Cited by 529Advanced Proteomics Techniques and ApplicationsMass Spectrometry Techniques and ApplicationsMetabolomics and Mass Spectrometry Studies

The DOI matches its Crossref record; 48 of the 48 references it cites were found in a registry or an index.

The One Hour Yeast Proteome

Open access

Hebert, Alexander S., Richards, Alicia L., Bailey, Derek J., Ulbrich, Arne, Coughlin, Emma E., Westphall, Michael S., Coon, Joshua J.·2014·Molecular & Cellular Proteomics

DOI 10.1074/mcp.m113.034769PMC PMC3879625

Open this paper in CoChat — free account

Abstract

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.

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

Integrity signals

Registry

Crossref · 10.1074/mcp.m113.034769

Cites

48 of 48 references verified0 citation errors · 0 not checkable

Statistics

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

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).”
Method
Universal 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
An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database
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).”
Background
Evaluation of Multidimensional Chromatography Coupled with Tandem Mass Spectrometry (LC/LC−MS/MS) for Large-Scale Protein Analysis: The Yeast Proteome
Peng, 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

Flagged first, then by citations

Show all 48 references

Sorted by citations

Items 101–200 of 529

Less is More: Membrane Protein Digestion Beyond Urea–Trypsin Solution for Next-level Proteomics
Zhang, X. (2015) · Molecular & Cellular Proteomics · doi:10.1074/mcp.r114.042572 · Cited by 67
Proteomics Standards Initiative at Twenty Years: Current Activities and Future Work
Deutsch, E. W., Vizcaíno, J. A., Jones, A. R., Binz, P., Lam, H., Klein, J., Bittremieux, W., Pérez‐Riverol, Y., Tabb, D. L., Walzer, M., et al. (2023) · Journal of Proteome Research · doi:10.1021/acs.jproteome.2c00637 · Cited by 67
Cell-free DNA in plasma as an essential immune system regulator
Korabečná, M., Zinková, A., Brynychova, I., Chylíková, B., Přikryl, P., Šedová, L., Neužil, P., & Šeda, O. (2020) · Scientific Reports · doi:10.1038/s41598-020-74288-2 · Cited by 64
Bottom-Up Proteomics (2013–2015): Keeping up in the Era of Systems Biology
Mayne, J., Ning, Z., Zhang, X., Starr, A. E., Chen, R., Deeke, S. A., Chiang, C., Xu, B., Wen, M., Cheng, K., et al. (2015) · Analytical Chemistry · doi:10.1021/acs.analchem.5b04230 · Cited by 64
Numerical Compression Schemes for Proteomics Mass Spectrometry Data
Teleman, J., Dowsey, A. W., González-Galarza, F. F., Perkins, S. R., Pratt, B. S., Röst, H. L., Malmström, L., Malmström, J. A., Jones, A. R., Deutsch, E. W., et al. (2014) · Molecular & Cellular Proteomics · doi:10.1074/mcp.o114.037879 · Cited by 62
One minute analysis of 200 histone posttranslational modifications by direct injection mass spectrometryPreprint
Sidoli, S., Kori, Y., Lopes, M. D. C., Yuan, Z., Kim, H. J., Kulej, K., Janssen, K. A., Agosto, L. M., da Cunha, J. P. C., Andrews, A. J., et al. (2019) · Genome Research · doi:10.1101/gr.247353.118 · Cited by 63
“Moreover, the throughput of such analyses has achieved ranges of 1 – 3 h per sample (Hebert et al. 2014), including for the analysis of protein posttranslational modifications (PTMs) like phosphorylation (Humphrey et al. 2018).”
The Negative Mode Proteome with Activated Ion Negative Electron Transfer Dissociation (AI-NETD)
Riley, N. M., Rush, M. J. P., Rose, C. M., Richards, A., Kwiecien, N. W., Bailey, D. J., Hebert, A. S., Westphall, M. S., & Coon, J. J. (2015) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m115.049726 · Cited by 61
Self-citation
Exploring antimicrobial resistance to beta-lactams, aminoglycosides and fluoroquinolones in E. coli and K. pneumoniae using proteogenomics
Foudraine, D. E., Strepis, N., Stingl, C., ten Kate, M. T., Verbon, A., Klaassen, C. H. W., Goessens, W. H. F., Luider, T. M., & Dekker, L. J. M. (2021) · Scientific Reports · doi:10.1038/s41598-021-91905-w · Cited by 60
Secretome of gingival epithelium in response to subgingival biofilms
