Improved visualization of protein consensus sequences by iceLogo

A Proteome-wide, Quantitative Survey of In Vivo Ubiquitylation Sites Reveals Widespread Regulatory Roles

Wagner, S. A., Beli, P., Weinert, B. T., Nielsen, M. L., Cox, J., Mann, M., & Choudhary, C. (2011) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m111.013284 · Cited by 889

Calorie restriction and SIRT3 trigger global reprogramming of the mitochondrial protein acetylome

Hebert, A. S., Dittenhafer-Reed, K. E., Yu, W., Bailey, D. J., Selen, E. S., Boersma, M. D., Carson, J. J., Tonelli, M., Balloon, A. J., Higbee, A. J., et al. (2013) · Molecular Cell · doi:10.1016/j.molcel.2012.10.024 · Cited by 636

An Optimized Shotgun Strategy for the Rapid Generation of Comprehensive Human Proteomes

Bekker-Jensen, D. B., Kelstrup, C. D., Batth, T. S., Larsen, S. C., Haldrup, C., Bramsen, J. B., Sørensen, K. D., Høyer, S., Ørntoft, T. F., Andersen, C. L., et al. (2017) · Cell Systems · doi:10.1016/j.cels.2017.05.009 · Cited by 490

Label-free quantitative proteomics of the lysine acetylome in mitochondria identifies substrates of SIRT3 in metabolic pathways

Rardin, M. J., Newman, J. C., Held, J. M., Cusack, M. P., Sorensen, D. J., Li, B., Schilling, B., Mooney, S. D., Kahn, C. R., Verdin, E., et al. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1302961110 · Cited by 445

A molecular basis for the association of the HLA-DRB1 locus, citrullination, and rheumatoid arthritis

Scally, S. W., Petersen, J., Law, S. C., Dudek, N. L., Nel, H. J., Loh, K. L., Wijeyewickrema, L. C., Eckle, S. B. G., van Heemst, J., Pike, R. N., et al. (2013) · Journal of Experimental Medicine · doi:10.1084/jem.20131241 · Cited by 429

Seq2Logo: a method for construction and visualization of amino acid binding motifs and sequence profiles including sequence weighting, pseudo counts and two-sided representation of amino acid enrichment and depletion

Thomsen, M. C. F., & Nielsen, M. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks469 · Cited by 431

Dynamic Adipocyte Phosphoproteome Reveals that Akt Directly Regulates mTORC2

Humphrey, S. J., Yang, G., Yang, P., Fazakerley, D. J., Stöckli, J., Yang, J. Y., & James, D. E. (2013) · Cell Metabolism · doi:10.1016/j.cmet.2013.04.010 · Cited by 411

Multi-omics analyses of the ulcerative colitis gut microbiome link Bacteroides vulgatus proteases with disease severity

Mills, R. H., Dulai, P. S., Vázquez-Baeza, Y., Sauceda, C., Daniel, N., Gerner, R. R., Batachari, L. E., Malfavon, M., Zhu, Q., Weldon, K., et al. (2022) · Nature Microbiology · doi:10.1038/s41564-021-01050-3 · Cited by 385

Site-specific mapping of the human SUMO proteome reveals co-modification with phosphorylation

Hendriks, I. A., Lyon, D., Young, C., Jensen, L. J., Vertegaal, A. C. O., & Nielsen, M. L. (2017) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.3366 · Cited by 382

Large-Scale Quantitative Assessment of Different In-Solution Protein Digestion Protocols Reveals Superior Cleavage Efficiency of Tandem Lys-C/Trypsin Proteolysis over Trypsin Digestion

Glatter, T., Ludwig, C., Ahrné, E., Aebersold, R., Heck, A. J. R., & Schmidt, A. (2012) · Journal of Proteome Research · doi:10.1021/pr300273g · Cited by 364

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

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 326

Proteome-wide analysis of arginine monomethylation reveals widespread occurrence in human cells

Larsen, S. C., Sylvestersen, K. B., Mund, A., Lyon, D., Mullari, M., Madsen, M. V., Daniel, J. A., Jensen, L. J., & Nielsen, M. L. (2016) · Science Signaling · doi:10.1126/scisignal.aaf7329 · Cited by 320

