Higher-energy C-trap dissociation for peptide modification analysis

Mass spectrometry-based proteomics

Aebersold, R., & Mann, M. (2003) · Nature · doi:10.1038/nature01511 · Cited by 6,955

Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics

Ong, S.-E., Blagoev, B., Kratchmarova, I., Kristensen, D. B., Steen, H., Pandey, A., & Mann, M. (2002) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m200025-mcp200 · Cited by 5,574

Lysine acetylation targets protein complexes and co-regulates major cellular functions

Choudhary, C., Kumar, C., Gnad, F., Nielsen, M. L., Rehman, M., Walther, T. C., Olsen, J. V., & Mann, M. (2009) · Science · doi:10.1126/science.1175371 · Cited by 4,040

Mass-spectrometric exploration of proteome structure and function

Aebersold, R., & Mann, M. (2016) · Nature · doi:10.1038/nature19949 · Cited by 2,334

L-Arginine Modulates T Cell Metabolism and Enhances Survival and Anti-tumor Activity

Geiger, R., Rieckmann, J. C., Wolf, T., Basso, C., Feng, Y., Fuhrer, T., Kogadeeva, M., Picotti, P., Meissner, F., Mann, M., et al. (2016) · Cell · doi:10.1016/j.cell.2016.09.031 · Cited by 1,775

Protein Analysis by Shotgun/Bottom-up Proteomics

Zhang, Y., Fonslow, B. R., Shan, B., Baek, M.-C., & Yates, J. R. (2013) · Chemical Reviews · doi:10.1021/cr3003533 · Cited by 1,491

Proteomics by Mass Spectrometry: Approaches, Advances, and Applications

Yates, J. R., Ruse, C. I., & Nakorchevsky, A. (2009) · Annual Review of Biomedical Engineering · doi:10.1146/annurev-bioeng-061008-124934 · Cited by 1,078

MS3 eliminates ratio distortion in isobaric multiplexed quantitative proteomics

Ting, L., Rad, R., Gygi, S. P., & Haas, W. (2011) · Nature Methods · doi:10.1038/nmeth.1714 · Cited by 1,009

Deep proteome and transcriptome mapping of a human cancer cell line

Nagaraj, N., Wisniewski, J. R., Geiger, T., Cox, J., Kircher, M., Kelso, J., Pääbo, S., & Mann, M. (2011) · Molecular Systems Biology · doi:10.1038/msb.2011.81 · Cited by 979

Mass spectrometry-based proteomics using Q Exactive, a high-performance benchtop quadrupole Orbitrap mass spectrometer

Michalski, A., Damoc, E., Hauschild, J.-P., Lange, O., Wieghaus, A., Makarov, A., Nagaraj, N., Cox, J., Mann, M., & Horning, S. (2011) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m111.011015 · Cited by 832

Quantitative mass spectrometry in proteomics: critical review update from 2007 to the present

Bantscheff, M., Lemeer, S., Savitski, M. M., & Kuster, B. (2012) · Analytical and Bioanalytical Chemistry · doi:10.1007/s00216-012-6203-4 · Cited by 801

Comparative Proteomic Analysis of Eleven Common Cell Lines Reveals Ubiquitous but Varying Expression of Most Proteins

Geiger, T., Wehner, A., Schaab, C., Cox, J., & Mann, M. (2012) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m111.014050 · Cited by 797

Quantitative, High-Resolution Proteomics for Data-Driven Systems Biology

Cox, J., & Mann, M. (2011) · Annual Review of Biochemistry · doi:10.1146/annurev-biochem-061308-093216 · Cited by 685

Targeted Proteomic Quantification on Quadrupole-Orbitrap Mass Spectrometer

Gallien, S., Duriez, E., Crone, C., Kellmann, M., Moehring, T., & Domon, B. (2012) · Molecular & Cellular Proteomics · doi:10.1074/mcp.o112.019802 · Cited by 510

Top Down proteomics: Facts and perspectives

Catherman, A. D., Skinner, O. S., & Kelleher, N. L. (2014) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2014.02.041 · Cited by 507

A dual pressure linear ion trap orbitrap instrument with very high sequencing speed

Olsen, J. V., Schwartz, J. C., Griep-Raming, J., Nielsen, M. L., Damoc, E., Denisov, E., Lange, O., Remes, P., Taylor, D., Splendore, M., et al. (2009) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m900375-mcp200 · Cited by 464

Precision proteomics: The case for high resolution and high mass accuracy

Mann, M., & Kelleher, N. L. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0800788105 · Cited by 450

