The PRIDE database and related tools and resources in 2019: improving support for quantification data

The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences

Perez-Riverol, Y., Bai, J., Bandla, C., García-Seisdedos, D., Hewapathirana, S., Kamatchinathan, S., Kundu, D. J., Prakash, A., Frericks-Zipper, A., Eisenacher, M., et al. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkab1038 · Cited by 6,125

Metabolic regulation of gene expression by histone lactylation

Zhang, D., Tang, Z., Huang, H., Zhou, G., Cui, C., Weng, Y., Liu, W., Kim, S., Lee, S., Perez-Neut, M., et al. (2019) · Nature · doi:10.1038/s41586-019-1678-1 · Cited by 4,371

GENCODE 2021

Frankish, A., Diekhans, M., Jungreis, I., Lagarde, J., Loveland, J. E., Mudge, J. M., Sisu, C., Wright, J. C., Armstrong, J., Barnes, I., et al. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkaa1087 · Cited by 1,334

Proteomics of SARS-CoV-2-infected host cells reveals therapy targets

Bojkova, D., Klann, K., Koch, B., Widera, M., Krause, D., Ciesek, S., Cinatl, J., & Münch, C. (2020) · Nature · doi:10.1038/s41586-020-2332-7 · Cited by 1,010

Specificities of exosome versus small ectosome secretion revealed by live intracellular tracking of CD63 and CD9

Mathieu, M., Névo, N., Jouve, M., Valenzuela, J. I., Maurin, M., Verweij, F. J., Palmulli, R., Lankar, D., Dingli, F., Loew, D., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-24384-2 · Cited by 910

Obesity Shapes Metabolism in the Tumor Microenvironment to Suppress Anti-Tumor Immunity

Ringel, A. E., Drijvers, J. M., Baker, G. J., Catozzi, A., García-Cañaveras, J. C., Gassaway, B. M., Miller, B. C., Juneja, V. R., Nguyen, T. H., Joshi, S., et al. (2020) · Cell · doi:10.1016/j.cell.2020.11.009 · Cited by 780

Cardioids reveal self-organizing principles of human cardiogenesis

Hofbauer, P., Jahnel, S. M., Papai, N., Giesshammer, M., Deyett, A., Schmidt, C., Penc, M., Tavernini, K., Grdseloff, N., Meledeth, C., et al. (2021) · Cell · doi:10.1016/j.cell.2021.04.034 · Cited by 588

Deep Visual Proteomics defines single-cell identity and heterogeneity

Mund, A., Coscia, F., Kriston, A., Hollandi, R., Kovács, F., Brunner, A.-D., Migh, E., Schweizer, L., Santos, A., Bzorek, M., et al. (2022) · Nature Biotechnology · doi:10.1038/s41587-022-01302-5 · Cited by 562

Ultra-High-Throughput Clinical Proteomics Reveals Classifiers of COVID-19 Infection

Messner, C. B., Demichev, V., Wendisch, D., Michalick, L., White, M., Freiwald, A., Textoris-Taube, K., Vernardis, S. I., Egger, A.-S., Kreidl, M., et al. (2020) · Cell Systems · doi:10.1016/j.cels.2020.05.012 · Cited by 561

Formation of a protein corona on the surface of extracellular vesicles in blood plasma

Tóth, E. Á., Turiák, L., Visnovitz, T., Cserép, C., Mázló, A., Sódar, B. W., Försönits, A. I., Petővári, G., Sebestyén, A., Komlósi, Z., et al. (2021) · Journal of Extracellular Vesicles · doi:10.1002/jev2.12140 · Cited by 522

Exercise plasma boosts memory and dampens brain inflammation via clusterin

De Miguel, Z., Khoury, N., Betley, M. J., Lehallier, B., Willoughby, D., Olsson, N., Yang, A. C., Hahn, O., Lu, N., Vest, R. T., et al. (2021) · Nature · doi:10.1038/s41586-021-04183-x · Cited by 422

Tau molecular diversity contributes to clinical heterogeneity in Alzheimer’s disease

Dujardin, S., Commins, C., Lathuiliere, A., Beerepoot, P., Fernandes, A. R., Kamath, T. V., De Los Santos, M. B., Klickstein, N., Corjuc, D. L., Corjuc, B. T., et al. (2020) · Nature Medicine · doi:10.1038/s41591-020-0938-9 · Cited by 438

Microfluidic device with brain extracellular matrix promotes structural and functional maturation of human brain organoids

Cho, A.-N., Jin, Y., An, Y., Kim, J., Choi, Y. S., Lee, J. S., Kim, J., Choi, W.-Y., Koo, D.-J., Yu, W., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-24775-5 · Cited by 397