Bostancı, N., Bao, K., Wåhlander, Å., Grossmann, J., Thurnheer, T., & Belibasakis, G. N. (2015) · Molecular Oral Microbiology · doi:10.1111/omi.12096 · Cited by 60
“With modern mass spectrometry (MS)-based methods, it is now possible to identify and quantify thousands of proteins from complex biological samples (Hebert et al., 2014).”
Background
Proteome-wide quantitative multiplexed profiling of protein expression: carbon-source dependency inSaccharomyces cerevisiae
Paulo, J. A., O’Connell, J. D., Gaun, A., & Gygi, S. P. (2015) · Molecular Biology of the Cell · doi:10.1091/mbc.e15-07-0499 · Cited by 57
“cerevisiae via mass spectrometry–based techniques (King et al., 2006; Nagaraj et al., 2012; Picotti et al., 2013; Webb et al., 2013; Hebert et al., 2014; Paulo and Gygi, 2014).”
Result
Elucidating Proteoform Families from Proteoform Intact-Mass and Lysine-Count Measurements
Shortreed, M. R., Frey, B. L., Scalf, M., Knoener, R. A., Cesnik, A. J., & Smith, L. M. (2016) · Journal of Proteome Research · doi:10.1021/acs.jproteome.5b01090 · Cited by 58
Serum Proteomes Distinguish Children Developing Type 1 Diabetes in a Cohort With HLA-Conferred Susceptibility
Moulder, R., Bhosale, S. D., Erkkilä, T., Laajala, E., Salmi, J., Nguyen, E. V., Kallionpää, H., Mykkänen, J., Vähä-Mäkilä, M., Hyöty, H., et al. (2015) · Diabetes · doi:10.2337/db14-0983 · Cited by 59
“Instrumental improvements (48), alternative fractionation strategies, and data-independent approaches have begun to address this problem (49).”
Background
Tapered-Tip Capillary Electrophoresis Nano-Electrospray Ionization Mass Spectrometry for Ultrasensitive Proteomics: the Mouse Cortex
Choi, S. B., Zamarbide, M., Manzini, M. C., & Nemes, P. (2016) · Journal of the American Society for Mass Spectrometry · doi:10.1007/s13361-016-1532-8 · Cited by 58
Ptc7p Dephosphorylates Select Mitochondrial Proteins to Enhance Metabolic Function
Guo, X. Q., Niemi, N. M., Hutchins, P. D., Condon, S. G. F., Jochem, A., Ulbrich, A., Higbee, A. J., Russell, J. D., Senes, A., Coon, J. J., et al. (2017) · Cell Reports · doi:10.1016/j.celrep.2016.12.049 · Cited by 59
“LC-MS/MS Proteomics Yeast were lysed, digested, and labeled with 8-plex TMTs as previously described (Hebert et al., 2014) with modification.”
Self-citation
Top-Down Characterization of Heavily Modified Histones Using 193 nm Ultraviolet Photodissociation Mass Spectrometry
Greer, S. M., & Brodbelt, J. S. (2018) · Journal of Proteome Research · doi:10.1021/acs.jproteome.7b00801 · Cited by 60
IdentiPy: An Extensible Search Engine for Protein Identification in Shotgun Proteomics
Levitsky, L. I., Ivanov, M. V., Lobas, A. A., Bubis, J. A., Tarasova, I. A., Solovyeva, E. M., Pridatchenko, M. L., & Gorshkov, M. V. (2018) · Journal of Proteome Research · doi:10.1021/acs.jproteome.7b00640 · Cited by 57
DeMix Workflow for Efficient Identification of Cofragmented Peptides in High Resolution Data-dependent Tandem Mass Spectrometry
Zhang, B., Pirmoradian, M., Chernobrovkin, A. L., & Zubarev, R. A. (2014) · Molecular & Cellular Proteomics · doi:10.1074/mcp.o114.038877 · Cited by 57
“But real breakthroughs in MS-based deep proteomics analysis can only come from hardware advances, such as higher acquisition rate (5), sensitivity (44), and mass accuracy (18), as well as better peptide separation (2), ionization (45), fragmentation (38), etc.”
BackgroundMethodInfluential
Cross-linking and other structural proteomics techniques: how chemistry is enabling mass spectrometry applications in structural biology
Leitner, A. (2016) · Chemical Science · doi:10.1039/c5sc04196a · Cited by 55
Multi-omic Mitoprotease Profiling Defines a Role for Oct1p in Coenzyme Q Production
Veling, M. T., Reidenbach, A. G., Freiberger, E. C., Kwiecien, N. W., Hutchins, P. D., Drahnak, M. J., Jochem, A., Ulbrich, A., Rush, M. J. P., Russell, J. D., et al. (2017) · Molecular Cell · doi:10.1016/j.molcel.2017.11.023 · Cited by 57
Self-citation
Proteomics and phosphoproteomics in precision medicine: applications and challenges
Giudice, G., & Petsalaki, E. (2017) · Briefings in Bioinformatics · doi:10.1093/bib/bbx141 · Cited by 56
“[32] were able to measure the entire yeast proteome comprising peptides from 3980 proteins in just over 1 h.”
