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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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Citations
Cites
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MethodUniversal sample preparation method for proteome analysis
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“Historically yeast, with its 6600 open reading frames, has been the preferred proteomic technology test-bed (8).”
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Cited by
Sorted by citations
Items 501–529 of 529
Pich-Bavastro, C., Meylan, P., Mastelic-Gavillet, B., Nguyễn, T. N., Loyon, R., Trang, B. K., Moser, H., Moret, C., Goepfert, C., Hafner, J., et al. (2023) · doi:10.1158/0008-5472.22420370
Pich-Bavastro, C., Meylan, P., Mastelic-Gavillet, B., Nguyễn, T. N., Loyon, R., Trang, B. K., Moser, H., Moret, C., Goepfert, C., Hafner, J., et al. (2023) · doi:10.1158/0008-5472.22420370.v1
Quantitative proteomic analysis of super soft kernel texture in soft white spring wheat
Aoun, M., Orenday‐Ortiz, J. M., Brown, K. J., Broeckling, C. D., Morris, C. F., & Kiszonas, A. M. (2023) · PLoS ONE · doi:10.1371/journal.pone.0289784
Mining Mass Spectra for Peptide FactsPreprint
Zumer, J., & Lemieux, S. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.10.27.564468
Pepid: a Highly Modifiable, Bioinformatics-Oriented Peptide Search EnginePreprint
Zumer, J., & Lemieux, S. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.10.30.564469
“The One Hour Yeast Proteome is a dataset of non-synthetic yeast peptides with a baseline generated by the Thermo Fisher version of the SEQUEST search engine [Hebert et al., 2014].”
MethodJiroušková, M., Harant, K., Cejnar, P., Ojha, S., Korelova, K., Sarnová, L., Sticová, E., Mayr, C. H., Schiller, H. B., & Gregor, M. (2025) · eLife · doi:10.7554/elife.98023.3
Marešová, A., Grulyová, M., Hradilová, M., Zemlianski, V., Princová, J., & Převorovský, M. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.03.25.586586
“…were acidified with trifluoroacetic acid (1% final concentration), desalted using in-house stage tips packed with C18 disks (Empore) according to (Rappsilber et al., 2007), and subjected to nano-liquid chromatography coupled to tandem mass spectrometry (nLC-MS2) analysis (Hebert et al., 2014).”
MethodVít, O., Talacko, P., Musil, Z., Hartmann, I., Pacák, K., & Petrák, J. (2023) · Figshare · doi:10.6084/m9.figshare.24196840
Stelate, A., Malínská, K., Tihlaříková, E., Müller, K., Vaculíková, R., Knirsch, M., Vondráková, Z., Vlčák, E., Retzer, K., Neubergerová, M., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.01.23.634346
Exploring chromatographic dimensions for state-of-the-art proteomics applicationsPreprint
Schebesta, A.-S., Korff, K., Itang, E. C. M., Albrecht, V., Geyer, P. E., & Mueller-Reif, J. B. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.08.16.670650
“To our knowledge, this is the first systematic evaluation under Astral DIA conditions, showing that analytical bottlenecks can shift from separation-limited to MS-limited performance, altering optimization priorities compared to those established over decades of method development 23,24 .”
Cytoplasmatic polyadenylation of mRNA by TENT5A is critical for enamel mineralizationPreprint
Novaliches, G. A., Gewartowska, O., Špoutil, F., Mroczek, S., Talacko, P., Harant, K., Augusto-Vale, A.-M., Krejzova, I., Trufen, C. E. M., Krawczyk, P. S., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2025.12.08.692968
Nwaora, H., Yu, Y., & Zhuang, Z. (2025) · PROTEOMICS · doi:10.1002/pmic.70089
“…proteome coverage, from the early report of less than 1500 protein identifications using LCQ ion trap MS [ 3 ], to over 4000 proteins using Orbitrap Tribrid mass spectrometer [ 6 ], and the latest identification of essentially the entire yeast proteome using Orbitrap Astral mass spectrometer [ 9 ].”
