Building high-quality assay libraries for targeted analysis of SWATH MS data von Schubert, Olga T, Gillet, Ludovic C, Collins, Ben C, Navarro, Pedro, Rosenberger, George, Wolski, Witold E, Lam, Henry, Amodei, Dario, Mallick, Parag, MacLean, Brendan, Aebersold, Ruedi

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rawDiag: An R Package Supporting Rational LC–MS Method Optimization for Bottom-up Proteomics von Trachsel, Christian, Panse, Christian, Kockmann, Tobias, Wolski, Witold E, Grossmann, Jonas, Schlapbach, Ralph

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Epigenetics and Proteomics Join Transcriptomics in the Quest for Tuberculosis Biomarkers von Esterhuyse, Maria M, Weiner, 3rd, January, Caron, Etienne, Loxton, Andre G, Iannaccone, Marco, Wagman, Chandre, Saikali, Philippe, Stanley, Kim, Wolski, Witold E, Mollenkopf, Hans-Joachim, Schick, Matthias, Aebersold, Ruedi, Linhart, Heinz, Walzl, Gerhard, Kaufmann, Stefan H E

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Precise Temporal Profiling of Signaling Complexes in Primary Cells Using SWATH Mass Spectrometry von Caron, Etienne, Roncagalli, Romain, Hase, Takeshi, Wolski, Witold E., Choi, Meena, Menoita, Marisa G., Durand, Stephane, García-Blesa, Antonio, Fierro-Monti, Ivo, Sajic, Tatjana, Heusel, Moritz, Weiss, Tobias, Malissen, Marie, Schlapbach, Ralph, Collins, Ben C., Ghosh, Samik, Kitano, Hiroaki, Aebersold, Ruedi, Malissen, Bernard, Gstaiger, Matthias

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Reduced CXCL4/PF4 expression as a driver of increased human hematopoietic stem and progenitor cell proliferation in polycythemia vera von Meier-Abt, Fabienne, Wolski, Witold E., Tan, Ge, Kummer, Sandra, Amon, Sabine, Manz, Markus G., Aebersold, Ruedi, Theocharides, Alexandre P. A.

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OpenMS: a flexible open-source software platform for mass spectrometry data analysis von Röst, Hannes L, Sachsenberg, Timo, Aiche, Stephan, Bielow, Chris, Weisser, Hendrik, Aicheler, Fabian, Andreotti, Sandro, Ehrlich, Hans-Christian, Gutenbrunner, Petra, Kenar, Erhan, Liang, Xiao, Nahnsen, Sven, Nilse, Lars, Pfeuffer, Julianus, Rosenberger, George, Rurik, Marc, Schmitt, Uwe, Veit, Johannes, Walzer, Mathias, Wojnar, David, Wolski, Witold E, Schilling, Oliver, Choudhary, Jyoti S, Malmström, Lars, Aebersold, Ruedi, Reinert, Knut, Kohlbacher, Oliver

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prolfqua: A Comprehensive R‑Package for Proteomics Differential Expression Analysis von Wolski, Witold E., Nanni, Paolo, Grossmann, Jonas, d’Errico, Maria, Schlapbach, Ralph, Panse, Christian

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Rapid mass spectrometric conversion of tissue biopsy samples into permanent quantitative digital proteome maps von Guo, Tiannan, Kouvonen, Petri, Koh, Ching Chiek, Gillet, Ludovic C, Wolski, Witold E, Röst, Hannes L, Rosenberger, George, Collins, Ben C, Blum, Lorenz C, Gillessen, Silke, Joerger, Markus, Jochum, Wolfram, Aebersold, Ruedi

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Modic type 2 changes are fibroinflammatory changes with complement system involvement adjacent to degenerated vertebral endplates von Heggli, Irina, Laux, Christoph J., Mengis, Tamara, Karol, Agnieszka, Cornaz, Frédéric, Herger, Nick, Aradi‐Vegh, Borbala, Widmer, Jonas, Burkhard, Marco D., Farshad‐Amacker, Nadja A., Pfammatter, Sibylle, Wolski, Witold E., Brunner, Florian, Distler, Oliver, Farshad, Mazda, Dudli, Stefan