System-wide perturbation analysis with nearly complete coverage of the yeast proteome by single-shot ultra HPLC runs on a bench top Orbitrap

Nagaraj, N., Alexander Kulak, N., Cox, J., Neuhauser, N., Mayr, K., Hoerning, O., Vorm, O., & Mann, M. (2012) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m111.013722 · Cited by 392

η-Secretase processing of APP inhibits neuronal activity in the hippocampus

Willem, M., Tahirovic, S., Busche, M. A., Ovsepian, S. V., Chafai, M., Kootar, S., Hornburg, D., Evans, L. D. B., Moore, S., Daria, A., et al. (2015) · Nature · doi:10.1038/nature14864 · Cited by 398

Quantitative maps of protein phosphorylation sites across 14 different rat organs and tissues

Lundby, A., Secher, A., Lage, K., Nordsborg, N. B., Dmytriyev, A., Lundby, C., & Olsen, J. V. (2012) · Nature Communications · doi:10.1038/ncomms1871 · Cited by 343

High Recovery FASP Applied to the Proteomic Analysis of Microdissected Formalin Fixed Paraffin Embedded Cancer Tissues Retrieves Known Colon Cancer Markers

Wiśniewski, J. R., Ostasiewicz, P., & Mann, M. (2011) · Journal of Proteome Research · doi:10.1021/pr200019m · Cited by 290

Extensive quantitative remodeling of the proteome between normal colon tissue and adenocarcinoma

Wiśniewski, J. R., Ostasiewicz, P., Duś, K., Zielińska, D. F., Gnad, F., & Mann, M. (2012) · Molecular Systems Biology · doi:10.1038/msb.2012.44 · Cited by 248

Proteome-wide Analysis of Lysine Acetylation Suggests its Broad Regulatory Scope in Saccharomyces cerevisiae

Henriksen, P., Wagner, S. A., Weinert, B. T., Sharma, S., Bačinskaja, G., Rehman, M., Juffer, A. H., Walther, T. C., Lisby, M., & Choudhary, C. (2012) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m112.017251 · Cited by 246

Ultrasensitive and Fast Bottom‐up Analysis of Femtogram Amounts of Complex Proteome Digests

Sun, L., Zhu, G., Zhao, Y., Yan, X., Mou, S., & Dovichi, N. J. (2013) · Angewandte Chemie International Edition · doi:10.1002/anie.201308139 · Cited by 212

Dynamics of ions of intact proteins in the Orbitrap mass analyzer

Makarov, A., & Denisov, E. (2009) · Journal of the American Society for Mass Spectrometry · doi:10.1016/j.jasms.2009.03.024 · Cited by 194

Top-Down Proteomics: Ready for Prime Time?

Chen, B., Brown, K. A., Lin, Z., & Ge, Y. (2018) · Analytical Chemistry · doi:10.1021/acs.analchem.7b04747 · Cited by 210

Proteins in Art, Archaeology, and Paleontology: From Detection to Identification

Dallongeville, S., Garnier, N., Rolando, C., & Tokarski, C. (2016) · Chemical Reviews · doi:10.1021/acs.chemrev.5b00037 · Cited by 172

Mass spectrometry for nutritional peptidomics: how to analyze food bioactives and their health effects.

Panchaud, A., Affolter, M., & Kussmann, M. (2012) · Journal of Proteomics · doi:10.1016/j.jprot.2011.12.022 · Cited by 159

Comprehensive Comparison of iTRAQ and Label-free LC-Based Quantitative Proteomics Approaches Using Two Chlamydomonas reinhardtii Strains of Interest for Biofuels Engineering

Wang, H., Alvarez, S., & Hicks, L. M. (2012) · Journal of Proteome Research · doi:10.1021/pr2008225 · Cited by 142

Systems‐wide analysis of BCR signalosomes and downstream phosphorylation and ubiquitylation

Satpathy, S., Wagner, S. A., Beli, P., Gupta, R., Kristiansen, T. A., Malinova, D., Francavilla, C., Tolar, P., Bishop, G. A., Hostager, B. S., et al. (2015) · Molecular Systems Biology · doi:10.15252/msb.20145880 · Cited by 124

Deep Top-Down Proteomics Using Capillary Zone Electrophoresis-Tandem Mass Spectrometry: Identification of 5700 Proteoforms from the Escherichia coli Proteome

McCool, E. N., Lubeckyj, R. A., Shen, X., Chen, D., Kou, Q., Liu, X., & Sun, L. (2018) · Analytical Chemistry · doi:10.1021/acs.analchem.8b00693 · Cited by 117