Regarding Emitter Positioning for Nanoflow Electrospray IonizationPreprint
Lancaster, N. M., Quarmby, S. T., Overmyer, K. A., & Coon, J. J. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2025.12.18.695161
“12 Experiments were conducted using an Orbitrap Ascend mass spectrometer, which features a nanoflow source and asymmetric inlet capillary (high-capacity transfer tube, HCTT).”
Self-citationDrastichová, Z., Rudajev, V., Pallag, G., & Novotny, J. (2021) · Figshare · doi:10.6084/m9.figshare.13788297
Drastichová, Z., Rudajev, V., Pallag, G., & Novotny, J. (2021) · Figshare · doi:10.6084/m9.figshare.13788318
Drastichová, Z., Rudajev, V., Pallag, G., & Novotny, J. (2021) · Figshare · doi:10.6084/m9.figshare.13788291
Additional file 1 of Comparison of false-discovery rates of various decoy databases
Lee, S., Park, H., & Kim, H. (2021) · Figshare · doi:10.6084/m9.figshare.16640806
Drastichová, Z., Rudajev, V., Pallag, G., & Novotny, J. (2021) · Figshare · doi:10.6084/m9.figshare.13788321
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Drastichová, Z., Rudajev, V., Pallag, G., & Novotny, J. (2021) · Figshare · doi:10.6084/m9.figshare.13788303
Vít, O., Talacko, P., Musil, Z., Hartmann, I., Pacak, K., & Petrak, J. (2023) · Figshare · doi:10.6084/m9.figshare.24196846
Kulej, K., Steinberg, A. P., Zhang, J., Casalena, G., Havasov, E., Shah, S. P., McPherson, A., & Kentsis, A. (2026) · eLife · doi:10.7554/elife.108878
Cytoplasmatic polyadenylation of mRNA by TENT5A is critical for enamel mineralizationPreprint
Novaliches, G. A., Gewartowska, O., Špoutil, F., Mroczek, S., Talacko, P., Harant, K., Augusto-Vale, A.-M., Krejzova, I., Trufen, C. E. M., Krawczyk, P., et al. (2026) · eLife · doi:10.7554/elife.110033
Cytoplasmatic polyadenylation of mRNA by TENT5A is critical for enamel mineralizationPreprint
Novaliches, G. A., Gewartowska, O., Špoutil, F., Mroczek, S., Talacko, P., Harant, K., Augusto-Vale, A.-M., Krejzova, I., Trufen, C. E. M., Krawczyk, P., et al. (2026) · eLife · doi:10.7554/elife.110033.1
Pythoud, N. (2020) · theses.fr (ABES) · doi:10.70675/659636cez02e9z4b19z9e6eze6ece92372f6
Limited Impact of Column Chemistry and Length on Proteome Coverage Under High-Speed DIA
Schebesta, A.-S., Korff, K., Itang, E. C. M., Albrecht, V., Geyer, P. E., & Mueller-Reif, J. B. (2026) · Molecular & Cellular Proteomics · doi:10.1016/j.mcpro.2026.101609 · Cited by 1
“…suggesting that within the range of modern sub-2 μ m stationary phases, the dependence of identification depth on chromatographic parameters is reduced compared to earlier-generation work-flows, though the extent of this effect beyond the materials tested here remains to be established (24, 25).”
Warmerdam, M., Pijman, Y. O., Pedersen, M. P., Wattel, K., Vieira‐Lara, M. A., & Pronk, J. T. (2026) · Applied and Environmental Microbiology · doi:10.1128/aem.00362-26
The mighty microproteins: from versatile cellular regulators to precision medicine therapeutics
Azhar, M., Hassan, F., & Arain, M. A. (2026) · 3 Biotech · doi:10.1007/s13205-026-05054-w
“Some commonly used methods include solid-phase extraction, urea-tricine poly - acrylamide gel electrophoresis (PAGE), acid precipitation, and molecular weight cut-off (MWCO) filtration (Aeber - sold and Mann 2016; Hebert et al. 2014).”
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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