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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
Items 301–400 of 529
Efficient CRISPR/Cas9-mediated gene disruption in the tetraploid protist Giardia intestinalis
Horáčková, V., Voleman, L., Hagen, K. D., Petrů, M., Vinopalová, M., Weisz, F., Janowicz, N. E., Marková, L., Motyčková, A., Najdrová, V., et al. (2022) · Open Biology · doi:10.1098/rsob.210361 · Cited by 18
Yang, J., Cheng, Z., Gong, F., & Fu, Y. (2023) · Analytical Chemistry · doi:10.1021/acs.analchem.2c03662 · Cited by 16
Rodríguez-Expósito, R. L., Sifaoui, I., Reyes-Batllé, M., Fuchs, F., Scheid, P. L., Piñero, J. E., Šuťák, R., & Lorenzo‐Morales, J. (2023) · Antioxidants · doi:10.3390/antiox12122081 · Cited by 16
“Perseus 1.6.15.0 software was used to analyze the data [54].”
MethodInfluentialLesur, A., Gallien, S., & Domon, B. (2016) · TrAC Trends in Analytical Chemistry · doi:10.1016/j.trac.2016.01.023 · Cited by 17
STAGE-diging: A novel in-gel digestion processing for proteomics samples
Soffientini, P., & Bachi, A. (2016) · Journal of Proteomics · doi:10.1016/j.jprot.2016.03.038 · Cited by 16
Global Ion Suppression Limits the Potential of Mass Spectrometry Based Phosphoproteomics
Dreier, R. F., Ahrné, E., Brož, P., & Schmidt, A. (2018) · Journal of Proteome Research · doi:10.1021/acs.jproteome.8b00812 · Cited by 16
Makukhin, N., Havelka, V., Poláchová, E., Rampírová, P., Tarallo, V., Stříšovský, K., & Míšek, J. (2019) · FEBS Journal · doi:10.1111/febs.14951 · Cited by 16
Comparative Integrated Omics Analysis of the Hfq Regulon in Bordetella pertussis
Dienstbier, A., Amman, F., Štipl, D., Petráčková, D., & Večerek, B. (2019) · International Journal of Molecular Sciences · doi:10.3390/ijms20123073 · Cited by 16
Porter, C. J., & Bereman, M. S. (2015) · Analytical and Bioanalytical Chemistry · doi:10.1007/s00216-015-8819-7 · Cited by 16
“Although conventional data-dependent-acquisition strategies are extremely powerful for surveying proteomes [2], methods based on independent acquisition offer specific benefits.”
BackgroundMethodRen, J., Zhang, M., Li, T., Zhang, J.-E., Lin, R., Chen, S., Luo, M., & Dong, M. (2016) · PLoS ONE · doi:10.1371/journal.pone.0163500 · Cited by 15
Solis, M. I. V., Giannone, R. J., Hettich, R. L., & Abraham, P. E. (2019) · Analytical Chemistry · doi:10.1021/acs.analchem.9b00819 · Cited by 15
Lombard‐Banek, C., & Schiel, J. E. (2020) · Molecules · doi:10.3390/molecules25061396 · Cited by 16
Kucera, J., Horská, K., Hruška, P., Kuruczová, D., Micale, V., Kučerová, J., & Vašků, J. B. (2020) · Progress in Neuro-Psychopharmacology and Biological Psychiatry · doi:10.1016/j.pnpbp.2020.110165 · Cited by 16
Orsburn, B. C., Jenkins, C., Miller, S. D., Neely, B. A., & Bumpus, N. N. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.03.08.980383 · Cited by 17
Proteome signatures—how are they obtained and what do they teach us?
