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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Benchtop Orbitrap mass spectrometers are the most common instrument for proteomics, bypass cryogenic cooling, and offer high resolution and faster acquisition.
“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]
Mass spectrometry of intact proteins cannot achieve the throughput of bottom-up proteomics, which may identify thousands of protein families in one experiment.
“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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The diverse and expanding role of mass spectrometry in structural and molecular biology
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“…of thousands of peptides can be analyzed by combining orthogonal separation meth-ods (e.g., reversed-phase, ion exchange and/or hydrophilic interaction chromatography) with modern mass spectrometers that perform high-speed tandem-MS experiments (see below for more details; Hebert et al , 2014).”
Topf, U., Suppanz, I., Samluk, Ł., Wróbel, L., Böser, A., Sakowska, P., Knapp, B. L., Pietrzyk, M. K., Chacińska, A., & Warscheid, B. (2018) · Nature Communications · doi:10.1038/s41467-017-02694-8 · Cited by 236 · see citing works
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“LC additives such as DMSO [128] and ammonium formate [129], to enhance the LC peak capacity without compromising MS sensitivity, have further improved the separation efficiency of RP, but are yet to be introduced into LC–MS/MS-based glycoproteomics.”
BackgroundMethodGallien, S., Kim, S.-Y., & Domon, B. (2015) · Molecular & Cellular Proteomics · doi:10.1074/mcp.o114.043968 · Cited by 206 · see citing works
Ting, Y. S., Egertson, J. D., Payne, S. H., Kim, S., MacLean, B., Käll, L., Aebersold, R., Smith, R. D., Noble, W. S., & MacCoss, M. J. (2015) · Molecular & Cellular Proteomics · doi:10.1074/mcp.o114.047035 · Cited by 175 · see citing works
Global detection of human variants and isoforms by deep proteome sequencing
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“Near-complete proteomes of simple organisms can be detected by mass spectrometry (MS) following only 1 h of analysis 1,2 .”
BackgroundSelf-citationBeck, S., Michalski, A., Raether, O., Lubeck, M., Kaspar, S., Goedecke, N., Baessmann, C., Hornburg, D., Meier, F., Paron, I., et al. (2015) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m114.047407 · Cited by 176 · see citing works
Metabolic Remodeling during Biofilm Development of Bacillus subtilis
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Self-citationTRIC: an automated alignment strategy for reproducible protein quantification in targeted proteomics
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Loss-less Nano-fractionator for High Sensitivity, High Coverage Proteomics
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“Current mass spectrometers with acquisition rates of approximately 20 Hz enable the detection of 10,000 peptides per hour LC-MS time [222], indicating that owing to technical advances, extensive fractionation might become less and less mandatory.”
BackgroundInteractive Peptide Spectral Annotator: A Versatile Web-based Tool for Proteomic Applications
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Top-down proteomics: challenges, innovations, and applications in basic and clinical research
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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].”
BackgroundMarx, H., Minogue, C. E., Jayaraman, D., Richards, A., Kwiecien, N. W., Siahpirani, A. F., Rajasekar, S., Maëda, J., Garcia, K., Valle-Echevarria, A. R. D., et al. (2016) · Nature Biotechnology · doi:10.1038/nbt.3681 · Cited by 150 · see citing works
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“For the different column and gradient length, the different stationary phases, the DIA methods were adapted to keep data points per peak constant, which also contributed to the differences in identifications in these acquisitions.”
MethodNow, More Than Ever, Proteomics Needs Better Chromatography
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Self-citationLens β-crystallins: The role of deamidation and related modifications in aging and cataract
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“While there have been dramatic improvements in mass spectrometry that have profound implications in studies of deamidation (Hebert et al., 2014; Robinson et al., 2005), the analysis of the resulting data can still be challenging.”
BackgroundSimple and Integrated Spintip-Based Technology Applied for Deep Proteome Profiling
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Mitochondrial protein functions elucidated by multi-omic mass spectrometry profiling
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“LC-MS/MS analyses were performed using previously described methodologies 1, 2 .”
Self-citationLipiDex: An Integrated Software Package for High-Confidence Lipid Identification
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Self-citationA Molecular Portrait of De Novo Genes in Yeasts
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“Other notable improvements are new versions of mass spectrometers with rapid scan rates, high sensitivity and high resolution (Hebert et al., 2014), and revised bioinformatics pipelines for MS data mining (Wang et al., 2014).”
BackgroundFlashPack: Fast and Simple Preparation of Ultrahigh-performance Capillary Columns for LC-MS*
Kovalchuk, S. I., Jensen, O. N., & Rogowska-Wrzesińska, A. (2018) · Molecular & Cellular Proteomics · doi:10.1074/mcp.tir118.000953 · Cited by 119 · see citing works
“separation using a 50 cm length capillary column packed with 2 m sorbent particles allowed profiling of the yeast proteome (~5,000 proteins) in just about one hour [2].”