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prolfquapp  A User-Friendly Command-Line Tool Simplifying Differential Expression Analysis in Quantitative Proteomics von Wolski, Witold E., Grossmann, Jonas, Schwarz, Leonardo, Leary, Peter, Türker, Can, Nanni, Paolo, Schlapbach, Ralph, Panse, Christian

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Targeted proteomics coming of age - SRM, PRM and DIA performance evaluated from a core facility perspective von Kockmann, Tobias, Trachsel, Christian, Panse, Christian, Wahlander, Asa, Selevsek, Nathalie, Grossmann, Jonas, Wolski, Witold E., Schlapbach, Ralph

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APOE2, E3, and E4 differentially modulate cellular homeostasis, cholesterol metabolism, and inflammatory response in isogenic iPSC-derived astrocytes von de Leeuw, Sherida M., Kirschner, Aron W.T., Lindner, Karina, Rust, Ruslan, Budny, Vanessa, Wolski, Witold E., Gavin, Anne-Claude, Nitsch, Roger M., Tackenberg, Christian

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Proceedings of the EuBIC-MS developers meeting 2023 von Beltrao, Pedro, Van Den Bossche, Tim, Gabriels, Ralf, Holstein, Tanja, Kockmann, Tobias, Nameni, Alireza, Panse, Christian, Schlapbach, Ralph, Lautenbacher, Ludwig, Mattanovich, Matthias, Nesvizhskii, Alexey, Van Puyvelde, Bart, Scheid, Jonas, Schwämmle, Veit, Strauss, Maximilian, Susmelj, Anna Klimovskaia, The, Matthew, Webel, Henry, Wilhelm, Mathias, Winkelhardt, Dirk, Wolski, Witold E., Xi, Muyao

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Calibration of mass spectrometric peptide mass fingerprint data without specific external or internal calibrants von Wolski, Witold E, Lalowski, Maciej, Jungblut, Peter, Reinert, Knut

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APOE2, E3, and E4 differentially modulate cellular homeostasis, cholesterol metabolism, and inflammatory response in isogenic iPSC-derived astrocytes von de Leeuw, Sherida M., Kirschner, Aron W.T., Lindner, Karina, Rust, Ruslan, Budny, Vanessa, Wolski, Witold E., Gavin, Anne-Claude, Nitsch, Roger M., Tackenberg, Christian

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Transformation and other factors of the peptide mass spectrometry pairwise peak-list comparison process von Wolski, Witold E, Lalowski, Maciej, Martus, Peter, Herwig, Ralf, Giavalisco, Patrick, Gobom, Johan, Sickmann, Albert, Lehrach, Hans, Reinert, Knut

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Proteomic identification of proliferation and progression markers in human polycythemia vera stem and progenitor cells von Tan, Ge, Wolski, Witold E., Kummer, Sandra, Hofstetter, Mara, Theocharides, Alexandre P.A., Manz, Markus G., Aebersold, Ruedi, Meier-Abt, Fabienne

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Analytical model of peptide mass cluster centres with applications von Wolski, Witold E, Farrow, Malcolm, Emde, Anne-Katrin, Lehrach, Hans, Lalowski, Maciej, Reinert, Knut

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Aggregatibacter actinomycetemcomitans H-NS promotes biofilm formation and alters protein dynamics of other species within a polymicrobial oral biofilm von Bao, Kai, Bostanci, Nagihan, Thurnheer, Thomas, Grossmann, Jonas, Wolski, Witold E., Thay, Bernard, Belibasakis, Georgios N., Oscarsson, Jan

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Proceedings of the EuBIC-MS developers meeting 2023 von Beltrao, Pedro, Van Den Bossche, Tim, Gabriels, Ralf, Holstein, Tanja, Kockmann, Tobias, Nameni, Alireza, Panse, Christian, Schlapbach, Ralph, Lautenbacher, Ludwig, Mattanovich, Matthias, Nesvizhskii, Alexey, Van Puyvelde, Bart, Scheid, Jonas, Schwammle, Veit, Strauss, Maximilian, Susmelj, Anna Klimovskaia, The, Matthew, Webel, Henry, Wilhelm, Mathias, Winkelhardt, Dirk, Wolski, Witold E, Xi, Muyao

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