da Costa, J. P., Carvalhais, V. M. D., Ferreira, R. M., Amado, F. M. L., Vilanova, M., Cerca, N., & Vitorino, R. M. P. (2015) · Applied Microbiology and Biotechnology · doi:10.1007/s00253-015-6795-7 · Cited by 15
Ma, F., Liu, F., Xu, W., & Li, L. (2018) · Journal of Proteome Research · doi:10.1021/acs.jproteome.8b00197 · Cited by 17
Machata, S., Müller, M. M., Lehmann, R., Sieber, P., Panagiotou, G., Carvalho, A., Cunha, C., Lagrou, K., Maertens, J. A., Slevogt, H., et al. (2020) · Virulence · doi:10.1080/21505594.2020.1824960 · Cited by 15
He, Y., Brademan, D. R., Hutchins, P. D., Overmyer, K. A., & Coon, J. J. (2022) · Analytical Chemistry · doi:10.1021/acs.analchem.1c05552 · Cited by 15
Self-citationden Ridder, M., Knibbe, E., van den Brandeler, W., Daran-Lapujade, P. A. S., & Pabst, M. (2022) · Journal of Proteomics · doi:10.1016/j.jprot.2022.104576 · Cited by 15
Tarasova, I. A., Surin, A. K., Fornelli, L., Pridatchenko, M. L., Suvorina, M. Y., & Gorshkov, M. V. (2015) · European Journal of Mass Spectrometry · doi:10.1255/ejms.1356 · Cited by 15
Mm, H., & Khatun, M. S. (2018) · Annals of Proteomics and Bioinformatics · doi:10.29328/journal.apb.1001005 · Cited by 15
Clinical implications of glycoproteomics forAcinetobacter baumannii
Kinsella, R. L., Scott, N. E., & Feldman, M. F. (2014) · Expert Review of Proteomics · doi:10.1586/14789450.2015.987756 · Cited by 15
“The application of these developments within the field of bacterial glycosylation analysis paired with continuous refinement of mass spectrometry instrumentation [15] enables higher quality data to be generated in shorter periods of time, facilitating the characterization of glycosylation within this genus.”
BackgroundMendes, M. L., Borrmann, K. F., & Dittmar, G. A. G. (2024) · Expert Review of Proteomics · doi:10.1080/14789450.2024.2413092 · Cited by 14
“The race to acquire full proteome data has been a driving force for the proteomics field, leading to the routine measurement of full proteomes of smaller, less complex organisms (yeast and different bacteria [40]).”
Sztacho, M., Červenka, J., Šalovská, B., Antiga, L., Hoboth, P., & Hozák, P. (2024) · PLoS Genetics · doi:10.1371/journal.pgen.1011462 · Cited by 16
“The instrument was run in top speed mode with 2 s cycles [65].”
Quantitative physiology and biomass composition of Cyberlindnera jadinii in ethanol-grown cultures
Vieira‐Lara, M. A., Warmerdam, M., de Hulster, E. A. F., van den Broek, M. A., Daran, J.-M. G., & Pronk, J. T. (2024) · Biotechnology for Biofuels and Bioproducts · doi:10.1186/s13068-024-02585-3 · Cited by 14
Zhang, S., Yuan, H., Zhao, B., Zhou, Y., Jiang, H., Zhang, L., Liang, Z., & Zhang, Y. (2015) · The Analyst · doi:10.1039/c5an00887e · Cited by 14
Proteomics: Tools of the Trade
Bose, U., Wijffels, G. L., Howitt, C. A., & Colgrave, M. L. (2019) · Advances in experimental medicine and biology · doi:10.1007/978-3-030-12298-0_1 · Cited by 18
Samperi, R., Capriotti, A. L., Cavaliere, C., Colapicchioni, V., Chiozzi, R. Z., & Laganà, A. (2015) · Comprehensive analytical chemistry · doi:10.1016/b978-0-444-63340-8.00006-6 · Cited by 15
Pellerin, D., Gagnon, H., Dubé, J., & Corbin, F. (2015) · F1000Research · doi:10.12688/f1000research.6529.1 · Cited by 15
Evaluating the use of HILIC in large-scale, multi dimensional proteomics: Horses for courses?
