Protocol for high-throughput semi-automated label-free- or TMT-based phosphoproteome profiling by Claire Koenig, Ana Martinez-Val, Previn Naicker, Stoyan Stoychev, Justin Jordaan, Jesper V. Olsen

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Proteomics of resistance to Notch1 inhibition in acute lymphoblastic leukemia reveals targetable kinase signatures by Giulia Franciosa, Jos G. A. Smits, Sonia Minuzzo, Ana Martinez-Val, Stefano Indraccolo, Jesper V. Olsen

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Dissection of two routes to naïve pluripotency using different kinase inhibitors by Ana Martinez-Val, Cian J. Lynch, Isabel Calvo, Pilar Ximénez-Embún, Fernando Garcia, Eduardo Zarzuela, Manuel Serrano, Javier Munoz

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PRMT5-mediated regulatory arginine methylation of RIPK3 by Chanchal Chauhan, Ana Martinez-Val, Rainer Niedenthal, Jesper Velgaard Olsen, Alexey Kotlyarov, Simon Bekker-Jensen, Matthias Gaestel, Manoj B. Menon

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Rapid and site-specific deep phosphoproteome profiling by data-independent acquisition without the need for spectral libraries by Dorte B. Bekker-Jensen, Oliver M. Bernhardt, Alexander Hogrebe, Ana Martinez-Val, Lynn Verbeke, Tejas Gandhi, Christian D. Kelstrup, Lukas Reiter, Jesper V. Olsen

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iSanXoT: A standalone application for the integrative analysis of mass spectrometry-based quantitative proteomics data by Jose Manuel Rodríguez, Inmaculada Jorge, Ana Martinez-Val, Rafael Barrero-Rodríguez, Ricardo Magni, Estefanía Núñez, Andrea Laguillo, Cristina A. Devesa, Juan A. López, Emilio Camafeita, Jesús Vázquez

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Hybrid-DIA: intelligent data acquisition integrates targeted and discovery proteomics to analyze phospho-signaling in single spheroids by Ana Martínez-Val, Kyle Fort, Claire Koenig, Leander Van der Hoeven, Giulia Franciosa, Thomas Moehring, Yasushi Ishihama, Yu-ju Chen, Alexander Makarov, Yue Xuan, Jesper V. Olsen

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The RNA Polymerase II Factor RPAP1 Is Critical for Mediator-Driven Transcription and Cell Identity by Cian J. Lynch, Raquel Bernad, Isabel Calvo, Sandrina Nóbrega-Pereira, Sergio Ruiz, Nuria Ibarz, Ana Martinez-Val, Osvaldo Graña-Castro, Gonzalo Gómez-López, Eduardo Andrés-León, Vladimir Espinosa Angarica, Antonio del Sol, Sagrario Ortega, Oscar Fernandez-Capetillo, Enrique Rojo, Javier Munoz, Manuel Serrano

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Spatial-proteomics reveals phospho-signaling dynamics at subcellular resolution by Ana Martinez-Val, Dorte B. Bekker-Jensen, Sophia Steigerwald, Claire Koenig, Ole Østergaard, Adi Mehta, Trung Tran, Krzysztof Sikorski, Estefanía Torres-Vega, Ewa Kwasniewicz, Sólveig Hlín Brynjólfsdóttir, Lisa B. Frankel, Rasmus Kjøbsted, Nicolai Krogh, Alicia Lundby, Simon Bekker-Jensen, Fridtjof Lund-Johansen, Jesper V. Olsen

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