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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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Cites
Quantitative Monitoring of Gene Expression Patterns with a Complementary DNA Microarray
Schena, M., Shalon, D., Davis, R. W., & Brown, P. O. (1995) · Science · doi:10.1126/science.270.5235.467 · Cited by 9,609 · cited 1×
“Owing to cost, speed, and accessibility, transcriptomic analysis is often used as a proteomic proxy (3, 4).”
MethodUniversal sample preparation method for proteome analysis
Wiśniewski, J. R., Zougman, A., Nagaraj, N., & Mann, M. (2009) · Nature Methods · doi:10.1038/nmeth.1322 · Cited by 8,352
Eng, J. K., McCormack, A. L., & Yates, J. R. (1994) · Journal of the American Society for Mass Spectrometry · doi:10.1016/1044-0305(94)80016-2 · Cited by 6,484
Exploring the metabolic and genetic control of gene expression on a genomic scale.
Derisi, J., Iyer, V., & Brown, P. (1997) · Science · doi:10.1126/science.278.5338.680 · Cited by 4,832
Large-scale analysis of the yeast proteome by multidimensional protein identification technology
Washburn, M. P., Wolters, D. A., & Yates, J. R. (2001) · Nature Biotechnology · doi:10.1038/85686 · Cited by 4,768
Correlation between Protein and mRNA Abundance in Yeast
Gygi, S. P., Rochon, Y., Franza, B. R., & Aebersold, R. (1999) · Molecular and Cellular Biology · doi:10.1128/mcb.19.3.1720 · Cited by 3,819
Global analysis of protein expression in yeast
Ghaemmaghami, S., Huh, W.-K., Bower, K., Howson, R. W., Belle, A., Dephoure, N., O'Shea, E. K., & Weissman, J. S. (2003) · Nature · doi:10.1038/nature02046 · Cited by 3,750
Direct analysis of protein complexes using mass spectrometry
Link, A. J., Eng, J. K., Schieltz, D. M., Carmack, E., Mize, G. J., Morris, D. R., Garvik, B. M., & Yates, J. R. (1999) · Nature Biotechnology · doi:10.1038/10890 · Cited by 2,218
Saccharomyces Genome Database: the genomics resource of budding yeast
Cherry, J., Hong, E., Amundsen, C., Balakrishnan, R., Binkley, G., Chan, E. T., Christie, K., Costanzo, M., Dwight, S., Engel, S., et al. (2011) · Nucleic Acids Res. · doi:10.1093/nar/gkr1029 · Cited by 1,886 · cited 1×
“Historically yeast, with its 6600 open reading frames, has been the preferred proteomic technology test-bed (8).”
BackgroundPeng, J., Elias, J. E., Thoreen, C. C., Licklider, L., & Gygi, S. P. (2002) · Journal of Proteome Research · doi:10.1021/pr025556v · Cited by 1,652
Cited by
Sorted by citations
The Perseus computational platform for comprehensive analysis of (prote)omics data
Tyanova, S., Temu, T., Sinitcyn, P., Carlson, A., Hein, M. Y., Geiger, T., Mann, M., & Cox, J. (2016) · Nature Methods · doi:10.1038/nmeth.3901 · Cited by 8,803
Mass-spectrometric exploration of proteome structure and function
Aebersold, R., & Mann, M. (2016) · Nature · doi:10.1038/nature19949 · Cited by 2,334
Ultrasensitive proteome analysis using paramagnetic bead technology
Hughes, C. S., Föehr, S., Garfield, D. A., Furlong, E. E. M., Steinmetz, L. M., & Krijgsveld, J. (2014) · Molecular Systems Biology · doi:10.15252/msb.20145625 · Cited by 1,226
Collins, B. C., Hunter, C. L., Liu, Y., Schilling, B., Rosenberger, G., Bader, S. L., Chan, D. W., Gibson, B. W., Gingras, A.-C., Held, J. M., et al. (2017) · Nature Communications · doi:10.1038/s41467-017-00249-5 · Cited by 576