Bensaddek, D., Nicolas, A., & Lamond, A. I. (2015) · International Journal of Mass Spectrometry · doi:10.1016/j.ijms.2015.07.029 · Cited by 17
Perfluorinated alcohol induced coacervates as extraction media for proteomic analysis
McCord, J. P., Muddiman, D. C., & Khaledi, M. G. (2017) · Journal of Chromatography A · doi:10.1016/j.chroma.2017.06.025 · Cited by 14
Giese, S. H., Ishihama, Y., & Rappsilber, J. (2018) · Analytical Chemistry · doi:10.1021/acs.analchem.7b05157 · Cited by 14
Li, B., Guo, F., Hu, H., Liu, P., Tan, M., Pan, J., & Zhai, L. (2019) · Journal of Mass Spectrometry · doi:10.1002/jms.4441 · Cited by 14
Xin, P., Schier, J., Šefrnová, Y., Kulich, I., DUBROVSKY, J. G., Vielle‐Calzada, J., & Soukup, A. (2022) · The Plant Journal · doi:10.1111/tpj.15980 · Cited by 14
Proteomics quality and standard: From a regulatory perspective
Gu, Q., & Yu, L. (2013) · Journal of Proteomics · doi:10.1016/j.jprot.2013.11.024 · Cited by 16
“These technologies were further improved more recently to achieve ultra high resolution, selectivity, sensitivity, and speed of peptide measurement [24-27], which resulted in higher throughput and nearly complete analysis of proteomes [28-31].”
BackgroundHamzeiy, H., & Cox, J. (2016) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2016.11.014 · Cited by 13
The progress and potential of proteomic biomarkers for type 1 diabetes in children
Moulder, R., Bhosale, S. D., Lahesmaa, R., & Goodlett, D. R. (2016) · Expert Review of Proteomics · doi:10.1080/14789450.2017.1265449 · Cited by 13
“having developed to the level that thousands of proteins can be detected per hour [87].”
BackgroundLewandowska, D., Zhang, R., Colas, I., Uzrek, N., & Waugh, R. (2019) · Frontiers in Plant Science · doi:10.3389/fpls.2019.00393 · Cited by 11
“Meiosis occurs over a restricted period of around 48 h in barley with recombination occurring in the earlier stages within the first 12–24 h (Higgins et al., 2012).”
BackgroundAcute and chronic blood serum proteome changes in patients with methanol poisoning
Cejnar, P., Smirnova, T. A., Kučková, Š., Procházka, A., Žák, I., Harant, K., & Zakharov, S. (2022) · Scientific Reports · doi:10.1038/s41598-022-25492-9 · Cited by 13
“The MS2 ion count target was set to 104, and the max injection time was 35 ms 33 .”
Parker, S. J., Raedschelders, K., & Eyk, J. E. V. (2014) · PROTEOMICS · doi:10.1002/pmic.201400448 · Cited by 13
Proteomics of the Roseobacter clade, a window to the marine microbiology landscape
Christie‐Oleza, J. A., & Armengaud, J. (2015) · PROTEOMICS · doi:10.1002/pmic.201500222 · Cited by 13
An optimization of the LC-MS/MS workflow for deep proteome profiling on an Orbitrap Fusion
Nie, L., Zhu, M., Sun, S., Zhai, L., Wu, Z., Qian, L., & Tan, M. (2015) · Analytical Methods · doi:10.1039/c5ay01900a · Cited by 16
Glycoproteins Enrichment and LC-MS/MS Glycoproteomics in Central Nervous System Applications
Zhu, R., Song, E., Hussein, A., Kobeissy, F. H., & Mechref, Y. S. (2017) · Methods in molecular biology · doi:10.1007/978-1-4939-6952-4_9 · Cited by 13
