DIA-NN: neural networks and interference correction enable deep proteome coverage in high throughput von Demichev, Vadim, Messner, Christoph B., Vernardis, Spyros I., Lilley, Kathryn S., Ralser, Markus

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MSnbase-an R/Bioconductor package for isobaric tagged mass spectrometry data visualization, processing and quantitation von Gatto, Laurent, Lilley, Kathryn S.

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dia-PASEF data analysis using FragPipe and DIA-NN for deep proteomics of low sample amounts von Demichev, Vadim, Szyrwiel, Lukasz, Yu, Fengchao, Teo, Guo Ci, Rosenberger, George, Niewienda, Agathe, Ludwig, Daniela, Decker, Jens, Kaspar-Schoenefeld, Stephanie, Lilley, Kathryn S., Mülleder, Michael, Nesvizhskii, Alexey I., Ralser, Markus

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Toward a Comprehensive Map of the Effectors of Rab GTPases von Gillingham, Alison K., Sinka, Rita, Torres, Isabel L., Lilley, Kathryn S., Munro, Sean

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Comprehensive identification of RNA–protein interactions in any organism using orthogonal organic phase separation (OOPS) von Queiroz, Rayner M. L., Smith, Tom, Villanueva, Eneko, Marti-Solano, Maria, Monti, Mie, Pizzinga, Mariavittoria, Mirea, Dan-Mircea, Ramakrishna, Manasa, Harvey, Robert F., Dezi, Veronica, Thomas, Gavin H., Willis, Anne E., Lilley, Kathryn S.

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Tracking the embryonic stem cell transition from ground state pluripotency von Kalkan, Tüzer, Olova, Nelly, Roode, Mila, Mulas, Carla, Lee, Heather J, Nett, Isabelle, Marks, Hendrik, Walker, Rachael, Stunnenberg, Hendrik G, Lilley, Kathryn S, Nichols, Jennifer, Reik, Wolf, Bertone, Paul, Smith, Austin

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Combining LOPIT with differential ultracentrifugation for high-resolution spatial proteomics von Geladaki, Aikaterini, Kočevar Britovšek, Nina, Breckels, Lisa M., Smith, Tom S., Vennard, Owen L., Mulvey, Claire M., Crook, Oliver M., Gatto, Laurent, Lilley, Kathryn S.

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Global analysis of protein-RNA interactions in SARS-CoV-2-infected cells reveals key regulators of infection von Kamel, Wael, Noerenberg, Marko, Cerikan, Berati, Chen, Honglin, Järvelin, Aino I., Kammoun, Mohamed, Lee, Jeffrey Y., Shuai, Ni, Garcia-Moreno, Manuel, Andrejeva, Anna, Deery, Michael J., Johnson, Natasha, Neufeldt, Christopher J., Cortese, Mirko, Knight, Michael L., Lilley, Kathryn S., Martinez, Javier, Davis, Ilan, Bartenschlager, Ralf, Mohammed, Shabaz, Castello, Alfredo

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Changes in the Arabidopsis RNA-binding proteome reveal novel stress response mechanisms von Marondedze, Claudius, Thomas, Ludivine, Gehring, Chris, Lilley, Kathryn S

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Ultra-High-Throughput Clinical Proteomics Reveals Classifiers of COVID-19 Infection von Messner, Christoph B., Demichev, Vadim, Wendisch, Daniel, Michalick, Laura, White, Matthew, Freiwald, Anja, Textoris-Taube, Kathrin, Vernardis, Spyros I., Egger, Anna-Sophia, Kreidl, Marco, Ludwig, Daniela, Kilian, Christiane, Agostini, Federica, Zelezniak, Aleksej, Thibeault, Charlotte, Pfeiffer, Moritz, Hippenstiel, Stefan, Hocke, Andreas, von Kalle, Christof, Campbell, Archie, Hayward, Caroline, Porteous, David J., Marioni, Riccardo E., Langenberg, Claudia, Lilley, Kathryn S., Kuebler, Wolfgang M., Mülleder, Michael, Drosten, Christian, Suttorp, Norbert, Witzenrath, Martin, Kurth, Florian, Sander, Leif Erik, Ralser, Markus

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A draft map of the mouse pluripotent stem cell spatial proteome von Christoforou, Andy, Mulvey, Claire M., Breckels, Lisa M., Geladaki, Aikaterini, Hurrell, Tracey, Hayward, Penelope C., Naake, Thomas, Gatto, Laurent, Viner, Rosa, Arias, Alfonso Martinez, Lilley, Kathryn S.

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Addressing Accuracy and Precision Issues in iTRAQ Quantitation von Karp, Natasha A., Huber, Wolfgang, Sadowski, Pawel G., Charles, Philip D., Hester, Svenja V., Lilley, Kathryn S.

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A proteomic approach identifies many novel palmitoylated proteins in Arabidopsis von Hemsley, Piers A., Weimar, Thilo, Lilley, Kathryn S., Dupree, Paul, Grierson, Claire S.

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A Bayesian mixture modelling approach for spatial proteomics von Crook, Oliver M, Mulvey, Claire M, Kirk, Paul D W, Lilley, Kathryn S, Gatto, Laurent

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Proteome Mapping of a Cyanobacterium Reveals Distinct Compartment Organization and Cell-Dispersed Metabolism von Baers, Laura L, Breckels, Lisa M, Mills, Lauren A, Gatto, Laurent, Deery, Michael J, Stevens, Tim J, Howe, Christopher J, Lilley, Kathryn S, Lea-Smith, David J

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Proteome labeling and protein identification in specific tissues and at specific developmental stages in an animal von Elliott, Thomas S, Townsley, Fiona M, Bianco, Ambra, Ernst, Russell J, Sachdeva, Amit, Elsässer, Simon J, Davis, Lloyd, Lang, Kathrin, Pisa, Rudolf, Greiss, Sebastian, Lilley, Kathryn S, Chin, Jason W

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Mapping diversity in African trypanosomes using high resolution spatial proteomics von Moloney, Nicola M., Barylyuk, Konstantin, Tromer, Eelco, Crook, Oliver M., Breckels, Lisa M., Lilley, Kathryn S., Waller, Ross F., MacGregor, Paula

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Spatial proteomics defines the content of trafficking vesicles captured by golgin tethers von Shin, John J. H., Crook, Oliver M., Borgeaud, Alicia C., Cattin-Ortolá, Jérôme, Peak-Chew, Sew Y., Breckels, Lisa M., Gillingham, Alison K., Chadwick, Jessica, Lilley, Kathryn S., Munro, Sean

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phage abortive infection system, ToxIN, functions as a protein-RNA toxin-antitoxin pair von Fineran, Peter C, Blower, Tim R, Foulds, Ian J, Humphreys, David P, Lilley, Kathryn S, Salmond, George P.C

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Spatiotemporal proteomic profiling of the pro-inflammatory response to lipopolysaccharide in the THP-1 human leukaemia cell line von Mulvey, Claire M., Breckels, Lisa M., Crook, Oliver M., Sanders, David J., Ribeiro, Andre L. R., Geladaki, Aikaterini, Christoforou, Andy, Britovšek, Nina Kočevar, Hurrell, Tracey, Deery, Michael J., Gatto, Laurent, Smith, Andrew M., Lilley, Kathryn S.

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