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Proteomics 4D: The proteome in context

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Publications

Systematic characterization of pan‐cancer mutation clusters

Author(s): Buljan, Marija; Blattmann, Peter; Aebersold, Ruedi; Boutros, Michael
Published in: Molecular Systems Biology, Issue 1, 2018, ISSN 1744-4292
DOI: 10.3929/ethz-b-000256182

Inference and quantification of peptidoforms in large sample cohorts by SWATH-MS

Author(s): George Rosenberger, Yansheng Liu, Hannes L Röst, Christina Ludwig, Alfonso Buil, Ariel Bensimon, Martin Soste, Tim D Spector, Emmanouil T Dermitzakis, Ben C Collins, Lars Malmström, Ruedi Aebersold
Published in: Nature Biotechnology, Issue 35/8, 2017, Page(s) 781-788, ISSN 1087-0156
DOI: 10.1038/nbt.3908

Systems Pharmacology Dissection of Cholesterol Regulation Reveals Determinants of Large Pharmacodynamic Variability between Cell Lines

Author(s): Blattmann, Peter; Henriques, David; Zimmermann, Michael; Frommelt, Fabian; Sauer, Uwe; Saez-Rodriguez, Julio; Aebersold, Ruedi
Published in: Cell Systems, Issue 11, 2017, ISSN 2405-4712
DOI: 10.3929/ethz-b-000228208

A Proteomic Connectivity Map

Author(s): Christian Feller, Ruedi Aebersold
Published in: Cell Systems, Issue 6/4, 2018, Page(s) 403-405, ISSN 2405-4712
DOI: 10.1016/j.cels.2018.04.007

Structures of human PRC2 with its cofactors AEBP2 and JARID2

Author(s): Vignesh Kasinath, Marco Faini, Simon Poepsel, Dvir Reif, Xinyu Ashlee Feng, Goran Stjepanovic, Ruedi Aebersold, Eva Nogales
Published in: Science, Issue 359/6378, 2018, Page(s) 940-944, ISSN 0036-8075
DOI: 10.1126/science.aar5700

Molecular basis for disassembly of an importin:ribosomal protein complex by the escortin Tsr2

Author(s): Sabina Schütz, Erich Michel, Fred F. Damberger, Michaela Oplová, Cohue Peña, Alexander Leitner, Ruedi Aebersold, Frederic H.-T. Allain, Vikram Govind Panse
Published in: Nature Communications, Issue 9/1, 2018, ISSN 2041-1723
DOI: 10.1038/s41467-018-06160-x

Epigenetic stress responses induce muscle stem-cell ageing by Hoxa9 developmental signals

Author(s): Simon Schwörer, Friedrich Becker, Christian Feller, Ali H. Baig, Ute Köber, Henriette Henze, Johann M. Kraus, Beibei Xin, André Lechel, Daniel B. Lipka, Christy S. Varghese, Manuel Schmidt, Remo Rohs, Ruedi Aebersold, Kay L. Medina, Hans A. Kestler, Francesco Neri, Julia von Maltzahn, Stefan Tümpel, K. Lenhard Rudolph
Published in: Nature, Issue 540/7633, 2016, Page(s) 428-432, ISSN 0028-0836
DOI: 10.1038/nature20603

Structure of a human cap-dependent 48S translation pre-initiation complex

Author(s): Boris Eliseev, Lahari Yeramala, Alexander Leitner, Manikandan Karuppasamy, Etienne Raimondeau, Karine Huard, Elena Alkalaeva, Ruedi Aebersold, Christiane Schaffitzel
Published in: Nucleic Acids Research, Issue 46/5, 2018, Page(s) 2678-2689, ISSN 0305-1048
DOI: 10.1093/nar/gky054

System-wide quantitative proteomics of the metabolic syndrome in mice: genotypic and dietary effects