Shen, X., & Sun, L. (2018) · PROTEOMICS · doi:10.1002/pmic.201700432 · Cited by 13
Amine-binding properties of salivary yellow-related proteins in phlebotomine sand flies
Sumová, P., Šíma, M., Kalousková, B., Polanská, N., Vaněk, O., Oliveira, F., Valenzuela, J. G., & Volf, P. (2019) · Insect Biochemistry and Molecular Biology · doi:10.1016/j.ibmb.2019.103245 · Cited by 13
Mixed-Data Acquisition: Next-Generation Quantitative Proteomics Data Acquisition
Santos, M. D. M., Camillo-Andrade, A. C., Kurt, L. U., Clasen, M. A., de Lyra, E. S. B., Gozzo, F. C., Batista, M., Valente, R. H., Brunoro, G. V. F., Barbosa, V. C., et al. (2020) · Journal of Proteomics · doi:10.1016/j.jprot.2020.103803 · Cited by 13
Drastichová, Z., Rudajev, V., Pallag, G., & Novotný, J. (2021) · Biological Research · doi:10.1186/s40659-021-00327-5 · Cited by 12
Shliaha, P. V., Jukes‐Jones, R., Christoforou, A., Fox, J., Hughes, C. J., Langridge, J., Cain, K., & Lilley, K. S. (2014) · Journal of Proteome Research · doi:10.1021/pr500220g · Cited by 14
Quantitative proteomics of model organisms
Feng, Y., Cappelletti, V., & Picotti, P. (2017) · Current Opinion in Systems Biology · doi:10.1016/j.coisb.2017.09.004 · Cited by 12
Peters-Clarke, T. M., Riley, N. M., Westphall, M. S., & Coon, J. J. (2021) · Journal of the American Society for Mass Spectrometry · doi:10.1021/jasms.1c00284 · Cited by 11
Self-citationGökmen‐Polar, Y., True, J. D., Vieth, E., Gu, Y., Gu, X., Qi, G. D., Mosley, A. L., & Badve, S. (2018) · PLoS ONE · doi:10.1371/journal.pone.0204658 · Cited by 12
Vít, O., Patel, M. A., Musil, Z., Hartmann, I., Fryšák, Z., Miettinen, M., Pacák, K., & Petrák, J. (2021) · Molecules · doi:10.3390/molecules26216567 · Cited by 12
Ždralević, M., Longo, V., Guaragnella, N., Giannattasio, S., Timperio, A. M., & Zolla, L. (2015) · Molecular BioSystems · doi:10.1039/c4mb00660g · Cited by 12
Protein turnover measurement using selected reaction monitoring-mass spectrometry (SRM-MS)
Holman, S. W., Hammond, D. E., Simpson, D. M., Waters, J., Hurst, J. L., & Beynon, R. J. (2016) · Philosophical Transactions of the Royal Society A Mathematical Physical and Engineering Sciences · doi:10.1098/rsta.2015.0362 · Cited by 12
Proteomic Profiling of Hsp90 Inhibitors
Voruganti, S., Kline, J. T., Balch, M., Rogers, J., Matts, R. L., & Hartson, S. D. (2017) · Methods in molecular biology · doi:10.1007/978-1-4939-7477-1_11 · Cited by 12
FractionOptimizer: a method for optimal peptide fractionation in bottom-up proteomics
Solovyeva, E. M., Lobas, A. A., Kopylov, A. T., Ilina, I. Y., Levitsky, L. I., Moshkovskii, S. A., & Gorshkov, M. V. (2018) · Analytical and Bioanalytical Chemistry · doi:10.1007/s00216-018-1054-2 · Cited by 12
Proteomic approaches in kidney disease biomarker discovery
Fenton, R. A. (2018) · American Journal of Physiology-Renal Physiology · doi:10.1152/ajprenal.00421.2018 · Cited by 12
“The sensitivity and acquisition speed of modern mass spectrometers (7) make it realistic to profile the whole human proteome (12).”