Protein Phosphorylation: A Major Switch Mechanism for Metabolic Regulation
Humphrey, S. J., James, D. E., & Mann, M. (2015) · Trends in Endocrinology and Metabolism · doi:10.1016/j.tem.2015.09.013 · Cited by 574
Bruderer, R., Bernhardt, O. M., Gandhi, T., Xuan, Y., Sondermann, J. R., Schmidt, M., Gómez‐Varela, D., & Reiter, L. (2017) · Molecular & Cellular Proteomics · doi:10.1074/mcp.ra117.000314 · Cited by 493
MS Amanda, a Universal Identification Algorithm Optimized for High Accuracy Tandem Mass Spectra
Dorfer, V., Pichler, P., Stranzl, T., Stadlmann, J., Taus, T., Winkler, S., & Mechtler, K. (2014) · Journal of Proteome Research · doi:10.1021/pr500202e · Cited by 485
An Optimized Shotgun Strategy for the Rapid Generation of Comprehensive Human Proteomes
Bekker‐Jensen, D. B., Kelstrup, C. D., Batth, T. S., Buch-Larsen, S. C., Haldrup, C., Bramsen, J. B., Sørensen, K. D., Høyer, S., Orntoft, T. F., Andersen, C. L., et al. (2017) · Cell Systems · doi:10.1016/j.cels.2017.05.009 · Cited by 480
“While it required a week of total mass spectrometry (MS) instrument time to obtain this original data, the complete yeast proteome can now be analyzed a hundred times faster, in 1.8 hr (Hebert et al., 2014).”
InfluentialDe novo peptide sequencing by deep learning
Tran, N. H., Zhang, X., Xin, L., Shan, B., & Li, M. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1705691114 · Cited by 451
A Scalable Approach for Protein False Discovery Rate Estimation in Large Proteomic Data Sets
Savitski, M. M., Wilhelm, M., Hahne, H., Küster, B., & Bantscheff, M. (2015) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m114.046995 · Cited by 441
Challenges and emergent solutions for LC‐MS/MS based untargeted metabolomics in diseases
Liang, C., Lu, H., & Lee, Y. H. (2018) · Mass Spectrometry Reviews · doi:10.1002/mas.21562 · Cited by 429
Multidimensional proteomics for cell biology
Larance, M., & Lamond, A. I. (2015) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm3970 · Cited by 420
Guzmán, U. H., Martínez‐Val, A., Ye, Z., Damoc, E., Arrey, T. N., Pashkova, A., Renuse, S., Denisov, E. V., Petzoldt, J., Peterson, A. C., et al. (2024) · Nature Biotechnology · doi:10.1038/s41587-023-02099-7 · Cited by 405
“The first complete proteome of a eukaryotic organism analyzed by MS was that of yeast 22 , and with state-of-the-art instrumentation it was possible to cover ~4,000 yeast proteins in approximately 1 h of LC–MS/MS time 23 .”
Tsiatsiani, L., & Heck, A. J. R. (2015) · FEBS Journal · doi:10.1111/febs.13287 · Cited by 353
A Single Kinase Generates the Majority of the Secreted Phosphoproteome
Tagliabracci, V. S., Wiley, S. E., Guo, X. Q., Kinch, L. N., Durrant, E. S., Wen, J., Xiao, J., Cui, J., Nguyen, K. B., Engel, J. D., et al. (2015) · Cell · doi:10.1016/j.cell.2015.05.028 · Cited by 347
Self-citationIlluminating the dark phosphoproteome
Needham, E. J., Parker, B. L., Burykin, T., James, D. E., & Humphrey, S. J. (2019) · Science Signaling · doi:10.1126/scisignal.aau8645 · Cited by 336
“Arguably, this shift is already underway, with deep proteome measurements now able to measure nearly all proteins in model organisms (22, 23) and well over 10,000 proteins in single human cell lines (24–27).”