Islet proteomics reveals genetic variation in dopamine production resulting in altered insulin secretion
Mitok, K. A., Freiberger, E. C., Schueler, K. L., Rabaglia, M. E., Stapleton, D. S., Kwiecien, N. W., Malec, P. A., Hebert, A. S., Broman, A. T., Kennedy, R. T., et al. (2018) · Journal of Biological Chemistry · doi:10.1074/jbc.ra117.001102 · Cited by 61
“However, recent developments in mass spectrometric technologies have improved sensitivity and permit deep profiling of single animals without the need for pooling, prefractionation, or heavy-isotope quantitative tagging (19,44).”
BackgroundSelf-citation
Over 2300 Phosphorylated Peptide Identifications with Single-Shot Capillary Zone Electrophoresis-Tandem Mass Spectrometry in a 100 min Separation
Ludwig, K. R., Sun, L., Zhu, G., Dovichi, N. J., & Hummon, A. B. (2015) · Analytical Chemistry · doi:10.1021/acs.analchem.5b02457 · Cited by 56
Proteomic Atlas of the Human Brain in Alzheimer’s Disease
McKetney, J., Runde, R. M., Hebert, A. S., Salamat, S. M., Roy, S., & Coon, J. J. (2019) · Journal of Proteome Research · doi:10.1021/acs.jproteome.9b00004 · Cited by 54
Self-citation
What are the 100 most cited fungal genera?
Bhunjun, C. S., Chen, Y. J., Phukhamsakda, C., Boekhout, T., Groenewald, J. Z., McKenzi, E. H. C., Francisco, E. C., Frisvad, J. C., Groenewald, M., Hurdeal, V. G., et al. (2024) · Studies in Mycology · doi:10.3114/sim.2024.108.01 · Cited by 58
Evaluation of Data-Dependent and -Independent Mass Spectrometric Workflows for Sensitive Quantification of Proteins and Phosphorylation Sites
Bauer, M., Ahrné, E., Baron, A. P., Glatter, T., Fava, L. L., Santamaría, A., Nigg, E. A., & Schmidt, A. (2014) · Journal of Proteome Research · doi:10.1021/pr500860c · Cited by 57
A Biologist's Field Guide to Multiplexed Quantitative Proteomics
Bakalarski, C. E., & Kirkpatrick, D. S. (2016) · Molecular & Cellular Proteomics · doi:10.1074/mcp.o115.056986 · Cited by 58
“…mixtures, improvements in mass spectrometry instrumentation have brought about dramatic improvements in cataloging the protein constituents of a sample; recent reports have shown the ability to identify the entire yeast proteome in an hour (20) and provided a draft of the human proteome (3, 4).”
Background
Improvement of Quantitative Measurements in Multiplex Proteomics Using High-Field Asymmetric Waveform Spectrometry
Pfammatter, S., Bonneil, É., & Thibault, P. (2016) · Journal of Proteome Research · doi:10.1021/acs.jproteome.6b00745 · Cited by 55
Benchmarking Quantitative Performance in Label-Free Proteomics
Dowell, J. A., Wright, L. J., Armstrong, E. A., & Denu, J. M. (2021) · ACS Omega · doi:10.1021/acsomega.0c04030 · Cited by 58
Anillin propels myosin-independent constriction of actin rings
Kučera, O., Siahaan, V., Janda, D., Dijkstra, S., Pilátová, E., Žatecká, E., Diez, S., Braun, M., & Lánský, Z. (2021) · Nature Communications · doi:10.1038/s41467-021-24474-1 · Cited by 54
Combination of FAIMS, Protein A Depletion, and Native Digest Conditions Enables Deep Proteomic Profiling of Host Cell Proteins in Monoclonal Antibodies
Johnson, R. O., Greer, T., Cejkov, M., Zheng, X., & Li, N. (2020) · Analytical Chemistry · doi:10.1021/acs.analchem.0c01175 · Cited by 55
Distinguishing Sulfotyrosine Containing Peptides from their Phosphotyrosine Counterparts Using Mass Spectrometry
Chen, G., Zhang, Y., Trinidad, J. C., & Dann, C. E. (2018) · Journal of the American Society for Mass Spectrometry · doi:10.1007/s13361-017-1854-1 · Cited by 54
Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses
MacGilvray, M. E., Shishkova, E., Place, M., Wagner, E. R., Coon, J. J., & Gasch, A. P. (2020) · Journal of Proteome Research · doi:10.1021/acs.jproteome.0c00253 · Cited by 53
Self-citation
From the Human Genome to the Human Proteome
Muñoz, J., & Heck, A. J. R. (2014) · Angewandte Chemie International Edition · doi:10.1002/anie.201406545 · Cited by 54
Vitreous humor in the pathologic scope: Insights from proteomic approaches
Monteiro, J. P., Santos, F. M., Rocha, A. S., Sousa, J. P. C., Queiroz, J. A., Passarinha, L. A., & Tomaz, C. T. (2014) · PROTEOMICS - CLINICAL APPLICATIONS · doi:10.1002/prca.201400133 · Cited by 55