BackgroundMaximizing Tandem Mass Spectrometry Acquisition Rates for Shotgun Proteomics
Trujillo, E. A., Hebert, A. S., Brademan, D. R., & Coon, J. J. (2019) · Analytical Chemistry · doi:10.1021/acs.analchem.9b02979 · Cited by 12
Self-citationChen, R., Stupak, J., Williamson, S., Twine, S. M., & Li, J. (2019) · Rapid Communications in Mass Spectrometry · doi:10.1002/rcm.8459 · Cited by 12
Four Areas of Engagement Requiring Strengthening in Modern Proteomics Today
Fehniger, T. E., Boja, E. S., Rodriguez, H., Baker, M. S., & Marko‐Varga, G. (2014) · Journal of Proteome Research · doi:10.1021/pr500472d · Cited by 13
Sun, Y., Yang, N., Li, S., Chen, F., Xie, Y., & Tang, C. (2024) · Journal of Experimental Botany · doi:10.1093/jxb/erae100 · Cited by 11
Loss of Wiz Function Affects Methylation Pattern in Palate Development and Leads to Cleft Palate
Buková, I., Szczerkowska, K. I., Procházková, M., Beck, I. M., Procházka, J., & Sedláček, R. (2021) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2021.620692 · Cited by 11
“Several studies have provided insight into the role of Wiz in mice, such as linking Wiz deficiency with behavioral phenotypes and anxiety (Isbel et al., 2016).”
BackgroundCardiovascular proteomics in the era of big data: experimental and computational advances
Lam, M. P. Y., Lau, E., Ng, D. C. M., Wang, D., & Ping, P. (2016) · Clinical Proteomics · doi:10.1186/s12014-016-9124-y · Cited by 11
“Fast-forward to today, a modern mass spectrometer can generate over a million spectra per day and quantify ~4000 proteins in the course of 1 h [2].”
BackgroundVošahlíková, M., Ujčíková, H., Chernyavskiy, O., Brejchová, J., Roubalová, L., Alda, M., & Svoboda, P. (2017) · Biochimica et Biophysica Acta (BBA) - General Subjects · doi:10.1016/j.bbagen.2017.02.011 · Cited by 11
Sulfur Pentafluoride is a Preferred Reagent Cation for Negative Electron Transfer Dissociation
Rush, M. J. P., Riley, N. M., Westphall, M. S., Syka, J. E. P., & Coon, J. J. (2017) · Journal of the American Society for Mass Spectrometry · doi:10.1007/s13361-017-1600-8 · Cited by 11
Self-citationPostnovo: Postprocessing Enables Accurate and FDR-Controlled de Novo Peptide Sequencing
Miller, S. E., Rizzo, A. I., & Waldbauer, J. (2018) · Journal of Proteome Research · doi:10.1021/acs.jproteome.8b00278 · Cited by 11
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 · doi:10.1002/ange.201409075 · Cited by 11
Self-citationManakov, D., Ujčíková, H., Pravenec, M., & Novotný, J. (2016) · Journal of Proteomics · doi:10.1016/j.jprot.2016.04.041 · Cited by 10
“The instrument was run in top speed mode with 2 s cycles [21].”
Affinity Selection from Synthetic Peptide Libraries Enabled by De Novo MS/MS Sequencing
Koh, L. Q., Lim, Y. W., & Gates, Z. P. (2022) · International Journal of Peptide Research and Therapeutics · doi:10.1007/s10989-022-10370-9 · Cited by 11
Label-Free Quantitative Proteomics in Yeast
Léger, T., Garcia, C., Videlier, M., & Camadro, J. (2015) · Methods in molecular biology · doi:10.1007/978-1-4939-3079-1_16 · Cited by 12
Predifferentiated Smooth Muscle-Like Adipose-Derived Stem Cells for Bladder Engineering
Smolar, J., Horst, M., Salemi, S., & Eberli, D. (2020) · Tissue Engineering Part A · doi:10.1089/ten.tea.2019.0216 · Cited by 10
“A modified top speed method (3s cycle time) was used[28].”