A blood atlas of COVID-19 defines hallmarks of disease severity and specificity

Ahern, D. J., Ai, Z., Ainsworth, M., Allan, C., Allcock, A., Angus, B., Ansari, M. A., Arancibia-Cárcamo, C. V., Aschenbrenner, D., Attar, M., et al. (2022) · Cell · doi:10.1016/j.cell.2022.01.012 · Cited by 328

Morphological, cellular and molecular basis of brain infection in COVID-19 patients

Crunfli, F., Carregari, V. C., Veras, F. P., Vendramini, P. H., Valença, A. G. F., Antunes, A. S. L. M., Brandão-Teles, C., da Silva Zuccoli, G., Reis-de-Oliveira, G., Silva-Costa, L. C., et al. (2020) · doi:10.1101/2020.10.09.20207464 · Cited by 331

Rapid and direct control of target protein levels with VHL-recruiting dTAG molecules

Nabet, B., Ferguson, F. M., Seong, B. K. A., Kuljanin, M., Leggett, A. L., Mohardt, M. L., Robichaud, A., Conway, A. S., Buckley, D. L., Mancias, J. D., et al. (2020) · doi:10.1101/2020.03.13.980946 · Cited by 312

The reductive glycine pathway allows autotrophic growth of Desulfovibrio desulfuricans

Sánchez-Andrea, I., Guedes, I. A., Hornung, B., Boeren, S., Lawson, C. E., Sousa, D. Z., Bar-Even, A., Claassens, N. J., & Stams, A. J. M. (2020) · Nature Communications · doi:10.1038/s41467-020-18906-7 · Cited by 306

HIF-1α and HIF-2α differently regulate tumour development and inflammation of clear cell renal cell carcinoma in mice

Hoefflin, R., Harlander, S., Schäfer, S., Metzger, P., Kuo, F., Schönenberger, D., Adlesic, M., Peighambari, A., Seidel, P., Chen, C.-Y., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-17873-3 · Cited by 292

Proteome Integral Solubility Alteration: A High-Throughput Proteomics Assay for Target Deconvolution

Gaetani, M., Sabatier, P., Saei, A. A., Beusch, C. M., Yang, Z., Lundström, S. L., & Zubarev, R. A. (2019) · Journal of Proteome Research · doi:10.1021/acs.jproteome.9b00500 · Cited by 287

Proteome profiling in cerebrospinal fluid reveals novel biomarkers of Alzheimer's disease

Bader, J. M., Geyer, P. E., Müller, J. B., Strauss, M. T., Koch, M., Leypoldt, F., Koertvelyessy, P., Bittner, D., Schipke, C. G., Incesoy, E. I., et al. (2020) · Molecular Systems Biology · doi:10.15252/msb.20199356 · Cited by 286

Faecal microbiota transplant from aged donor mice affects spatial learning and memory via modulating hippocampal synaptic plasticity- and neurotransmission-related proteins in young recipients

D’Amato, A., Di Cesare Mannelli, L., Lucarini, E., Man, A. L., Le Gall, G., Branca, J. J. V., Ghelardini, C., Amedei, A., Bertelli, E., Regoli, M., et al. (2020) · Microbiome · doi:10.1186/s40168-020-00914-w · Cited by 269

Mechanism of adrenergic CaV1.2 stimulation revealed by proximity proteomics

Liu, G., Papa, A., Katchman, A. N., Zakharov, S. I., Roybal, D., Hennessey, J. A., Kushner, J., Yang, L., Chen, B.-X., Kushnir, A., et al. (2020) · Nature · doi:10.1038/s41586-020-1947-z · Cited by 243

Adipocyte extracellular vesicles carry enzymes and fatty acids that stimulate mitochondrial metabolism and remodeling in tumor cells

Clement, E., Lazar, I., Attané, C., Carrié, L., Dauvillier, S., Ducoux‐Petit, M., Esteve, D., Menneteau, T., Moutahir, M., Le Gonidec, S., et al. (2020) · The EMBO Journal · doi:10.15252/embj.2019102525 · Cited by 240

HLA Ligand Atlas: a benign reference of HLA-presented peptides to improve T-cell-based cancer immunotherapy

Marcu, A., Bichmann, L., Kuchenbecker, L., Kowalewski, D. J., Freudenmann, L. K., Backert, L., Mühlenbruch, L., Szolek, A., Lübke, M., Wagner, P., et al. (2021) · Journal for ImmunoTherapy of Cancer · doi:10.1136/jitc-2020-002071 · Cited by 250

Expression Atlas update: from tissues to single cells

Papatheodorou, I., Moreno, P., Manning, J., Fuentes, A. M.-P., George, N., Fexova, S., Fonseca, N. A., Füllgrabe, A., Green, M., Huang, N., et al. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz947 · Cited by 224