BackgroundLian, J., Mishra, S., & Zhao, H. (2018) · Metabolic Engineering · doi:10.1016/j.ymben.2018.04.011 · Cited by 342
Off-Line High-pH Reversed-Phase Fractionation for In-Depth Phosphoproteomics
Batth, T. S., Francavilla, C., & Olsen, J. V. (2014) · Journal of Proteome Research · doi:10.1021/pr500893m · Cited by 328
Zhang, Z., Wu, S., Stenoien, D. L., & Paša‐Tolić, L. (2014) · Annual Review of Analytical Chemistry · doi:10.1146/annurev-anchem-071213-020216 · Cited by 336
Ultra-fast proteomics with Scanning SWATH
Messner, C. B., Demichev, V., Bloomfield, N., Yu, J., White, M. E. H., Kreidl, M., Egger, A.-S., Freiwald, A., Ivosev, G., Wasim, F., et al. (2021) · Nature Biotechnology · doi:10.1038/s41587-021-00860-4 · Cited by 314
Parallel reaction monitoring using quadrupole‐Orbitrap mass spectrometer: Principle and applications
Bourmaud, A., Gallien, S., & Domon, B. (2016) · PROTEOMICS · doi:10.1002/pmic.201500543 · Cited by 324
Animal board invited review: advances in proteomics for animal and food sciences
de Almeida, A. M., Bassols, A., Bendixen, E., Bhide, M. R., Ceciliani, F., Cristóbal, S., Eckersall, P. D., Hollung, K., Lisacek, F., Mazzucchelli, G., et al. (2014) · animal · doi:10.1017/s1751731114002602 · Cited by 302
“%) per analysis hour covering 4 to 6 orders of protein abundance (Hebert et al., 2014).”
BackgroundFeist, P. E., & Hummon, A. B. (2015) · International Journal of Molecular Sciences · doi:10.3390/ijms16023537 · Cited by 306
Integrated analysis of shotgun proteomic data with PatternLab for proteomics 4.0
Carvalho, P. C., Lima, D. B., Leprevost, F. D. V., Santos, M. D. M., Fischer, J. D. S. D. G., de Aquino, P. F., Moresco, J. J., Yates, J. R., & Barbosa, V. C. (2015) · Nature Protocols · doi:10.1038/nprot.2015.133 · Cited by 280
“Shotgun proteomics has revolutionized biochemical and bio-medical research by enabling the identification and quantification of thousands of proteins in complex biological samples such as organelles, cell lysates, biological fluids and tissues 1 .”
BackgroundComprehensive Single-Shot Proteomics with FAIMS on a Hybrid Orbitrap Mass Spectrometer
Hebert, A. S., Prasad, S., Belford, M. W., Bailey, D. J., McAlister, G. C., Abbatiello, S. E., Huguet, R., Wouters, E. R., Dunyach, J., Brademan, D. R., et al. (2018) · Analytical Chemistry · doi:10.1021/acs.analchem.8b02233 · Cited by 278
Self-citationMALDI imaging mass spectrometry: Spatial molecular analysis to enable a new age of discovery
Gessel, M. M., Norris, J. L., & Caprioli, R. M. (2014) · Journal of Proteomics · doi:10.1016/j.jprot.2014.03.021 · Cited by 280
“[3] Hebert AS, Richards AL, Bailey DJ, Ulbrich A, Coughlin EE, Westphall MS, et al.”