RAD51 Inhibition Induces R-Loop Formation in Early G1 Phase of the Cell Cycle
Naščáková, Z., Boleslavska, B., Urban, V., Oravetzova, A., Vlachova, E., Janščák, P., & Dobrovolná, J. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms22073740 · Cited by 10
Comparison of false-discovery rates of various decoy databases
Lee, S., Park, H., & Kim, H. (2021) · Proteome Science · doi:10.1186/s12953-021-00179-7 · Cited by 10
Namane, A., & Saveanu, C. (2022) · Methods in molecular biology · doi:10.1007/978-1-0716-2257-5_13 · Cited by 10
Willen, L., Basáñez, M.-G., Dvořák, V., Veriegh, F. B. D., Aboagye, F. T., Idun, B. K., Osman, M. E., Osei-Atweneboana, M. Y., Courtenay, O., & Volf, P. (2021) · PLoS neglected tropical diseases · doi:10.1371/journal.pntd.0009512 · Cited by 9
“The instrument was run in top speed mode with 2 s cycles [42].”
MethodYang, Y., Su, Y., Wang, X., Gao, W., Lu, X. M., Lam, H., & Tian, R. (2022) · Analytica Chimica Acta · doi:10.1016/j.aca.2022.339615 · Cited by 8
Choi, S. B., Vatan, T., Alexander, T. A., Zhang, C., Mitchell, S. M., Speer, C. M., & Nemes, P. (2023) · Analytical Chemistry · doi:10.1021/acs.analchem.3c01987 · Cited by 9
Tissue Specific Labeling in Proteomics
Ramberger, E., & Dittmar, G. (2017) · Proteomes · doi:10.3390/proteomes5030017 · Cited by 9
“The first comprehensive analysis of the yeast proteome was reported in 2008 [1], and with state-of-the art technology, this benchmark can now be reached with a very limited analysis time of one hour [2].”
BackgroundZhang, Y., Wen, Z., Washburn, M. P., & Florens, L. A. (2019) · Journal of Proteome Research · doi:10.1021/acs.jproteome.9b00036 · Cited by 9
O’Brien, E. T., Wang, Y., Ying, H., & Yue, B. Y. J. T. (2014) · Journal of Ocular Pharmacology and Therapeutics · doi:10.1089/jop.2013.0189 · Cited by 9
“The shortcoming of looking only at the transcription level to infer cell function can now be partially overcome by coupling such experiments with recently greatly improved techniques for identifying the portfolio of expressed proteins and glycoproteins from tissues and cells using mass spectrometry.(69,70) It is hoped…”
BackgroundCharacterization of human pineal gland proteome
Yelamanchi, S. D., Kumar, M., Madugundu, A. K., Gopalakrishnan, L., Dey, G., Chavan, S., Sathe, G. J., Mathur, P. P., Gowda, H., Mahadevan, A., et al. (2016) · Molecular BioSystems · doi:10.1039/c6mb00507a · Cited by 9
Li, Q., Yu, F., Tan, M., & Zhai, L. (2017) · Chinese Journal of Analytical Chemistry · doi:10.1016/s1872-2040(17)60998-8 · Cited by 11
Quantitative Proteomics Data in the Public Domain: Challenges and Opportunities
Jarnuczak, A. F., Ternent, T., & Vizcaíno, J. A. (2019) · Methods in molecular biology · doi:10.1007/978-1-4939-9232-4_14 · Cited by 10
Beeck, J. O. D., Pauwels, J., Landuyt, N. V., Jacobs, P., Malsche, W. D., Desmet, G., Argentini, A., Staes, A., Martens, L., Impens, F., et al. (2018) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/472134 · Cited by 9
Perera, V. R., Lapek, J. D., Newton, G. L., Gonzalez, D. J., & Pogliano, K. (2018) · PLoS ONE · doi:10.1371/journal.pone.0192977 · Cited by 9
Shin, J., Marx, H., Richards, A., Vaneechoutte, D., Jayaraman, D., Maëda, J., Chakraborty, S., Sussman, M. R., Vandepoele, K., Ané, J., et al. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa1041 · Cited by 10
Self-citationMetabolic Remodeling during Nitrogen Fixation in Zymomonas mobilis
Martien, J. I., Trujillo, E. A., Jacobson, T. B., Tatli, M., Hebert, A. S., Stevenson, D. M., Coon, J. J., & Amador‐Noguez, D. (2021) · mSystems · doi:10.1128/msystems.00987-21 · Cited by 7
“LC-MS raw files were converted to mzXML format and visualized using MAVEN (109).”