Single-Shot Proteomics Using Capillary Zone Electrophoresis–Electrospray Ionization-Tandem Mass Spectrometry with Production of More than 1 250 Escherichia coli Peptide Identifications in a 50 min Separation

Zhu, G., Sun, L., Yan, X., & Dovichi, N. J. (2013) · Analytical Chemistry · doi:10.1021/ac303750g · Cited by 103

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

Advancing Top-down Analysis of the Human Proteome Using a Benchtop Quadrupole-Orbitrap Mass Spectrometer

Fornelli, L., Durbin, K. R., Fellers, R. T., Early, B. P., Greer, J. B., LeDuc, R. D., Compton, P. D., & Kelleher, N. L. (2017) · Journal of Proteome Research · doi:10.1021/acs.jproteome.6b00698 · Cited by 88

A comprehensive pipeline for translational top-down proteomics from a single blood draw

Toby, T. K., Fornelli, L., Srzentić, K., DeHart, C. J., Levitsky, J., Friedewald, J., & Kelleher, N. L. (2019) · Nature Protocols · doi:10.1038/s41596-018-0085-7 · Cited by 86

Native Proteomics in Discovery Mode Using Size-Exclusion Chromatography–Capillary Zone Electrophoresis–Tandem Mass Spectrometry

Shen, X., Kou, Q., Guo, R., Yang, Z., Chen, D., Liu, X., Hong, H., & Sun, L. (2018) · Analytical Chemistry · doi:10.1021/acs.analchem.8b02725 · Cited by 78

Unabridged Analysis of Human Histone H3 by Differential Top-Down Mass Spectrometry Reveals Hypermethylated Proteoforms from MMSET/NSD2 Overexpression

Zheng, Y., Fornelli, L., Compton, P. D., Sharma, S., Canterbury, J., Mullen, C., Zabrouskov, V., Fellers, R. T., Thomas, P. M., Licht, J. D., et al. (2016) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m115.053819 · Cited by 73

pTop 1.0: A High-Accuracy and High-Efficiency Search Engine for Intact Protein Identification

Sun, R.-X., Luo, L., Wu, L., Wang, R.-M., Zeng, W.-F., Chi, H., Liu, C., & He, S.-M. (2016) · Analytical Chemistry · doi:10.1021/acs.analchem.5b03963 · Cited by 71

Annotation of loci from genome-wide association studies using tissue-specific quantitative interaction proteomics

The QT Interval International GWAS Consortium (QT-IGC), Lundby, A., Rossin, E. J., Steffensen, A. B., Acha, M. R., Newton-Cheh, C., Pfeufer, A., Lynch, S. N., Olesen, S.-P., Brunak, S., et al. (2014) · Nature Methods · doi:10.1038/nmeth.2997 · Cited by 71

Proteomics in heart failure: top-down or bottom-up?

Gregorich, Z. R., Chang, Y.-H., & Ge, Y. (2014) · Pflügers Archiv - European Journal of Physiology · doi:10.1007/s00424-014-1471-9 · Cited by 69

Coupling Capillary Zone Electrophoresis with Electron Transfer Dissociation and Activated Ion Electron Transfer Dissociation for Top-Down Proteomics

Zhao, Y., Riley, N. M., Sun, L., Hebert, A. S., Yan, X., Westphall, M. S., Rush, M. J. P., Zhu, G., Champion, M. M., Medie, F. M., et al. (2015) · Analytical Chemistry · doi:10.1021/acs.analchem.5b00883 · Cited by 55

Disruption of nucleocytoplasmic trafficking as a cellular senescence driver.

Park, J.-H., Ryu, S. J., Kim, B. J., Cho, H.-J., Park, C. H., Choi, H. J. C., Jang, E.-J., Yang, E. J., Hwang, J.-A., Woo, S.-H., et al. (2021) · Experimental & Molecular Medicine · doi:10.1038/s12276-021-00643-6 · Cited by 44

PLK1-mediated phosphorylation cascade activates Mis18 complex to ensure centromere inheritance

Parashara, P., Medina-Pritchard, B., Abad, M. A., Sotelo-Parrilla, P., Thamkachy, R., Grundei, D., Zou, J., Spanos, C., Kumar, C. N., Basquin, C., et al. (2024) · Science · doi:10.1126/science.ado8270 · Cited by 36

Substrate specificity of the TRAMP nuclear surveillance complexes

Delan-Forino, C., Spanos, C., Rappsilber, J., & Tollervey, D. (2020) · Nature Communications · doi:10.1038/s41467-020-16965-4 · Cited by 36

Extending the Isotopically Resolved Mass Range of Orbitrap Mass Spectrometers

Shaw, J. B., & Brodbelt, J. S. (2013) · Analytical Chemistry · doi:10.1021/ac401634b · Cited by 28