Identification of differentially expressed peptides in high-throughput proteomics data
van Ooijen, M. P., Jong, V. L., Eijkemans, M. J. C., Heck, A. J. R., Andeweg, A. C., Binai, N. A., & van den Ham, H. (2017) · Briefings in Bioinformatics · doi:10.1093/bib/bbx031 · Cited by 63
An overview of technologies for MS-based proteomics-centric multi-omics
Rajczewski, A. T., Jagtap, P. D., & Griffin, T. J. (2022) · Expert Review of Proteomics · doi:10.1080/14789450.2022.2070476 · Cited by 57
“performances such as detection of the entire yeast proteome in as little as an hour [56].”
Background
Varroa destructor parasitism has a greater effect on proteome changes than the deformed wing virus and activates TGF-β signaling pathways
Erban, T., Sopko, B., Kadlikova, K., Talacko, P., & Harant, K. (2019) · Scientific Reports · doi:10.1038/s41598-019-45764-1 · Cited by 53
Implementation of Activated Ion Electron Transfer Dissociation on a Quadrupole-Orbitrap-Linear Ion Trap Hybrid Mass Spectrometer
Riley, N. M., Westphall, M. S., Hebert, A. S., & Coon, J. J. (2017) · Analytical Chemistry · doi:10.1021/acs.analchem.7b00213 · Cited by 52
Self-citation
Decoupling Yeast Cell Division and Stress Defense Implicates mRNA Repression in Translational Reallocation during Stress
Ho, Y., Shishkova, E., Hose, J., Coon, J. J., & Gasch, A. P. (2018) · Current Biology · doi:10.1016/j.cub.2018.06.044 · Cited by 50
Self-citation
DeepDigest: Prediction of Protein Proteolytic Digestion with Deep Learning
Yang, J., Gao, Z., Ren, X., Sheng, J., Xu, P., Chang, C., & Fu, Y. (2021) · Analytical Chemistry · doi:10.1021/acs.analchem.0c04704 · Cited by 51
High-Resolution Fourier Transform Ion Cyclotron Resonance Mass Spectrometry with Increased Throughput for Biomolecular Analysis
Nagornov, K. O., Gorshkov, M. V., Kozhinov, A. N., & Tsybin, Y. O. (2014) · Analytical Chemistry · doi:10.1021/ac501579h · Cited by 51
Comprehensive and Scalable Highly Automated MS-Based Proteomic Workflow for Clinical Biomarker Discovery in Human Plasma
Dayon, L., Galindo, A. N., Corthésy, J., Cominetti, O., & Kussmann, M. (2014) · Journal of Proteome Research · doi:10.1021/pr500635f · Cited by 51
A Calibration Routine for Efficient ETD in Large-Scale Proteomics
Rose, C. M., Rush, M. J. P., Riley, N. M., Merrill, A. E., Kwiecien, N. W., Holden, D. D., Mullen, C., Westphall, M. S., & Coon, J. J. (2015) · Journal of the American Society for Mass Spectrometry · doi:10.1007/s13361-015-1183-1 · Cited by 53
Self-citation
Label-Free Protein Quantification for Plant Golgi Protein Localization and Abundance
Nikolovski, N., Shliaha, P. V., Gatto, L., Dupree, P., & Lilley, K. S. (2014) · PLANT PHYSIOLOGY · doi:10.1104/pp.114.245589 · Cited by 51
“Although LC-MS instruments has demonstrated truly remarkable improvements in sensitivity over the recent years it is nonetheless challenging to quantify a proteome comprehensively, due to its large dynamic range of greater than six orders of magnitude (Hebert et al., 2014; Huh et al., 2003).”
Background
Genome Sequence and Analysis of a Stress-Tolerant, Wild-Derived Strain ofSaccharomyces cerevisiaeUsed in Biofuels Research
McIlwain, S. J., Peris, D., Sardi, M. I., Moskvin, O. V., Zhan, F., Myers, K. S., Riley, N. M., Buzzell, A., Parreiras, L. S., Ong, I. M., et al. (2016) · G3 Genes Genomes Genetics · doi:10.1534/g3.116.029389 · Cited by 50
Self-citation
Chronic exposure of bumblebees to neonicotinoid imidacloprid suppresses the entire mevalonate pathway and fatty acid synthesis
Erban, T., Sopko, B., Talacko, P., Harant, K., Kadlikova, K., Halešová, T., Riddellová, K., & Pekas, A. (2018) · Journal of Proteomics · doi:10.1016/j.jprot.2018.12.022 · Cited by 51
The One Hour Human Proteome
Serrano, L. R., Peters-Clarke, T. M., Arrey, T. N., Damoc, E., Robinson, M. L., Lancaster, N. M., Shishkova, E., Moss, C. E., Pashkova, A., Sinitcyn, P. G., et al. (2024) · Molecular & Cellular Proteomics · doi:10.1016/j.mcpro.2024.100760 · Cited by 48
“This system offered tandem mass spectrometry (MS/MS) scan rates of 20 Hz, allowing detection of nearly 4000 proteins after a 70-min liquid chromatography tandem mass spectrometry (LC-MS/MS) experiment (6, 7).”