MethodMaxQuant.Live Enables Global Targeting of More Than 25,000 Peptides
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Decoding the Transcriptional Response to Ischemic Stroke in Young and Aged Mouse Brain
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One-hour proteome analysis in yeast
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Self-citationDefining mitochondrial protein functions through deep multiomic profiling
Rensvold, J. W., Shishkova, E., Sverchkov, Y., Miller, I. J., Çetinkaya, A., Pyle, A., Manicki, M., Brademan, D. R., Alanay, Y., Raiman, J., et al. (2022) · Nature · doi:10.1038/s41586-022-04765-3 · Cited by 113 · see citing works
Self-citationQuantitation and Identification of Thousands of Human Proteoforms below 30 kDa
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NeuCode Labels for Relative Protein Quantification
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Self-citationIon Mobility Tandem Mass Spectrometry Enhances Performance of Bottom-up Proteomics
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The Deep Thioredoxome in Chlamydomonas reinhardtii: New Insights into Redox Regulation
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“Peptides were eluted with gradient of 5–50% B over 70 or 100 minutes for anaerobic and aerobic samples, respectively, followed by a 100% B wash and re-equilibration with 0% B [88].”
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Self-citationConfetti: A Multiprotease Map of the HeLa Proteome for Comprehensive Proteomics
Guo, X., Trudgian, D. C., Lemoff, A. S., Yadavalli, S., & Mirzaei, H. (2014) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m113.035170 · Cited by 103 · see citing works
An Augmented Multiple-Protease-Based Human Phosphopeptide Atlas
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“Immense progress in both mass spectrometric instrumentation (Hebert et al., 2014; Michalski et al., 2011, 2012) and sample preparation and analysis (Di Palma et al.”
BackgroundApplying Label-Free Quantitation to Top Down Proteomics
Ntai, I., Kim, K., Fellers, R. T., Skinner, O. S., Smith, A. D., Early, B. P., Savaryn, J. P., LeDuc, R. D., Thomas, P. M., & Kelleher, N. L. (2014) · Analytical Chemistry · doi:10.1021/ac500395k · Cited by 102 · see citing works
Wang, H., Yang, Y., Li, Y., Bai, B., Wang, X., Tan, H., Liu, T., Beach, T. G., Peng, J., & Wu, Z. (2015) · Journal of Proteome Research · doi:10.1021/pr500882h · Cited by 96 · see citing works
Comprehensive Temporal Protein Dynamics during the Diauxic Shift in Saccharomyces cerevisiae
Murphy, J. P., Stepanova, E., Everley, R. A., Paulo, J. A., & Gygi, S. P. (2015) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m114.045849 · Cited by 94 · see citing works
Proton Transfer Charge Reduction Enables High-Throughput Top-Down Analysis of Large Proteoforms
Huguet, R., Mullen, C., Srzentić, K., Greer, J. B., Fellers, R. T., Zabrouskov, V., Syka, J. E. P., Kelleher, N. L., & Fornelli, L. (2019) · Analytical Chemistry · doi:10.1021/acs.analchem.9b03925 · Cited by 94 · see citing works
Fornelli, L., Durbin, K. R., Fellers, R. T., Early, B. P., Greer, J. B., LeDuc, R. D., Compton, P. D., & Kelleher, N. L. (2017) · Journal of Proteome Research · doi:10.1021/acs.jproteome.6b00698 · Cited by 88 · see citing works
Sun, L., Hebert, A. S., Yan, X., Zhao, Y., Westphall, M. S., Rush, M. J. P., Zhu, G., Champion, M. M., Coon, J. J., & Dovic̀hi, N. J. (2014) · Angewandte Chemie International Edition · doi:10.1002/anie.201409075 · Cited by 91 · see citing works
Self-citationDirect and Absolute Quantification of over 1800 Yeast Proteins via Selected Reaction Monitoring
Lawless, C., Holman, S. W., Brownridge, P., Lanthaler, K., Harman, V. M., Watkins, R. H., Hammond, D. E., Miller, R. L., Sims, P. F. G., Grant, C. M., et al. (2016) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m115.054288 · Cited by 87 · see citing works
“…quantitative data to complete the comprehensive absolute quantification of the yeast proteome to define a gold standard, exploiting the SRM-derived data to calibrate label-free approaches pro-teome-wide (7), a strategy that has shown promise with considerably fewer proteins as calibrants (8, 13).”
Davis, S. A., Charles, P. D., He, L., Mowlds, P., Kessler, B. M., & Fischer, R. (2017) · Journal of Proteome Research · doi:10.1021/acs.jproteome.6b00915 · Cited by 83 · see citing works
“Despite the advent of high-speed mass spectrometers, 7,8 prefractionation of biological samples is still necessary to overcome the dynamic range of protein abundance and to grant the mass spectrometer enough time for comprehensive sampling.”