A high-stringency blueprint of the human proteome

Adhikari, S., Nice, E. C., Deutsch, E. W., Lane, L., Omenn, G. S., Pennington, S. R., Paik, Y.-K., Overall, C. M., Corrales, F. J., Cristea, I. M., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-19045-9 · Cited by 210

Restoration of energy homeostasis by SIRT6 extends healthy lifespan

Roichman, A., Elhanati, S., Aon, M. A., Abramovich, I., Di Francesco, A., Shahar, Y., Avivi, M. Y., Shurgi, M., Rubinstein, A., Wiesner, Y., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-23545-7 · Cited by 214

Microtubules tune mechanosensitive cell responses

Seetharaman, S., Vianay, B., Roca, V., Farrugia, A. J., De Pascalis, C., Boëda, B., Dingli, F., Loew, D., Vassilopoulos, S., Bershadsky, A., et al. (2022) · Nature Materials · doi:10.1038/s41563-021-01108-x · Cited by 210

Protein synthesis rates and ribosome occupancies reveal determinants of translation elongation rates

Riba, A., Di Nanni, N., Mittal, N., Arhné, E., Schmidt, A., & Zavolan, M. (2019) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1817299116 · Cited by 209

A genome-wide atlas of co-essential modules assigns function to uncharacterized genes

Wainberg, M., Kamber, R. A., Balsubramani, A., Meyers, R. M., Sinnott-Armstrong, N., Hornburg, D., Jiang, L., Chan, J., Jian, R., Gu, M., et al. (2021) · Nature Genetics · doi:10.1038/s41588-021-00840-z · Cited by 204

A microenvironment-inspired synthetic three-dimensional model for pancreatic ductal adenocarcinoma organoids

Below, C. R., Kelly, J., Brown, A., Humphries, J. D., Hutton, C., Xu, J., Lee, B. Y., Cintas, C., Zhang, X., Hernandez-Gordillo, V., et al. (2022) · Nature Materials · doi:10.1038/s41563-021-01085-1 · Cited by 194

A time-resolved proteomic and prognostic map of COVID-19

Demichev, V., Tober-Lau, P., Lemke, O., Nazarenko, T., Thibeault, C., Whitwell, H., Röhl, A., Freiwald, A., Szyrwiel, L., Ludwig, D., et al. (2021) · Cell Systems · doi:10.1016/j.cels.2021.05.005 · Cited by 200

BacPROTACs mediate targeted protein degradation in bacteria

Morreale, F. E., Kleine, S., Leodolter, J., Junker, S., Hoi, D. M., Ovchinnikov, S., Okun, A., Kley, J., Kurzbauer, R., Junk, L., et al. (2022) · Cell · doi:10.1016/j.cell.2022.05.009 · Cited by 196

Senescent immune cells release grancalcin to promote skeletal aging

Li, C.-J., Xiao, Y., Sun, Y.-C., He, W.-Z., Liu, L., Huang, M., He, C., Huang, M., Chen, K.-X., Hou, J., et al. (2021) · Cell Metabolism · doi:10.1016/j.cmet.2021.08.009 · Cited by 190

TMTpro: Design, Synthesis, and Initial Evaluation of a Proline-Based Isobaric 16-Plex Tandem Mass Tag Reagent Set

Thompson, A., Wölmer, N., Koncarevic, S., Selzer, S., Böhm, G., Legner, H., Schmid, P., Kienle, S., Penning, P., Höhle, C., et al. (2019) · Analytical Chemistry · doi:10.1021/acs.analchem.9b04474 · Cited by 186

Expedited mapping of the ligandable proteome using fully functionalized enantiomeric probe pairs

Wang, Y., Dix, M. M., Bianco, G., Remsberg, J. R., Lee, H.-Y., Kalocsay, M., Gygi, S. P., Forli, S., Vite, G., Lawrence, R. M., et al. (2019) · Nature Chemistry · doi:10.1038/s41557-019-0351-5 · Cited by 179

Identifying drug targets in tissues and whole blood with thermal-shift profiling

Perrin, J., Werner, T., Kurzawa, N., Rutkowska, A., Childs, D. D., Kalxdorf, M., Poeckel, D., Stonehouse, E., Strohmer, K., Heller, B., et al. (2020) · Nature Biotechnology · doi:10.1038/s41587-019-0388-4 · Cited by 178

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

Defining the Adult Neural Stem Cell Niche Proteome Identifies Key Regulators of Adult Neurogenesis