MethodSelf-citation
Quantitative Proteomics Reveal Distinct Protein Regulations Caused by Aggregatibacter actinomycetemcomitans within Subgingival Biofilms
Bao, K., Bostancı, N., Selevsek, N., Thurnheer, T., & Belibasakis, G. N. (2015) · PLoS ONE · doi:10.1371/journal.pone.0119222 · Cited by 48
“With the utilization of mass spectrometry-based technologies, it is possible to identify and quantify thousands of proteins from complex biological samples in one run [29–32].”
Background
Intelligent Data Acquisition Blends Targeted and Discovery Methods
Bailey, D. J., McDevitt, M. T., Westphall, M. S., Pagliarini, D. J., & Coon, J. J. (2014) · Journal of Proteome Research · doi:10.1021/pr401278j · Cited by 49
Self-citation
DDX17 helicase promotes resolution of R-loop-mediated transcription–replication conflicts in human cells
Boleslavska, B., Oravetzova, A., Shukla, K., Naščáková, Z., Ibini, O., Hašanová, Z., Andrš, M., Kanagaraj, R., Dobrovolná, J., & Janščák, P. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac1116 · Cited by 50
Mass spectrometry methods for predicting antibiotic resistance
Charretier, Y., & Schrenzel, J. (2016) · PROTEOMICS - CLINICAL APPLICATIONS · doi:10.1002/prca.201600041 · Cited by 48
Large-Scale Metabolite Analysis of Standards and Human Serum by Laser Desorption Ionization Mass Spectrometry from Silicon Nanopost Arrays
Korte, A. R., Stopka, S. A., Morris, N. J., Trust T. Razunguzwa, & Vértes, Á. (2016) · Analytical Chemistry · doi:10.1021/acs.analchem.6b01186 · Cited by 46
Analysis of Intrinsic Peptide Detectability via Integrated Label-Free and SRM-Based Absolute Quantitative Proteomics
Jarnuczak, A. F., Lee, D. C. H., Lawless, C., Holman, S. W., Eyers, C. E., & Hubbard, S. J. (2016) · Journal of Proteome Research · doi:10.1021/acs.jproteome.6b00048 · Cited by 43
Algorithms for de-novo sequencing of peptides by tandem mass spectrometry: A review
Ng, C. C. A., Zhou, Y. Z., & Yao, Z. (2023) · Analytica Chimica Acta · doi:10.1016/j.aca.2023.341330 · Cited by 44
Unraveling snake venom complexity with ‘omics’ approaches: Challenges and perspectives
Zelanis, A., & Tashima, A. K. (2014) · Toxicon · doi:10.1016/j.toxicon.2014.05.011 · Cited by 47
Comparative Proteomic Analyses of Avirulent, Virulent, and Clinical Strains of Mycobacterium tuberculosis Identify Strain-specific Patterns
Jhingan, G. D., Kumari, S., Jamwal, S. V., Kalam, H., Arora, D., Jain, N., Kumaar, L. K., Samal, A., Rao, K. V. S., Kumar, D., et al. (2016) · Journal of Biological Chemistry · doi:10.1074/jbc.m115.666123 · Cited by 45
Abundant Lysine Methylation and N-Terminal Acetylation in Sulfolobus islandicus Revealed by Bottom-Up and Top-Down Proteomics
Vorontsov, E. A., Rensen, E., Prangishvili, D. A., Krupovìč, M., & Chamot‐Rooke, J. (2016) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m116.058073 · Cited by 44
ABRF Proteome Informatics Research Group (iPRG) 2015 Study: Detection of Differentially Abundant Proteins in Label-Free Quantitative LC–MS/MS Experiments
Choi, M., DOĞU, Z. F. E., Colangelo, C. M., Cottrell, J. S., Hoopmann, M. R., Kapp, E. A., Kim, S., Lam, H., Neubert, T. A., Palmblad, M., et al. (2016) · Journal of Proteome Research · doi:10.1021/acs.jproteome.6b00881 · Cited by 47
Two serine residues in P seudomonas syringae effector HopZ1a are required for acetyltransferase activity and association with the host co‐factor
Ma, K., Jiang, S., Hawara, E., Lee, D., Pan, S., Coaker, G., Song, J., & Ma, W. (2015) · New Phytologist · doi:10.1111/nph.13528 · Cited by 44
“(2012) and the MS survey scan using data-dependent acquisition (DDA) was described previously (Hebert et al., 2014).”
BackgroundMethod
Comparison of sample preparation techniques for large‐scale proteomics
Kuljanin, M., Dieters‐Castator, D. Z., Hess, D. A., Postovit, L.-M. M., & Lajoie, G. (2016) · PROTEOMICS · doi:10.1002/pmic.201600337 · Cited by 43
OptSSeq explores enzyme expression and function landscapes to maximize isobutanol production rate
Ghosh, I. N., Martien, J. I., Hebert, A. S., Zhang, Y., Coon, J. J., Amador‐Noguez, D., & Landick, R. C. (2018) · Metabolic Engineering · doi:10.1016/j.ymben.2018.12.008 · Cited by 45