BackgroundMass Spectrometry-Based Detection and Assignment of Protein Posttranslational Modifications
Doll, S., & Burlingame, A. L. (2014) · ACS Chemical Biology · doi:10.1021/cb500904b · Cited by 266
Phosphoproteomics in the Age of Rapid and Deep Proteome Profiling
Riley, N. M., & Coon, J. J. (2016) · Analytical Chemistry · doi:10.1021/acs.analchem.5b04123 · Cited by 265
Self-citationIon Activation Methods for Peptides and Proteins
Brodbelt, J. S. (2015) · Analytical Chemistry · doi:10.1021/acs.analchem.5b04563 · Cited by 259
Senko, M. W., Remes, P. M., Canterbury, J. D., Mathur, R., Song, Q., Eliuk, S. M., Mullen, C., Earley, L., Hardman, M., Blethrow, J. D., et al. (2013) · Analytical Chemistry · doi:10.1021/ac403115c · Cited by 243
The diverse and expanding role of mass spectrometry in structural and molecular biology
Lössl, P., van de Waterbeemd, M., & Heck, A. J. (2016) · The EMBO Journal · doi:10.15252/embj.201694818 · Cited by 222
“…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 246
Lombard‐Banek, C., Moody, S. A., & Nemes, P. (2016) · Angewandte Chemie International Edition · doi:10.1002/anie.201510411 · Cited by 214
Paulo, J. A., O’Connell, J. D., Everley, R. A., O’Brien, J. J., Gygi, M. A., & Gygi, S. P. (2016) · Journal of Proteomics · doi:10.1016/j.jprot.2016.07.005 · Cited by 203
Thaysen‐Andersen, M., & Packer, N. H. (2014) · Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics · doi:10.1016/j.bbapap.2014.05.002 · Cited by 207
“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 213
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
Global detection of human variants and isoforms by deep proteome sequencing
Sinitcyn, P. G., Richards, A., Weatheritt, R. J., Brademan, D. R., Marx, H., Shishkova, E., Meyer, J. G., Hebert, A. S., Westphall, M. S., Blencowe, B. J., et al. (2023) · Nature Biotechnology · doi:10.1038/s41587-023-01714-x · Cited by 193
“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 181
Metabolic Remodeling during Biofilm Development of Bacillus subtilis
Pisithkul, T., Schroeder, J. W., Trujillo, E. A., Yeesin, P., Stevenson, D. M., Chaiamarit, T., Coon, J. J., Wang, J. D., & Amador‐Noguez, D. (2019) · mBio · doi:10.1128/mbio.00623-19 · Cited by 171
Self-citationTRIC: an automated alignment strategy for reproducible protein quantification in targeted proteomics
Röst, H. L., Liu, Y., D’Agostino, G. A., Zanella, M., Navarro, P., Rosenberger, G., Collins, B. C., Gillet, L. C. J., Testa, G., Malmström, L., et al. (2016) · Nature Methods · doi:10.1038/nmeth.3954 · Cited by 166
Loss-less Nano-fractionator for High Sensitivity, High Coverage Proteomics
Kulak, N. A., Geyer, P. E., & Mann, M. (2017) · Molecular & Cellular Proteomics · doi:10.1074/mcp.o116.065136 · Cited by 173
Kelstrup, C. D., Jersie-Christensen, R., Batth, T. S., Arrey, T. N., Kuehn, A., Kellmann, M., & Olsen, J. V. (2014) · Journal of Proteome Research · doi:10.1021/pr500985w · Cited by 173
Pagel, O., Loroch, S., Sickmann, A., & Zahedi, R. P. (2015) · Expert Review of Proteomics · doi:10.1586/14789450.2015.1042867 · Cited by 163
“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
Brademan, D. R., Riley, N. M., Kwiecien, N. W., & Coon, J. J. (2019) · Molecular & Cellular Proteomics · doi:10.1074/mcp.tir118.001209 · Cited by 164
Self-citationMuntel, J., Gandhi, T., Verbeke, L., Bernhardt, O. M., Treiber, T., Bruderer, R., & Reiter, L. (2019) · Molecular Omics · doi:10.1039/c9mo00082h · Cited by 164
Top-down proteomics: challenges, innovations, and applications in basic and clinical research
Brown, K. A., Melby, J. A., Roberts, D. S., & Ge, Y. (2020) · Expert Review of Proteomics · doi:10.1080/14789450.2020.1855982 · Cited by 152
“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 153
Self-citationBruderer, R., Bernhardt, O. M., Gandhi, T., & Reiter, L. (2016) · PROTEOMICS · doi:10.1002/pmic.201500488 · Cited by 141
“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
Shishkova, E., Hebert, A. S., & Coon, J. J. (2016) · Cell Systems · doi:10.1016/j.cels.2016.10.007 · Cited by 145
Self-citationLens β-crystallins: The role of deamidation and related modifications in aging and cataract
Lampi, K. J., Wilmarth, P. A., Murray, M. R., & David, L. L. (2014) · Progress in Biophysics and Molecular Biology · doi:10.1016/j.pbiomolbio.2014.02.004 · Cited by 138
“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
Chen, W., Wang, S., Adhikari, S., Deng, Z., Wang, L., Chen, L., Ke, M., Yang, P., & Tian, R. (2016) · Analytical Chemistry · doi:10.1021/acs.analchem.6b00631 · Cited by 138
Mitochondrial protein functions elucidated by multi-omic mass spectrometry profiling
Stefely, J. A., Kwiecien, N. W., Freiberger, E. C., Richards, A., Jochem, A., Rush, M. J. P., Ulbrich, A., Robinson, K. P., Hutchins, P. D., Veling, M. T., et al. (2016) · Nature Biotechnology · doi:10.1038/nbt.3683 · Cited by 133
“LC-MS/MS analyses were performed using previously described methodologies 1, 2 .”