Proteomic Analyses Reveal Divergent Ubiquitylation Site Patterns in Murine Tissues

Wagner, S. A., Beli, P., Weinert, B. T., Schölz, C., Kelstrup, C. D., Young, C., Nielsen, M. L., Olsen, J. V., Brakebusch, C., & Choudhary, C. (2012) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m112.017905 · Cited by 285

HLA-DR15 Molecules Jointly Shape an Autoreactive T Cell Repertoire in Multiple Sclerosis

Wang, J., Jelcic, I., Mühlenbruch, L., Haunerdinger, V., Toussaint, N. C., Zhao, Y., Cruciani, C., Faigle, W., Naghavian, R., Foege, M., et al. (2020) · Cell · doi:10.1016/j.cell.2020.09.054 · Cited by 268

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

Dominant protection from HLA-linked autoimmunity by antigen-specific regulatory T cells

Ooi, J. D., Petersen, J., Tan, Y. H., Huynh, M., Willett, Z. J., Ramarathinam, S. H., Eggenhuizen, P. J., Loh, K. L., Watson, K. A., Gan, P. Y., et al. (2017) · Nature · doi:10.1038/nature22329 · Cited by 218

Active site specificity profiling of the matrix metalloproteinase family: Proteomic identification of 4300 cleavage sites by nine MMPs explored with structural and synthetic peptide cleavage analyses.

Eckhard, U., Huesgen, P. F., Schilling, O., Bellac, C. L., Butler, G. S., Cox, J. H., Dufour, A., Goebeler, V., Kappelhoff, R., Keller, U. A. D., et al. (2016) · Matrix Biology · doi:10.1016/j.matbio.2015.09.003 · Cited by 212

Early Pleistocene enamel proteome from Dmanisi resolves Stephanorhinus phylogeny

Cappellini, E., Welker, F., Pandolfi, L., Ramos-Madrigal, J., Samodova, D., Rüther, P. L., Fotakis, A. K., Lyon, D., Moreno-Mayar, J. V., Bukhsianidze, M., et al. (2019) · Nature · doi:10.1038/s41586-019-1555-y · Cited by 205

A PP2A-B55 recognition signal controls substrate dephosphorylation kinetics during mitotic exit

Cundell, M. J., Hutter, L. H., Nunes Bastos, R., Poser, E., Holder, J., Mohammed, S., Novak, B., & Barr, F. A. (2016) · Journal of Cell Biology · doi:10.1083/jcb.201606033 · Cited by 193

Microbial peptides activate tumour-infiltrating lymphocytes in glioblastoma

Naghavian, R., Faigle, W., Oldrati, P., Wang, J., Toussaint, N. C., Qiu, Y., Medici, G., Wacker, M., Freudenmann, L. K., Bonté, P.-E., et al. (2023) · Nature · doi:10.1038/s41586-023-06081-w · Cited by 163

Multi-omic Profiling Reveals Dynamics of the Phased Progression of Pluripotency

Yang, P., Humphrey, S. J., Cinghu, S., Pathania, R., Oldfield, A. J., Kumar, D., Perera, D., Yang, J. Y. H., James, D. E., Mann, M., et al. (2019) · Cell Systems · doi:10.1016/j.cels.2019.03.012 · Cited by 146

Tripartite degrons confer diversity and specificity on regulated protein degradation in the ubiquitin-proteasome system

Guharoy, M., Bhowmick, P., Sallam, M., & Tompa, P. (2016) · Nature Communications · doi:10.1038/ncomms10239 · Cited by 145

Mechanisms of site‐specific dephosphorylation and kinase opposition imposed by PP2A regulatory subunits

Kruse, T., Gnosa, S. P., Nasa, I., Garvanska, D. H., Hein, J. B., Nguyen, H., Samsøe‐Petersen, J., Lopez‐Mendez, B., Hertz, E. P. T., Schwarz, J., et al. (2020) · The EMBO Journal · doi:10.15252/embj.2019103695 · Cited by 97

Drosophila Sirt2/mammalian SIRT3 deacetylates ATP synthase β and regulates complex V activity