Self-citation
Peroxiredoxin 6 protects irradiated cells from oxidative stress and shapes their senescence-associated cytokine landscape
Šalovská, B., Kondelová, A., Pimková, K., Liblova, Z., Přibyl, M., Fabrik, I., Bártek, J., Vajrychová, M., & Hodný, Z. (2021) · Redox Biology · doi:10.1016/j.redox.2021.102212 · Cited by 47
“The instrument was run in a top speed mode with 2 s cycles [66].”
Method
The Value of Activated Ion Electron Transfer Dissociation for High-Throughput Top-Down Characterization of Intact Proteins
Riley, N. M., Sikora, J. W., Seckler, H. S., Greer, J. B., Fellers, R. T., LeDuc, R. D., Westphall, M. S., Thomas, P. M., Kelleher, N. L., & Coon, J. J. (2018) · Analytical Chemistry · doi:10.1021/acs.analchem.8b01638 · Cited by 43
Self-citation
Cross-compartment signal propagation in the mitotic exit network
Zhou, X., Li, W., Liu, Y., & Amon, A. (2021) · eLife · doi:10.7554/elife.63645 · Cited by 45
Generation of Multiple Reporter Ions from a Single Isobaric Reagent Increases Multiplexing Capacity for Quantitative Proteomics
Braun, C. R., Bird, G. H., Wühr, M., Erickson, B. K., Rad, R., Walensky, L. D., Gygi, S. P., & Haas, W. (2015) · Analytical Chemistry · doi:10.1021/acs.analchem.5b02307 · Cited by 43
Proteomics Moves into the Fast Lane
Riley, N. M., Hebert, A. S., & Coon, J. J. (2016) · Cell Systems · doi:10.1016/j.cels.2016.03.002 · Cited by 44
Self-citation
AP3: An Advanced Proteotypic Peptide Predictor for Targeted Proteomics by Incorporating Peptide Digestibility
Gao, Z., Chang, C., Yang, J., Zhu, Y., & Fu, Y. (2019) · Analytical Chemistry · doi:10.1021/acs.analchem.9b02520 · Cited by 43
Set of Novel Automated Quantitative Microproteomics Protocols for Small Sample Amounts and Its Application to Kidney Tissue Substructures
de Graaf, E. L., Pellegrini, D., & McDonnell, L. A. (2016) · Journal of Proteome Research · doi:10.1021/acs.jproteome.6b00889 · Cited by 42
Parasitoid Jewel Wasp Mounts Multipronged Neurochemical Attack to Hijack a Host Brain
Arvidson, R. S., Kaiser, M., Lee, S., Urenda, J., Dail, C., Mohammed, H., Nolan, C., Pan, S., Stajich, J., Libersat, F., et al. (2018) · Molecular & Cellular Proteomics · doi:10.1074/mcp.ra118.000908 · Cited by 42
Microscale Reversed-Phase Liquid Chromatography/Capillary Zone Electrophoresis-Tandem Mass Spectrometry for Deep and Highly Sensitive Bottom–Up Proteomics: Identification of 7500 Proteins with Five Micrograms of an MCF7 Proteome Digest
Yang, Z., Shen, X., Chen, D., & Sun, L. (2018) · Analytical Chemistry · doi:10.1021/acs.analchem.8b02466 · Cited by 43
Rewired cellular signaling coordinates sugar and hypoxic responses for anaerobic xylose fermentation in yeast
Myers, K. S., Riley, N. M., MacGilvray, M. E., Sato, T. K., McGee, M. A., Heilberger, J., Coon, J. J., & Gasch, A. P. (2019) · PLoS Genetics · doi:10.1371/journal.pgen.1008037 · Cited by 43
Self-citation
Architecture and dynamics of overlapped RNA regulatory networks
Lapointe, C. P., Preston, M. A., Wilinski, D., Saunders, H. A. J., Campbell, Z. T., & Wickens, M. (2017) · RNA · doi:10.1261/rna.062687.117 · Cited by 39
“Our data agree with the relative abundances of the endogenous proteins and mRNAs (Hebert et al. 2014; Kulak et al. 2014; Lapointe et al. 2015).”
Result
The proteome under translational control
Fijałkowska, D., Gevaert, K., & Damme, P. V. (2014) · PROTEOMICS · doi:10.1002/pmic.201400165 · Cited by 41
PepExplorer: A Similarity-driven Tool for Analyzing de Novo Sequencing Results
Leprevost, F. D. V., Valente, R. H., Lima, D. B., Perales, J., Melani, R. D., Yates, J. R., Barbosa, V. C., Junqueira, M., & Carvalho, P. C. (2014) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m113.037002 · Cited by 40
“The authors mention events in which they identified up to 19 sequences within less than a second, enabling them to achieve 90% coverage of the yeast proteome in one hour (49).”
Background
Development of a 45kpsi ultrahigh pressure liquid chromatography instrument for gradient separations of peptides using long microcapillary columns and sub-2μm particles
Grinias, K. M., Godinho, J. M., Franklin, E. G., Stobaugh, J. T., & Jorgenson, J. W. (2016) · Journal of Chromatography A · doi:10.1016/j.chroma.2016.09.053 · Cited by 40