BackgroundMethodInfluentialSelf-citationFBXO38 Ubiquitin Ligase Controls Centromere Integrity via ZXDA/B Stability
Dibus, N., Kořínek, V., & C̆ermák, L. (2022) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2022.929288 · Cited by 8
“The instrument was run in top speed mode with 2 s cycles (Hebert et al., 2014).”
Refining Transcriptome Gene Catalogs by MS‐Validation of Expressed Proteins
Tse, S. P.-K., Beauchemin, M., Morse, D., & Lo, S. C. (2017) · PROTEOMICS · doi:10.1002/pmic.201700271 · Cited by 8
Dubisova, M., Boháčová, K., Nahácka, Z., Kraus, D., Novák, J., Dvořáková, Š., Brisudová, P., Danesova, N., Selvi, S., Hrysiuk, M., et al. (2025) · Cancer Research · doi:10.1158/0008-5472.can-24-0737 · Cited by 7
“The instrument was run at top speed mode with 2-second cycles (32).”
Identification of Protease Cleavage Sites and Substrates in Cancer by Carboxy-TAILS (C-TAILS)
Solis, N., & Overall, C. M. (2018) · Methods in molecular biology · doi:10.1007/978-1-4939-7595-2_2 · Cited by 7
In-depth structural proteomics integrating mass spectrometry and polyacrylamide gel electrophoresis
Takemori, N., & Takemori, A. (2023) · Frontiers in Analytical Science · doi:10.3389/frans.2022.1107183 · Cited by 8
Vít, O., Talacko, P., Musil, Z., Hartmann, I., Pacák, K., & Petrák, J. (2023) · Clinical Proteomics · doi:10.1186/s12014-023-09428-7 · Cited by 7
“The instrument was run in the top-speed mode with 2 s cycles [11].”
MethodHigh-throughput N-glycoproteomics with fast liquid chromatographic separation
Bi, M., & Tian, Z. (2023) · Analytica Chimica Acta · doi:10.1016/j.aca.2023.342129 · Cited by 7
Novel DNA coding regions and protein arginylation reveal unexplored T. cruzi proteome and PTMs
de Oliveira, G. S., Kawahara, R., Rosa-Fernandes, L., Avila, C. C., Larsen, M. R., Alves, J. M. P., & Palmisano, G. (2016) · International Journal of Mass Spectrometry · doi:10.1016/j.ijms.2016.11.020 · Cited by 7
Proteomics of Eosinophil Activation
Mosher, D. F., Wilkerson, E., Turton, K. B., Hebert, A. S., & Coon, J. J. (2017) · Frontiers in Medicine · doi:10.3389/fmed.2017.00159 · Cited by 7
“For instance, our group is able to quantify nearly 90% of the estimated 4,500 proteins in the yeast proteome in ~1 h of analysis (12, 15).”
BackgroundSelf-citationVít, O., Harant, K., Klener, P., Man, P., & Petrák, J. (2019) · Journal of Proteomics · doi:10.1016/j.jprot.2019.103411 · Cited by 7
Virus systems biology: Proteomics profiling of dynamic protein networks during infection
Klann, K., Tascher, G., & Münch, C. (2021) · Advances in virus research · doi:10.1016/bs.aivir.2020.12.001 · Cited by 7
Chen, J., Wang, F., Liu, Z., Liu, J., Zhu, Y., Zhang, Y., & Zou, H. (2016) · Journal of Chromatography A · doi:10.1016/j.chroma.2016.12.075 · Cited by 7
Petrusová, J., Havalda, R., Flachs, P., Venit, T., Darášová, A., Hůlková, L., Sztacho, M., & Hozák, P. (2022) · Cells · doi:10.3390/cells11132013 · Cited by 6
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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