Shishkova, E., Hebert, A. S., Westphall, M. S., & Coon, J. J. (2018) · Analytical Chemistry · doi:10.1021/acs.analchem.8b02766 · Cited by 90 · see citing works
Self-citationLombard‐Banek, C., Reddy, S., Moody, S. A., & Nemes, P. (2016) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m115.057760 · Cited by 87 · see citing works
The Peripheral Blood Eosinophil Proteome
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Self-citationYang, S., Vera, J. M., Grass, J., Savvakis, G., Moskvin, O. V., Yang, Y., McIlwain, S. J., Lyu, Y., Zinonos, I., Hebert, A. S., et al. (2018) · Biotechnology for Biofuels · doi:10.1186/s13068-018-1116-x · Cited by 85 · see citing works
“Peptides were eluted with in increasing gradient of acetonitrile from 0 to 53% B over 75 min followed by a 5 min 100% B wash and a 10-min equilibration in 0% B [65].”
MethodSelf-citationThe emergence of proteome-wide technologies: systematic analysis of proteins comes of age
Breker, M., & Schuldiner, M. (2014) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm3821 · Cited by 82 · see citing works
Ferries, S., Perkins, S. R., Brownridge, P., Campbell, A. E., Eyers, P. A., Jones, A. R., & Eyers, C. E. (2017) · Journal of Proteome Research · doi:10.1021/acs.jproteome.7b00337 · Cited by 84 · see citing works
Instrumentation at the leading edge of proteomics
Peters-Clarke, T. M., Coon, J., & Riley, N. (2024) · Analytical Chemistry · doi:10.1021/acs.analchem.3c04497 · Cited by 78 · see citing works
Self-citationDickinson, Q., Bottoms, S., Hinchman, L., McIlwain, S. J., Li, S. C., Myers, C. L., Boone, C. M., Coon, J. J., Hebert, A. S., Sato, T. K., et al. (2016) · Microbial Cell Factories · doi:10.1186/s12934-016-0417-7 · Cited by 83 · see citing works
“We grew cells to mid-log with or without 0.25 % [EMIM] Cl and then measured the levels of cellular proteins using high-throughput quantitative proteomics [31].”
InfluentialSelf-citationOpposing roles of nuclear receptor HNF4α isoforms in colitis and colitis-associated colon cancer
Chellappa, K., Deol, P., Evans, J. R., Vuong, L. M., Chen, G., Briançon, N., Bolotin, E., Lytle, C. Y., Nair, M. G., & Sladek, F. M. (2016) · eLife · doi:10.7554/elife.10903 · Cited by 80 · see citing works
“Data were acquired using Orbitrap fusion method (Hebert et al., 2014) with acquisition time set from 1–70 min.”
MethodImproved Precursor Characterization for Data-Dependent Mass Spectrometry
Hebert, A. S., Thöing, C., Riley, N. M., Kwiecien, N. W., Shiskova, E., Huguet, R., Cardasis, H. L., Kuehn, A., Eliuk, S., Zabrouskov, V., et al. (2018) · Analytical Chemistry · doi:10.1021/acs.analchem.7b04808 · Cited by 67 · see citing works
Self-citationQuantitative shotgun proteome analysis by direct infusion
Meyer, J. G., Niemi, N. M., Pagliarini, D. J., & Coon, J. J. (2020) · Nature Methods · doi:10.1038/s41592-020-00999-z · Cited by 73 · see citing works
Self-citationErban, T., Shcherbachenko, E., Talacko, P., & Harant, K. (2019) · Journal of Natural Products · doi:10.1021/acs.jnatprod.8b00968 · Cited by 76 · see citing works
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Benchmarking the Orbitrap Tribrid Eclipse for Next Generation Multiplexed Proteomics
Yu, Q., Paulo, J. A., Navarrete-Perea, J., McAlister, G. C., Canterbury, J. D., Bailey, D. J., Robitaille, A. M., Huguet, R., Zabrouskov, V., Gygi, S. P., et al. (2020) · Analytical Chemistry · doi:10.1021/acs.analchem.9b05685 · Cited by 75 · see citing works
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“02 Da (FT MS/MS)[68].”
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“All separations were performed with a Thermo Dionex Ultimate 3000 RSLC-nano liquid chromatography instrument and an in house fabricated column heater to perform separations at 50 °C (Hebert et al., 2014).”
MethodSelf-citationSimon, O., Klaiber, I., Huber, A., & Pfannstiel, J. (2014) · Journal of Proteomics · doi:10.1016/j.jprot.2014.07.006 · Cited by 72 · see citing works
“[63] Hebert AS, Richards AL, Bailey DJ, Ulbrich A, Coughlin EE, Westphall MS, et al.”
BackgroundRecent advances in capillary ultrahigh pressure liquid chromatography
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Pptc7 is an essential phosphatase for promoting mammalian mitochondrial metabolism and biogenesis
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Chen, D., Shen, X., & Sun, L. (2017) · The Analyst · doi:10.1039/c7an00509a · Cited by 67 · see citing works
- 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 · 2013: 2
- 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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