“Even with developments including nano-ESI [9–12], ion mobility [13], and programs developed by bioinformaticians to aid in identification [14], the most advanced proteomic workflows still cannot map an entire proteome with a single analysis of even simple organisms such as yeast [15].”
Background
Proteomic analyses of CSF aimed at biomarker development for pediatric brain tumors
Samuel, N., Remke, M., Rutka, J. T., Raught, B., & Malkin, D. M. (2014) · Journal of Neuro-Oncology · doi:10.1007/s11060-014-1432-3 · Cited by 41
Rapid Multi-Omics Sample Preparation for Mass Spectrometry
Muehlbauer, L. K., Jen, A., Zhu, Y., He, Y., Shishkova, E., Overmyer, K. A., & Coon, J. J. (2023) · Analytical Chemistry · doi:10.1021/acs.analchem.2c02042 · Cited by 39
Self-citation
Evaluation of the Orbitrap Ascend Tribrid Mass Spectrometer for Shotgun Proteomics
He, Y., Shishkova, E., Peters-Clarke, T. M., Brademan, D. R., Westphall, M. S., Bergen, D., Huang, J., Huguet, R., Senko, M. W., Zabrouskov, V., et al. (2023) · Analytical Chemistry · doi:10.1021/acs.analchem.3c01155 · Cited by 39
Self-citation
Micro‐proteomics with iterative data analysis: Proteome analysis in C. elegans at the single worm level
Bensaddek, D., Narayan, V., Nicolas, A., Murillo, A. B., Gartner, A., Kenyon, C. J., & Lamond, A. I. (2015) · PROTEOMICS · doi:10.1002/pmic.201500264 · Cited by 39
Salivary proteomics of healthy dogs: An in depth catalog
Torres, S. M., Furrow, E., Souza, C. P., Granick, J., de Jong, E. P., Griffin, T. J., & Wang, X. (2018) · PLoS ONE · doi:10.1371/journal.pone.0191307 · Cited by 37
Global Analysis of Cellular Proteolysis by Selective Enzymatic Labeling of Protein N-Termini
Wiita, A. P., Seaman, J. E., & Wells, J. A. (2014) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/b978-0-12-417158-9.00013-3 · Cited by 38
“In tandem, new highly sensitive mass spectrometers will allow for both more comprehensive substrate identification and potentially label-free quantification with less protein input (Gallien et al., 2012; Hebert et al., 2014; Peterson, Russell, Bailey, Westphall, & Coon, 2012).”
Identification of 7 000–9 000 Proteins from Cell Lines and Tissues by Single-Shot Microflow LC–MS/MS
Bian, Y., The, M., Giansanti, P., Mergner, J., Zheng, R., Wilhelm, M., Boychenko, A., & Küster, B. (2021) · Analytical Chemistry · doi:10.1021/acs.analchem.1c00738 · Cited by 38
Tools for monitoring system suitability in LC MS/MS centric proteomic experiments
Bereman, M. S. (2014) · PROTEOMICS · doi:10.1002/pmic.201400373 · Cited by 36
Comparative proteomics reveals signature metabolisms of exponentially growing and stationary phase marine bacteria
Muthusamy, S., Lundin, D., Branca, R. M., Baltar, F., González, J. M., Lehtiö, J., & Pinhassi, J. (2017) · Environmental Microbiology · doi:10.1111/1462-2920.13725 · Cited by 37
“At the heart of this development has been an increase in the number of detectable proteins (Hebert et al., 2014; Beck et al., 2015), especially apparent for membrane proteins and low abundance proteins (Gilmore and Washburn, 2010).”
Background
Optimization of Search Engines and Postprocessing Approaches to Maximize Peptide and Protein Identification for High-Resolution Mass Data
Tu, C., Sheng, Q., Li, J., Ma, D., Shen, X., Wang, X., Shyr, Y., Yi, Z., & Qu, J. (2015) · Journal of Proteome Research · doi:10.1021/acs.jproteome.5b00536 · Cited by 35
Optimization and Modeling of Quadrupole Orbitrap Parameters for Sensitive Analysis toward Single-Cell Proteomics
Sun, B., Kovatch, J. R., Badiong, A., & Merbouh, N. (2017) · Journal of Proteome Research · doi:10.1021/acs.jproteome.7b00416 · Cited by 36
Beyond Self-Resistance: ABCF ATPase LmrC Is a Signal-Transducing Component of an Antibiotic-Driven Signaling Cascade Accelerating the Onset of Lincomycin Biosynthesis
Koběrská, M., Veselá, L., Vimberg, V., Lenart, J., Vesela, J., Kameník, Z., Janata, J., & Novotna, G. B. (2021) · mBio · doi:10.1128/mbio.01731-21 · Cited by 36
“The instrument was run in the top speed mode with 2-s cycles (69).”
Method