Kjell, J., Fischer-Sternjak, J., Thompson, A. J., Friess, C., Sticco, M. J., Salinas, F., Cox, J., Martinelli, D. C., Ninkovic, J., Franze, K., et al. (2020) · Cell Stem Cell · doi:10.1016/j.stem.2020.01.002 · Cited by 163

Structural basis of TFIIH activation for nucleotide excision repair

Kokic, G., Chernev, A., Tegunov, D., Dienemann, C., Urlaub, H., & Cramer, P. (2019) · Nature Communications · doi:10.1038/s41467-019-10745-5 · Cited by 163

Pro-inflammatory activation following demyelination is required for myelin clearance and oligodendrogenesis

Cunha, M. I., Su, M., Cantuti-Castelvetri, L., Müller, S. A., Schifferer, M., Djannatian, M., Alexopoulos, I., van der Meer, F., Winkler, A., van Ham, T. J., et al. (2020) · Journal of Experimental Medicine · doi:10.1084/jem.20191390 · Cited by 160

Proteomic analysis of urinary extracellular vesicles reveal biomarkers for neurologic disease

Wang, S., Kojima, K., Mobley, J. A., & West, A. B. (2019) · EBioMedicine · doi:10.1016/j.ebiom.2019.06.021 · Cited by 145

Structures of rhodopsin in complex with G-protein-coupled receptor kinase 1

Chen, Q., Plasencia, M., Li, Z., Mukherjee, S., Patra, D., Chen, C.-L., Klose, T., Yao, X.-Q., Kossiakoff, A. A., Chang, L., et al. (2021) · Nature · doi:10.1038/s41586-021-03721-x · Cited by 152

TREM2 interacts with TDP-43 and mediates microglial neuroprotection against TDP-43-related neurodegeneration

Xie, M., Liu, Y. U., Zhao, S., Zhang, L., Bosco, D. B., Pang, Y.-P., Zhong, J., Sheth, U., Martens, Y. A., Zhao, N., et al. (2022) · Nature Neuroscience · doi:10.1038/s41593-021-00975-6 · Cited by 157

Neuronal ribosomes exhibit dynamic and context-dependent exchange of ribosomal proteins

Fusco, C. M., Desch, K., Dörrbaum, A. R., Wang, M., Staab, A., Chan, I. C. W., Vail, E., Villeri, V., Langer, J. D., & Schuman, E. M. (2021) · Nature Communications · doi:10.1038/s41467-021-26365-x · Cited by 157

Effect of MSCs and MSC-Derived Extracellular Vesicles on Human Blood Coagulation

Silachev, D., Goryunov, K., Shpilyuk, M., Beznoschenko, O., Morozova, N., Kraevaya, E., Popkov, V., Pevzner, I., Zorova, L., Evtushenko, E., et al. (2019) · Cells · doi:10.3390/cells8030258 · Cited by 154

Fibrillar Aβ triggers microglial proteome alterations and dysfunction in Alzheimer mouse models

Sebastian Monasor, L., Müller, S. A., Colombo, A. V., Tanrioever, G., König, J., Roth, S., Liesz, A., Berghofer, A., Piechotta, A., Prestel, M., et al. (2020) · eLife · doi:10.7554/elife.54083 · Cited by 147

FAK activity sustains intrinsic and acquired ovarian cancer resistance to platinum chemotherapy

Diaz Osterman, C. J., Ozmadenci, D., Kleinschmidt, E. G., Taylor, K. N., Barrie, A. M., Jiang, S., Bean, L. M., Sulzmaier, F. J., Jean, C., Tancioni, I., et al. (2019) · eLife · doi:10.7554/elife.47327 · Cited by 145

Enzymatic Dissociation Induces Transcriptional and Proteotype Bias in Brain Cell Populations

Mattei, D., Ivanov, A., van Oostrum, M., Pantelyushin, S., Richetto, J., Mueller, F., Beffinger, M., Schellhammer, L., vom Berg, J., Wollscheid, B., et al. (2020) · International Journal of Molecular Sciences · doi:10.3390/ijms21217944 · Cited by 145

Enzymatic dissociation induces transcriptional and proteotype bias in brain cell populations

Mattei, D., Ivanov, A., van Oostrum, M., Pantelyushin, S., Richetto, J., Mueller, F., Beffinger, M. M., Schellhammer, L., vom Berg, J., Wollscheid, B., et al. (2020) · doi:10.1101/2020.05.14.095422 · Cited by 143

Mechanisms governing the pioneering and redistribution capabilities of the non-classical pioneer PU.1

Minderjahn, J., Schmidt, A., Fuchs, A., Schill, R., Raithel, J., Babina, M., Schmidl, C., Gebhard, C., Schmidhofer, S., Mendes, K., et al. (2020) · Nature Communications · doi:10.1038/s41467-019-13960-2 · Cited by 136