Large-scale Top-down Proteomics Using Capillary Zone Electrophoresis Tandem Mass Spectrometry

McCool, E. N., Lubeckyj, R., Shen, X., Kou, Q., Liu, X., & Sun, L. (2018) · Journal of Visualized Experiments · doi:10.3791/58644 · Cited by 26

Mapping the invisible chromatin transactions of prophase chromosome remodeling

Samejima, I., Spanos, C., Samejima, K., Rappsilber, J., Kustatscher, G., & Earnshaw, W. C. (2022) · Molecular Cell · doi:10.1016/j.molcel.2021.12.039 · Cited by 21

Proteasome-dependent truncation of the negative heterochromatin regulator Epe1 mediates antifungal resistance

Yaseen, I., White, S. A., Torres-Garcia, S., Spanos, C., Lafos, M., Gaberdiel, E., Yeboah, R., El Karoui, M., Rappsilber, J., Pidoux, A. L., et al. (2022) · Nature Structural & Molecular Biology · doi:10.1038/s41594-022-00801-y · Cited by 20

Proteomic Discovery and Validation of Novel Fluid Biomarkers for Improved Patient Selection and Prediction of Clinical Outcomes in Alzheimer’s Disease Patient Cohorts

(2022) · doi:10.3390/proteomes10030026 · Cited by 20

Nucleosomal asymmetry shapes histone mark binding and promotes poising at bivalent domains

Bryan, E., Valsakumar, D., Idigo, N. J., Warburton, M., Webb, K. M., McLaughlin, K. A., Spanos, C., Lenci, S., Major, V., Ambrosi, C., et al. (2025) · Molecular Cell · doi:10.1016/j.molcel.2024.12.002 · Cited by 16

Molecular mechanism targeting condensin for chromosome condensation

(2024) · doi:10.1038/s44318-024-00336-6 · Cited by 10

Structure of the yeast ceramide synthase

Schäfer, J.-H., Clausmeyer, L., Körner, C., Esch, B. M., Wolf, V. N., Sapia, J., Ahmed, Y., Walter, S., Vanni, S., Januliene, D., et al. (2025) · Nature Structural & Molecular Biology · doi:10.1038/s41594-024-01415-2 · Cited by 10

The kinetoplastid kinetochore protein KKT23 acetyltransferase is a structural homolog of GCN5 that acetylates the histone H2A C-terminal tail

Ludzia, P., Ishii, M., Deák, G., Spanos, C., Wilson, M. D., Redfield, C., & Akiyoshi, B. (2025) · Structure · doi:10.1016/j.str.2024.10.031 · Cited by 6

Differentiation granules, a dynamic regulator of T. brucei development

Cayla, M., Spanos, C., McWilliam, K., Waskett, E., Rappsilber, J., & Matthews, K. R. (2024) · Nature Communications · doi:10.1038/s41467-024-47309-1 · Cited by 5

Fission yeast Caprin protein is required for efficient heterochromatin establishment

Zhang, H., Kapitonova, E., Orrego, A., Spanos, C., Strachan, J., & Bayne, E. H. (2025) · PLOS Genetics · doi:10.1371/journal.pgen.1011620 · Cited by 1

Tetramerisation governs SALL transcription factor function in development and disease

Giuliani, S., Chhatbar, K., Wear, M., Guy, J., Mathieson, T., Burdett, H., George, L., Alston, G., Spanos, C., McHugh, T., et al. (2025) · bioRxiv · doi:10.1101/2025.10.27.684836

Dysfunction of a SET3-like complex underlies a family of related neurological disorders

Paton, K. M., Alexander-Howden, B., Hare, J. I., Guy, J., Chhatbar, K., Yudina, M., Morris, S. T., Walls, R., Mathieson, T., Spanos, C., et al. (2026) · Nature Communications · doi:10.1038/s41467-026-73227-5

Hap2-Ino80 facilitated transcription promotes de novo establishment of CENP-A chromatin

Singh, P. P., Shukla, M., White, S. A., Tong, P., Auchynnikava, T., Spanos, C., Rappsilber, J., Pidoux, A. L., & Allshire, R. C. (2019) · doi:10.1101/778639

Defining the chromatin-associated protein landscapes on Trypanosoma brucei repetitive elements using synthetic TALE proteins

Carloni, R., Devlin, T., Tong, P., Spanos, C., Auchynnikava, T., Rappsilber, J., Matthews, K. R., & Allshire, R. C. (2026) · eLife · doi:10.7554/elife.109950.2