Highly Sensitive Phosphoproteomics by Tailoring Solid-Phase Extraction to Electrostatic Repulsion-Hydrophilic Interaction Chromatography
Loroch, S., Zahedi, R. P., & Sickmann, A. (2014) · Analytical Chemistry · doi:10.1021/ac502708m · Cited by 35
Orthogonal Proteomic Platforms and Their Implications for the Stable Classification of High-Grade Serous Ovarian Cancer Subtypes
Thomas, S. N., Friedrich, B., Schnaubelt, M., Chan, D. W., Zhang, H., & Aebersold, R. H. (2020) · iScience · doi:10.1016/j.isci.2020.101079 · Cited by 34
“Although more rapid proteomic workflows have been developed (Anagnostopoulos et al., 2017; Hebert et al., 2014; Kulak et al., 2014; Richards et al., 2015), they have not yet been deployed for large-scale clinical proteomic studies.”
Pectin lyase enhances cotton resistance to Verticillium wilt by inducing cell apoptosis of Verticillium dahliae
Zhang, J., Yu, X., Zhang, C., Zhang, Q., Sun, Y., Zhu, H., & Tang, C. (2020) · Journal of Hazardous Materials · doi:10.1016/j.jhazmat.2020.124029 · Cited by 34
Proteome-wide Systems Genetics to Identify Functional Regulators of Complex Traits
Molendijk, J., & Parker, B. L. (2021) · Cell Systems · doi:10.1016/j.cels.2020.10.005 · Cited by 35
Depolarization-dependent Induction of Site-specific Changes in Sialylation on N-linked Glycoproteins in Rat Nerve Terminals
Boll, I., Jensen, P., Schwämmle, V., & Larsen, M. R. (2020) · Molecular & Cellular Proteomics · doi:10.1074/mcp.ra119.001896 · Cited by 32
Why proteomics is not the new genomics and the future of mass spectrometry in cell biology
Sidoli, S., Kulej, K., & Garcia, B. A. (2016) · The Journal of Cell Biology · doi:10.1083/jcb.201612010 · Cited by 38
A review of the role of chemical modification methods in contemporary mass spectrometry-based proteomics research
Leitner, A. (2017) · Analytica Chimica Acta · doi:10.1016/j.aca.2017.08.026 · Cited by 34
Survival Following Traumatic Brain Injury in Drosophila Is Increased by Heterozygosity for a Mutation of the NF-κB Innate Immune Response Transcription Factor Relish
Swanson, L. C., Trujillo, E. A., Thiede, G. H., Katzenberger, R. J., Shishkova, E., Coon, J. J., Ganetzky, B., & Wassarman, D. A. (2020) · Genetics · doi:10.1534/genetics.120.303776 · Cited by 32
Self-citation
Limited Proteolysis-Coupled Mass Spectrometry Identifies Phosphatidylinositol 4,5-Bisphosphate Effectors in Human Nuclear Proteome
Sztacho, M., Šalovská, B., Červenka, J., Balaban, C., Hoboth, P., & Hozák, P. (2021) · Cells · doi:10.3390/cells10010068 · Cited by 32
Recent advances in mass spectrometry analysis of neuropeptides
Phetsanthad, A., Vu, N. Q., Yu, Q., Buchberger, A. R., Chen, Z., Keller, C., & Li, L. (2021) · Mass Spectrometry Reviews · doi:10.1002/mas.21734 · Cited by 37
Proteomics of Skeletal Muscle: Focus on Insulin Resistance and Exercise Biology
Deshmukh, A. S. (2016) · Proteomes · doi:10.3390/proteomes4010006 · Cited by 35
Optimized Fragmentation Regime for Diazirine Photo-Cross-Linked Peptides
Giese, S. H., Belsom, A., & Rappsilber, J. (2016) · Analytical Chemistry · doi:10.1021/acs.analchem.6b02082 · Cited by 33
Benefits of Iterative Searches of Large Databases to Interpret Large Human Gut Metaproteomic Data Sets
Bassignani, A., Plancade, S., Berland, M., Blein‐Nicolas, M., Guillot, A., Chevret, D., Moritz, C., Huet, S., Rizkalla, S. W., Clément, K., et al. (2021) · Journal of Proteome Research · doi:10.1021/acs.jproteome.0c00669 · Cited by 32

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.
ORCID: Hebert, Alexander S.
Richards, Alicia L.
Coughlin, Emma E.
Westphall, Michael S.
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)
DOI: 10.1074/mcp.m113.034769
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: cc-by
www.elsevier.com/tdm/userlicense/1.0/ (tdm)
www.elsevier.com/legal/tdmrep-license (tdm)
creativecommons.org/licenses/by/4.0/ (vor, 2460 d)
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

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review

The One Hour Yeast Proteome

Abstract

Overview

Integrity signals

Verification

Claims the paper makes

Claims other papers make about this one

Self-check

Citations

Cites

Cited by

Related

Metadata

Record

About these checks