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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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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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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Understudied proteins: opportunities and challenges for functional proteomics von Kustatscher, Georg, Collins, Tom, Gingras, Anne-Claude, Guo, Tiannan, Hermjakob, Henning, Ideker, Trey, Lilley, Kathryn S., Lundberg, Emma, Marcotte, Edward M., Ralser, Markus, Rappsilber, Juri

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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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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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The RNA-binding protein repertoire of Arabidopsis thaliana von Marondedze, Claudius, Thomas, Ludivine, Serrano, Natalia L., Lilley, Kathryn S., Gehring, Chris

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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 Comprehensive Subcellular Atlas of the Toxoplasma Proteome via hyperLOPIT Provides Spatial Context for Protein Functions von Barylyuk, Konstantin, Koreny, Ludek, Ke, Huiling, Butterworth, Simon, Crook, Oliver M., Lassadi, Imen, Gupta, Vipul, Tromer, Eelco, Mourier, Tobias, Stevens, Tim J., Breckels, Lisa M., Pain, Arnab, Lilley, Kathryn S., Waller, Ross F.

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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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The proteomic landscape of genome-wide genetic perturbations von Messner, Christoph B., Demichev, Vadim, Muenzner, Julia, Aulakh, Simran K., Barthel, Natalie, Röhl, Annika, Herrera-Domínguez, Lucía, Egger, Anna-Sophia, Kamrad, Stephan, Hou, Jing, Tan, Guihong, Lemke, Oliver, Calvani, Enrica, Szyrwiel, Lukasz, Mülleder, Michael, Lilley, Kathryn S., Boone, Charles, Kustatscher, Georg, Ralser, Markus

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Moving Profiling Spatial Proteomics Beyond Discrete Classification von Crook, Oliver M., Smith, Tom, Elzek, Mohamed, 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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Ultra-fast proteomics with Scanning SWATH von Messner, Christoph B., Demichev, Vadim, Bloomfield, Nic, Yu, Jason S. L., White, Matthew, Kreidl, Marco, Egger, Anna-Sophia, Freiwald, Anja, Ivosev, Gordana, Wasim, Fras, Zelezniak, Aleksej, Jürgens, Linda, Suttorp, Norbert, Sander, Leif Erik, Kurth, Florian, Lilley, Kathryn S., Mülleder, Michael, Tate, Stephen, Ralser, Markus

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Assessing sub-cellular resolution in spatial proteomics experiments von Gatto, Laurent, Breckels, Lisa M., Lilley, Kathryn S.

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