Liver-fibrosis-activated transcriptional networks govern hepatocyte reprogramming and intra-hepatic communication

Loft, A., Alfaro, A. J., Schmidt, S. F., Pedersen, F. B., Terkelsen, M. K., Puglia, M., Chow, K. K., Feuchtinger, A., Troullinaki, M., Maida, A., et al. (2021) · Cell Metabolism · doi:10.1016/j.cmet.2021.06.005 · Cited by 129

The proteomic landscape of synaptic diversity across brain regions and cell types

van Oostrum, M., Blok, T. M., Giandomenico, S. L., tom Dieck, S., Tushev, G., Fürst, N., Langer, J. D., & Schuman, E. M. (2023) · Cell · doi:10.1016/j.cell.2023.09.028 · Cited by 135

Coordination of fungal biofilm development by extracellular vesicle cargo

Zarnowski, R., Noll, A., Chevrette, M. G., Sanchez, H., Jones, R., Anhalt, H., Fossen, J., Jaromin, A., Currie, C., Nett, J. E., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-26525-z · Cited by 123

Human Proteome Project Mass Spectrometry Data Interpretation Guidelines 3.0

Deutsch, E. W., Lane, L., Overall, C. M., Bandeira, N., Baker, M. S., Pineau, C., Moritz, R. L., Corrales, F., Orchard, S., Van Eyk, J. E., et al. (2019) · Journal of Proteome Research · doi:10.1021/acs.jproteome.9b00542 · Cited by 122

Whole-cell modeling in yeast predicts compartment-specific proteome constraints that drive metabolic strategies

Elsemman, I. E., Rodriguez Prado, A., Grigaitis, P., Garcia Albornoz, M., Harman, V., Holman, S. W., van Heerden, J., Bruggeman, F. J., Bisschops, M. M. M., Sonnenschein, N., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-28467-6 · Cited by 120

Niche stiffening compromises hair follicle stem cell potential during ageing by reducing bivalent promoter accessibility

Koester, J., Miroshnikova, Y. A., Ghatak, S., Chacón-Martínez, C. A., Morgner, J., Li, X., Atanassov, I., Altmüller, J., Birk, D. E., Koch, M., et al. (2021) · Nature Cell Biology · doi:10.1038/s41556-021-00705-x · Cited by 117

Targeted protein acetylation in cells using heterobifunctional molecules

Wang, W. W., Chen, L.-Y., Wozniak, J. M., Jadhav, A. M., Anderson, H., Malone, T. E., & Parker, C. G. (2021) · Journal of the American Chemical Society · doi:10.1021/jacs.1c07850 · Cited by 114

ELOF1 is a transcription-coupled DNA repair factor that directs RNA polymerase II ubiquitylation

van der Weegen, Y., de Lint, K., van den Heuvel, D., Nakazawa, Y., Mevissen, T. E. T., van Schie, J. J. M., San Martin Alonso, M., Boer, D. E. C., González-Prieto, R., Narayanan, I. V., et al. (2021) · Nature Cell Biology · doi:10.1038/s41556-021-00688-9 · Cited by 114

White matter integrity in mice requires continuous myelin synthesis at the inner tongue

Meschkat, M., Steyer, A. M., Weil, M.-T., Kusch, K., Jahn, O., Piepkorn, L., Agüi-Gonzalez, P., Phan, N. T. N., Ruhwedel, T., Sadowski, B., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-28720-y · Cited by 112

Indisulam targets RNA splicing and metabolism to serve as a therapeutic strategy for high-risk neuroblastoma

Nijhuis, A., Sikka, A., Yogev, O., Herendi, L., Balcells, C., Ma, Y., Poon, E., Eckold, C., Valbuena, G. N., Xu, Y., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-28907-3 · Cited by 110

Cell Type–Specific Adaptive Signaling Responses to KRASG12C Inhibition

Solanki, H. S., Welsh, E. A., Fang, B., Izumi, V., Darville, L., Stone, B., Franzese, R., Chavan, S., Kinose, F., Imbody, D., et al. (2021) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-20-3872 · Cited by 106

Extensive remodeling of the extracellular matrix during aging contributes to age-dependent impairments of muscle stem cell functionality

Schüler, S. C., Kirkpatrick, J. M., Schmidt, M., Santinha, D., Koch, P., Di Sanzo, S., Cirri, E., Hemberg, M., Ori, A., & von Maltzahn, J. (2021) · Cell Reports · doi:10.1016/j.celrep.2021.109223 · Cited by 106

Comparative profiling of the synaptic proteome from Alzheimer’s disease patients with focus on the APOE genotype

