteomics
- Publisher
- Elsevier BV
- Published
- 2014-01
- Volume
- 13
- Issue
- 1
- Pages
- 339-347
- ISSN
- 1535-9476 (ISSN-L)
- PMC
- PMC3879625
- OpenAlex
- W1991502938
- Cited by
- 528
- References
- 48
- Citations by year
- 2026: 9 · 2025: 13 · 2024: 18 · 2023: 26 · 2022: 23 · 2021: 47 · 2020: 40 · 2019: 49 · 2018: 44 · 2017: 55 · 2016: 77 · 2015: 60 · 2014: 64
- FWCI
- 30.34
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Molecular & Cellular Proteomics (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Human Genome Research Institute (T32HG002760)
- National Institute of General Medical Sciences (R01GM080148)
- Topics
- Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
- Physical Sciences › Chemistry › Spectroscopy › Mass Spectrometry Techniques and Applications
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Metabolomics and Mass Spectrometry Studies
- Keywords
- yeast proteome, peptide identification, sample preparation optimization, chromatographic separation, human proteome
- MeSH terms
- Amino Acid Sequence, Humans, Molecular Weight, Peptides, Saccharomyces cerevisiae, Proteome, Tandem Mass Spectrometry
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