Self-citationLipiDex: An Integrated Software Package for High-Confidence Lipid Identification
Hutchins, P. D., Russell, J. D., & Coon, J. J. (2018) · Cell Systems · doi:10.1016/j.cels.2018.03.011 · Cited by 133
Self-citationA Molecular Portrait of De Novo Genes in Yeasts
Vakirlis, N., Hebert, A. S., Opulente, D. A., Achaz, G., Hittinger, C. T., Fischer, G., Coon, J. J., & Lafontaine, I. (2017) · Molecular Biology and Evolution · doi:10.1093/molbev/msx315 · Cited by 126
Self-citationRuprecht, B., Koch, H., Médard, G., Mundt, M., Küster, B., & Lemeer, S. (2014) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m114.043109 · Cited by 132
Bai, B., Tan, H., Pagala, V., High, A. A., Ichhaporia, V. P., Hendershot, L. M., & Peng, J. (2016) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/bs.mie.2016.10.007 · Cited by 119
“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
“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
Wichmann, C., Meier, F., Winter, S. V., Brunner, A., Cox, J., & Mann, M. (2019) · Molecular & Cellular Proteomics · doi:10.1074/mcp.tir118.001131 · Cited by 119
Decoding the Transcriptional Response to Ischemic Stroke in Young and Aged Mouse Brain
Androvic, P., Kirdajova, D., Tureckova, J., Zucha, D., Rohlova, E., Abaffy, P., Kriska, J., Valny, M., Anderova, M., Kubista, M., et al. (2020) · Cell Reports · doi:10.1016/j.celrep.2020.107777 · Cited by 118
One-hour proteome analysis in yeast
Richards, A., Hebert, A. S., Ulbrich, A., Bailey, D. J., Coughlin, E. E., Westphall, M. S., & Coon, J. J. (2015) · Nature Protocols · doi:10.1038/nprot.2015.040 · Cited by 122
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 106
Self-citationQuantitation and Identification of Thousands of Human Proteoforms below 30 kDa
Durbin, K. R., Fornelli, L., Fellers, R. T., Doubleday, P. F., Narita, M., & Kelleher, N. L. (2016) · Journal of Proteome Research · doi:10.1021/acs.jproteome.5b00997 · Cited by 111
NeuCode Labels for Relative Protein Quantification
Merrill, A. E., Hebert, A. S., MacGilvray, M. E., Rose, C. M., Bailey, D. J., Bradley, J. C., Wood, W. W., Masri, M. E., Westphall, M. S., Gasch, A. P., et al. (2014) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m114.040287 · Cited by 111
Self-citationIon Mobility Tandem Mass Spectrometry Enhances Performance of Bottom-up Proteomics
Helm, D., Vissers, J. P. C., Hughes, C. J., Hahne, H., Ruprecht, B., Pachl, F., Grzyb, A., Richardson, K., Wildgoose, J. L., Maier, S. K., et al. (2014) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m114.041038 · Cited by 111
The Deep Thioredoxome in Chlamydomonas reinhardtii: New Insights into Redox Regulation
Pérez‐Pérez, M. E., Mauriès, A., Maes, A., Tourasse, N. J., Hamon, M., Lemaire, S. D., & Marchand, C. H. (2017) · Molecular Plant · doi:10.1016/j.molp.2017.07.009 · Cited by 110
Sato, T. K., Tremaine, M. T., Parreiras, L. S., Hebert, A. S., Myers, K. S., Higbee, A. J., Sardi, M. I., McIlwain, S. J., Ong, I. M., Breuer, R. J., et al. (2016) · PLoS Genetics · doi:10.1371/journal.pgen.1006372 · Cited by 107
“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].”