Hesse, R., Hurtado, M. L., Jackson, R. J., Eaton, S. L., Herrmann, A. G., Colom-Cadena, M., Tzioras, M., King, D., Rose, J., Tulloch, J., et al. (2019) · Acta Neuropathologica Communications · doi:10.1186/s40478-019-0847-7 · Cited by 107

Identification of two pathways mediating protein targeting from ER to lipid droplets

Song, J., Mizrak, A., Lee, C.-W., Cicconet, M., Lai, Z. W., Tang, W.-C., Lu, C.-H., Mohr, S. E., Farese, R. V., & Walther, T. C. (2022) · Nature Cell Biology · doi:10.1038/s41556-022-00974-0 · Cited by 106

Bone Marrow Mesenchymal Stem Cells' Secretome Exerts Neuroprotective Effects in a Parkinson's Disease Rat Model

Mendes-Pinheiro, B., Anjo, S. I., Manadas, B., Da Silva, J. D., Marote, A., Behie, L. A., Teixeira, F. G., & Salgado, A. J. (2019) · Frontiers in Bioengineering and Biotechnology · doi:10.3389/fbioe.2019.00294 · Cited by 103

Mitochondrial membrane proteins and VPS35 orchestrate selective removal of mtDNA

Sen, A., Kallabis, S., Gaedke, F., Jüngst, C., Boix, J., Nüchel, J., Maliphol, K., Hofmann, J., Schauss, A. C., Krüger, M., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-34205-9 · Cited by 102

Biogeographic venom variation in Russell’s viper (Daboia russelii) and the preclinical inefficacy of antivenom therapy in snakebite hotspots

Senji Laxme, R. R., Khochare, S., Attarde, S., Suranse, V., Iyer, A., Casewell, N. R., Whitaker, R., Martin, G., & Sunagar, K. (2021) · PLOS Neglected Tropical Diseases · doi:10.1371/journal.pntd.0009247 · Cited by 101

Light-mediated discovery of surfaceome nanoscale organization and intercellular receptor interaction networks

Müller, M., Gräbnitz, F., Barandun, N., Shen, Y., Wendt, F., Steiner, S. N., Severin, Y., Vetterli, S. U., Mondal, M., Prudent, J. R., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-27280-x · Cited by 101

The 10q26 Risk Haplotype of Age-Related Macular Degeneration Aggravates Subretinal Inflammation by Impairing Monocyte Elimination

Beguier, F., Housset, M., Roubeix, C., Augustin, S., Zagar, Y., Nous, C., Mathis, T., Eandi, C., Benchaboune, M., Drame-Maigné, A., et al. (2020) · Immunity · doi:10.1016/j.immuni.2020.07.021 · Cited by 87

Sirtuin-1 sensitive lysine-136 acetylation drives phase separation and pathological aggregation of TDP-43

Garcia Morato, J., Hans, F., von Zweydorf, F., Feederle, R., Elsässer, S. J., Skodras, A. A., Gloeckner, C. J., Buratti, E., Neumann, M., & Kahle, P. J. (2022) · Nature Communications · doi:10.1038/s41467-022-28822-7 · Cited by 94

Structure of the endosomal Commander complex linked to Ritscher-Schinzel syndrome

Healy, M. D., McNally, K. E., Butkovič, R., Chilton, M., Kato, K., Sacharz, J., McConville, C., Moody, E. R. R., Shaw, S., Planelles-Herrero, V. J., et al. (2023) · Cell · doi:10.1016/j.cell.2023.04.003 · Cited by 91

A multi-omics analysis reveals the unfolded protein response regulon and stress-induced resistance to folate-based antimetabolites

Reich, S., Nguyen, C. D. L., Has, C., Steltgens, S., Soni, H., Coman, C., Freyberg, M., Bichler, A., Seifert, N., Conrad, D., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-16747-y · Cited by 90

ATP13A3 is a major component of the enigmatic mammalian polyamine transport system

Hamouda, N. N., Van den Haute, C., Vanhoutte, R., Sannerud, R., Azfar, M., Mayer, R., Cortés Calabuig, Á., Swinnen, J. V., Agostinis, P., Baekelandt, V., et al. (2021) · Journal of Biological Chemistry · doi:10.1074/jbc.ra120.013908 · Cited by 85

Region-Specific Proteome Changes of the Intestinal Epithelium during Aging and Dietary Restriction

Gebert, N., Cheng, C.-W., Kirkpatrick, J. M., Di Fraia, D., Yun, J., Schädel, P., Pace, S., Garside, G. B., Werz, O., Rudolph, K. L., et al. (2020) · Cell Reports · doi:10.1016/j.celrep.2020.107565 · Cited by 88