Rahman, M., Nirala, N. K., Singh, A., Zhu, L. J., Taguchi, K., Bamba, T., Fukusaki, E., Shaw, L. M., Lambright, D. G., Acharya, J. K., et al. (2014) · Journal of Cell Biology · doi:10.1083/jcb.201404118 · Cited by 116

SmSP2: A serine protease secreted by the blood fluke pathogen Schistosoma mansoni with anti-hemostatic properties

Leontovyč, A., Ulrychová, L., O’Donoghue, A. J., Vondrášek, J., Marešová, L., Hubálek, M., Fajtová, P., Chanová, M., Jiang, Z., Craik, C. S., et al. (2018) · PLOS Neglected Tropical Diseases · doi:10.1371/journal.pntd.0006446 · Cited by 45

A quantitative and site-specific atlas of the citrullinome reveals widespread existence of citrullination and insights into PADI4 substrates

Rebak, A. S., Hendriks, I. A., Elsborg, J. D., Buch-Larsen, S. C., Nielsen, C. H., Terslev, L., Kirsch, R., Damgaard, D., Doncheva, N. T., Lennartsson, C., et al. (2024) · Nature Structural & Molecular Biology · doi:10.1038/s41594-024-01214-9 · Cited by 45

Proteomic analysis of lysine acetylation provides strong evidence for involvement of acetylated proteins in plant meiosis and tapetum function

Li, X., Ye, J., Ma, H., & Lu, P. (2018) · The Plant Journal · doi:10.1111/tpj.13766 · Cited by 39

Proteins and Proteoforms: New Separation Challenges

Regnier, F. E., & Kim, J. (2018) · Analytical Chemistry · doi:10.1021/acs.analchem.7b05007 · Cited by 36

Mutations in α-synuclein, TDP-43 and tau prolong protein half-life through diminished degradation by lysosomal proteases

Sampognaro, P. J., Arya, S., Knudsen, G. M., Gunderson, E. L., Sandoval-Perez, A., Hodul, M., Bowles, K., Craik, C. S., Jacobson, M. P., & Kao, A. W. (2023) · Molecular Neurodegeneration · doi:10.1186/s13024-023-00621-8 · Cited by 35

Enzymatic debittering of cheese flavoring and bitterness characterization of peptide mixture using sensory and peptidomics approach

Xiang, Q., Xia, Y., Fang, S., & Zhong, F. (2024) · Food Chemistry · doi:10.1016/j.foodchem.2023.138229 · Cited by 34

Exploring the landscape of ectodomain shedding by quantitative protein terminomics

Tsumagari, K., Chang, C.-H., & Ishihama, Y. (2021) · iScience · doi:10.1016/j.isci.2021.102259 · Cited by 24

Chemoproteomic identification of a DPP4 homolog in Bacteroides thetaiotaomicron

Keller, L. J., Nguyen, T. H., Liu, L. J., Hurysz, B. M., Lakemeyer, M., Guerra, M., Gelsinger, D. J., Chanin, R., Ngo, N., Lum, K. M., et al. (2023) · Nature Chemical Biology · doi:10.1038/s41589-023-01357-8 · Cited by 24

Early Pleistocene enamel proteome sequences from Dmanisi resolve Stephanorhinus phylogeny

Cappellini, E., Welker, F., Pandolfi, L., Madrigal, J. R., Fotakis, A. K., Lyon, D., Moreno Mayar, V. J., Bukhsianidze, M., Jersie-Christensen, R. R., Mackie, M., et al. (2018) · doi:10.1101/407692 · Cited by 20

Evolutionary crossroads of cell signaling: PP1 and PP2A substrate sites in intrinsically disordered regions

Hoermann, B., & Köhn, M. (2021) · Biochemical Society Transactions · doi:10.1042/bst20200175 · Cited by 14

Deep learning guided design of protease substrates

Martin-Alonso, C., Alamdari, S., Samad, T. S., Yang, K. K., Bhatia, S. N., & Amini, A. P. (2026) · Nature Communications · doi:10.1038/s41467-025-67226-1 · Cited by 14