Self-citationRichards, A., Merrill, A. E., & Coon, J. J. (2014) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2014.10.017 · Cited by 106
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 105
An Augmented Multiple-Protease-Based Human Phosphopeptide Atlas
Giansanti, P., Aye, T. T., van den Toorn, H., Peng, M., van Breukelen, B., & Heck, A. J. R. (2015) · Cell Reports · doi:10.1016/j.celrep.2015.05.029 · Cited by 105
“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 104
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
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
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
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
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 89
“…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
“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 84
Self-citationFornelli, 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
Lombard‐Banek, C., Reddy, S., Moody, S. A., & Nemes, P. (2016) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m115.057760 · Cited by 87
The Peripheral Blood Eosinophil Proteome
Wilkerson, E., Johansson, M. W., Hebert, A. S., Westphall, M. S., Mathur, S. K., Jarjour, N. N., Schwantes, E. A., Mosher, D. F., & Coon, J. J. (2016) · Journal of Proteome Research · doi:10.1021/acs.jproteome.6b00006 · Cited by 88
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 84
“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 85
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
Instrumentation at the Leading Edge of Proteomics
Peters-Clarke, T. M., Coon, J. J., & Riley, N. M. (2024) · Analytical Chemistry · doi:10.1021/acs.analchem.3c04497 · Cited by 89
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
“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 84
“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
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 77
Self-citationErban, T., Shcherbachenko, E., Talacko, P., & Harant, K. (2019) · Journal of Natural Products · doi:10.1021/acs.jnatprod.8b00968 · Cited by 80
Amorim, F. G., Costa, T. R., Baiwir, D., Pauw, E. D., Quinton, L., & Sampaio, S. V. (2018) · Toxins · doi:10.3390/toxins10050177 · Cited by 82
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 74
Self-citationMondal, A., Potts, G. K., Dawson, A. R., Coon, J. J., & Mehle, A. (2015) · PLoS Pathogens · doi:10.1371/journal.ppat.1004826 · Cited by 77
“02 Da (FT MS/MS)[68].”
Self-citationShen, X., Shen, S., Li, J., Hu, Q., Nie, L., Tu, C., Wang, X., Orsburn, B. C., Wang, J., & Qu, J. (2017) · Journal of Proteome Research · doi:10.1021/acs.jproteome.7b00061 · Cited by 73
Reidenbach, A. G., Kemmerer, Z. A., Aydın, D., Jochem, A., McDevitt, M. T., Hutchins, P. D., Stark, J. L., Stefely, J. A., Reddy, T. R., Hebert, A. S., et al. (2017) · Cell chemical biology · doi:10.1016/j.chembiol.2017.11.001 · Cited by 74
“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
“[63] Hebert AS, Richards AL, Bailey DJ, Ulbrich A, Coughlin EE, Westphall MS, et al.”
BackgroundRecent advances in capillary ultrahigh pressure liquid chromatography
Blue, L. E., Franklin, E. G., Godinho, J. M., Grinias, J. P., Grinias, K. M., Lunn, D. B., & Moore, S. (2017) · Journal of Chromatography A · doi:10.1016/j.chroma.2017.05.039 · Cited by 73
Pptc7 is an essential phosphatase for promoting mammalian mitochondrial metabolism and biogenesis
Niemi, N. M., Wilson, G. M., Overmyer, K. A., Vögtle, F. ‐., Myketin, L., Lohman, D. C., Schueler, K. L., Attie, A., Meisinger, C., Coon, J. J., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-11047-6 · Cited by 71
Self-citationWilliamson, J. C., Edwards, A. V. G., Verano‐Braga, T., Schwämmle, V., Kjeldsen, F., Jensen, O. N., & Larsen, M. R. (2016) · PROTEOMICS · doi:10.1002/pmic.201400545 · Cited by 69
Chen, D., Shen, X., & Sun, L. (2017) · The Analyst · doi:10.1039/c7an00509a · Cited by 67
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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