Systematic detection of functional proteoform groups from bottom-up proteomic datasets

Bludau, I., Frank, M., Dörig, C., Cai, Y., Heusel, M., Rosenberger, G., Picotti, P., Collins, B. C., Röst, H., & Aebersold, R. (2021) · Nature Communications · doi:10.1038/s41467-021-24030-x · Cited by 88

SUGAR-seq enables simultaneous detection of glycans, epitopes, and the transcriptome in single cells

Kearney, C. J., Vervoort, S. J., Ramsbottom, K. M., Todorovski, I., Lelliott, E. J., Zethoven, M., Pijpers, L., Martin, B. P., Semple, T., Martelotto, L., et al. (2021) · Science Advances · doi:10.1126/sciadv.abe3610 · Cited by 87

Estimating the number of protein molecules in a plant cell: protein and amino acid homeostasis during drought

Heinemann, B., Künzler, P., Eubel, H., Braun, H.-P., & Hildebrandt, T. M. (2020) · Plant Physiology · doi:10.1093/plphys/kiaa050 · Cited by 87

DamC reveals principles of chromatin folding in vivo without crosslinking and ligation

Redolfi, J., Zhan, Y., Valdes-Quezada, C., Kryzhanovska, M., Guerreiro, I., Iesmantavicius, V., Pollex, T., Grand, R. S., Mulugeta, E., Kind, J., et al. (2019) · Nature Structural & Molecular Biology · doi:10.1038/s41594-019-0231-0 · Cited by 86

Targeting of Scavenger Receptors Stabilin-1 and Stabilin-2 Ameliorates Atherosclerosis by a Plasma Proteome Switch Mediating Monocyte/Macrophage Suppression

Manta, C.-P., Leibing, T., Friedrich, M., Nolte, H., Adrian, M., Schledzewski, K., Krzistetzko, J., Kirkamm, C., David Schmid, C., Xi, Y., et al. (2022) · Circulation · doi:10.1161/circulationaha.121.058615 · Cited by 84

De novo protein identification in mammalian sperm using in situ cryoelectron tomography and AlphaFold2 docking

Chen, Z., Shiozaki, M., Haas, K. M., Skinner, W. M., Zhao, S., Guo, C., Polacco, B. J., Yu, Z., Krogan, N. J., Lishko, P. V., et al. (2023) · Cell · doi:10.1016/j.cell.2023.09.017 · Cited by 82

Temporal multi-omics identifies LRG1 as a vascular niche instructor of metastasis

Singhal, M., Gengenbacher, N., Abdul Pari, A. A., Kamiyama, M., Hai, L., Kuhn, B. J., Kallenberg, D. M., Kulkarni, S. R., Camilli, C., Preuß, S. F., et al. (2021) · Science Translational Medicine · doi:10.1126/scitranslmed.abe6805 · Cited by 80

Multistep mechanism of G-quadruplex resolution during DNA replication

Sato, K., Martin-Pintado, N., Post, H., Altelaar, M., & Knipscheer, P. (2021) · Science Advances · doi:10.1126/sciadv.abf8653 · Cited by 80

Proteomics characterisation of the L929 cell supernatant and its role in BMDM differentiation

Heap, R. E., Marín-Rubio, J. L., Peltier, J., Heunis, T., Dannoura, A., Moore, A., & Trost, M. (2021) · Life Science Alliance · doi:10.26508/lsa.202000957 · Cited by 80

Modeling the CRL4A ligase complex to predict target protein ubiquitination induced by cereblon-recruiting PROTACs

Bai, N., Riching, K. M., Makaju, A., Wu, H., Acker, T. M., Ou, S.-C., Zhang, Y., Shen, X., Bulloch, D. N., Rui, H., et al. (2022) · Journal of Biological Chemistry · doi:10.1016/j.jbc.2022.101653 · Cited by 77

A size-exclusion-based approach for purifying extracellular vesicles from human plasma

Vanderboom, P. M., Dasari, S., Ruegsegger, G. N., Pataky, M. W., Lucien, F., Heppelmann, C. J., Lanza, I. R., & Nair, K. S. (2021) · Cell Reports Methods · doi:10.1016/j.crmeth.2021.100055 · Cited by 75

Identification of long-lived proteins in the mitochondria reveals increased stability of the electron transport chain

Krishna, S., Arrojo e Drigo, R., Capitanio, J. S., Ramachandra, R., Ellisman, M., & Hetzer, M. W. (2021) · Developmental Cell · doi:10.1016/j.devcel.2021.10.008 · Cited by 73

Colocalization of different neurotransmitter transporters on synaptic vesicles is sparse except for VGLUT1 and ZnT3

Upmanyu, N., Jin, J., Emde, H. V. D., Ganzella, M., Bösche, L., Malviya, V. N., Zhuleku, E., Politi, A. Z., Ninov, M., Silbern, I., et al. (2022) · Neuron · doi:10.1016/j.neuron.2022.02.008 · Cited by 69

The Autophagy-Initiating Kinase ULK1 Controls RIPK1-Mediated Cell Death

Wu, W., Wang, X., Berleth, N., Deitersen, J., Wallot-Hieke, N., Böhler, P., Schlütermann, D., Stuhldreier, F., Cox, J., Schmitz, K., et al. (2020) · Cell Reports · doi:10.1016/j.celrep.2020.107547 · Cited by 72

In Vitro Kinase-to-Phosphosite Database (iKiP-DB) Predicts Kinase Activity in Phosphoproteomic Datasets

Mari, T., Mösbauer, K., Wyler, E., Landthaler, M., Drosten, C., & Selbach, M. (2022) · Journal of Proteome Research · doi:10.1021/acs.jproteome.2c00198 · Cited by 70

A CSB-PAF1C axis restores processive transcription elongation after DNA damage repair

van den Heuvel, D., Spruijt, C. G., González-Prieto, R., Kragten, A., Paulsen, M. T., Zhou, D., Wu, H., Apelt, K., van der Weegen, Y., Yang, K., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-21520-w · Cited by 70

A CSB-PAF1C axis restores processive transcription elongation after DNA damage repair

van den Heuvel, D., Spruijt, C. G., González-Prieto, R., Kragten, A., Paulsen, M. T., Zhou, D., Wu, H., Apelt, K., van der Weegen, Y., Yang, K., et al. (2020) · doi:10.1101/2020.01.04.894808 · Cited by 69

Bassoon contributes to tau-seed propagation and neurotoxicity

Martinez, P., Patel, H., You, Y., Jury, N., Perkins, A., Lee-Gosselin, A., Taylor, X., You, Y., Viana Di Prisco, G., Huang, X., et al. (2022) · Nature Neuroscience · doi:10.1038/s41593-022-01191-6 · Cited by 68

Mass Spectrometry Based Immunopeptidomics Leads to Robust Predictions of Phosphorylated HLA Class I Ligands

Solleder, M., Guillaume, P., Racle, J., Michaux, J., Pak, H.-S., Müller, M., Coukos, G., Bassani-Sternberg, M., & Gfeller, D. (2020) · Molecular & Cellular Proteomics · doi:10.1074/mcp.tir119.001641 · Cited by 68

A framework for ultra-low-input spatial tissue proteomics

Makhmut, A., Qin, D., Fritzsche, S., Nimo, J., König, J., & Coscia, F. (2023) · Cell Systems · doi:10.1016/j.cels.2023.10.003 · Cited by 67

A common vesicle proteome drives fungal biofilm development

Zarnowski, R., Sanchez, H., Jaromin, A., Zarnowska, U. J., Nett, J. E., Mitchell, A. P., & Andes, D. (2022) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2211424119 · Cited by 63

Hallstatt miners consumed blue cheese and beer during the Iron Age and retained a non-Westernized gut microbiome until the Baroque period

Maixner, F., Sarhan, M. S., Huang, K. D., Tett, A., Schoenafinger, A., Zingale, S., Blanco-Míguez, A., Manghi, P., Cemper-Kiesslich, J., Rosendahl, W., et al. (2021) · Current Biology · doi:10.1016/j.cub.2021.09.031 · Cited by 62

What Are We Missing by Using Hydrophilic Enrichment? Improving Bacterial Glycoproteome Coverage Using Total Proteome and FAIMS Analyses

Ahmad Izaham, A. R., Ang, C.-S., Nie, S., Bird, L. E., Williamson, N. A., & Scott, N. E. (2021) · Journal of Proteome Research · doi:10.1021/acs.jproteome.0c00565 · Cited by 62

Human METTL18 is a histidine-specific methyltransferase that targets RPL3 and affects ribosome biogenesis and function

Małecki, J. M., Odonohue, M.-F., Kim, Y., Jakobsson, M. E., Gessa, L., Pinto, R., Wu, J., Davydova, E., Moen, A., Olsen, J. V., et al. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkab088 · Cited by 59

Metabolic coessentiality mapping identifies C12orf49 as a regulator of SREBP processing and cholesterol metabolism

Bayraktar, E. C., La, K., Karpman, K., Unlu, G., Ozerdem, C., Ritter, D. J., Alwaseem, H., Molina, H., Hoffmann, H.-H., Millner, A., et al. (2020) · Nature Metabolism · doi:10.1038/s42255-020-0206-9 · Cited by 60