Author(s): Terfve C, Sabidó E, Wu Y, Gonçalves E, Choi M, Vaga S, Vitek O, Saez-Rodriguez J, Aebersold R.
Published in: Journal of Proteome Research, 2016, ISSN 1535-3893

Data‐independent acquisition‐based SWATH‐MS for quantitative proteomics: a tutorial

Author(s): Christina Ludwig, Ludovic Gillet, George Rosenberger, Sabine Amon, Ben C Collins, Ruedi Aebersold
Published in: Molecular Systems Biology, Issue 14/8, 2018, Page(s) e8126, ISSN 1744-4292
DOI: 10.15252/msb.20178126

Integrative Structural Investigation on the Architecture of Human Importin4_Histone H3/H4_Asf1a Complex and Its Histone H3 Tail Binding

Author(s): Jungmin Yoon, Seung Joong Kim, Sojin An, Saehyun Cho, Alexander Leitner, Taeyang Jung, Ruedi Aebersold, Hans Hebert, Uhn-Soo Cho, Ji-Joon Song
Published in: Journal of Molecular Biology, Issue 430/6, 2018, Page(s) 822-841, ISSN 0022-2836
DOI: 10.1016/j.jmb.2018.01.015

Systematic proteome and proteostasis profiling in human Trisomy 21 fibroblast cells

Author(s): Yansheng Liu, Christelle Borel, Li Li, Torsten Müller, Evan G. Williams, Pierre-Luc Germain, Marija Buljan, Tatjana Sajic, Paul J. Boersema, Wenguang Shao, Marco Faini, Giuseppe Testa, Andreas Beyer, Stylianos E. Antonarakis, Ruedi Aebersold
Published in: Nature Communications, Issue 8/1, 2017, ISSN 2041-1723
DOI: 10.1038/s41467-017-01422-6

Molecular basis of AKAP79 regulation by calmodulin

Author(s): Neha Patel, Florian Stengel, Ruedi Aebersold, Matthew G. Gold
Published in: Nature Communications, Issue 8/1, 2017, ISSN 2041-1723
DOI: 10.1038/s41467-017-01715-w

Structural insights into the assembly and polyA signal recognition mechanism of the human CPSF complex

Author(s): Marcello Clerici, Marco Faini, Ruedi Aebersold, Martin Jinek
Published in: eLife, Issue 6, 2017, ISSN 2050-084X
DOI: 10.7554/eLife.33111

Statistical control of peptide and protein error rates in large-scale targeted data-independent acquisition analyses

Author(s): George Rosenberger, Isabell Bludau, Uwe Schmitt, Moritz Heusel, Christie L Hunter, Yansheng Liu, Michael J MacCoss, Brendan X MacLean, Alexey I Nesvizhskii, Patrick G A Pedrioli, Lukas Reiter, Hannes L Röst, Stephen Tate, Ying S Ting, Ben C Collins, Ruedi Aebersold
Published in: Nature Methods, Issue 14/9, 2017, Page(s) 921-927, ISSN 1548-7091
DOI: 10.1038/NMETH.4398

Impact of Alternative Splicing on the Human Proteome

Author(s): Yansheng Liu, Mar Gonzàlez-Porta, Sergio Santos, Alvis Brazma, John C. Marioni, Ruedi Aebersold, Ashok R. Venkitaraman, Vihandha O. Wickramasinghe
Published in: Cell Reports, Issue 20/5, 2017, Page(s) 1229-1241, ISSN 2211-1247
DOI: 10.1016/j.celrep.2017.07.025

Quantitative proteomics: challenges and opportunities in basic and applied research

Author(s): Olga T Schubert, Hannes L Röst, Ben C Collins, George Rosenberger, Ruedi Aebersold
Published in: Nature Protocols, Issue 12/7, 2017, Page(s) 1289-1294, ISSN 1754-2189
DOI: 10.1038/nprot.2017.040

Multi-laboratory assessment of reproducibility, qualitative and quantitative performance of SWATH-mass spectrometry

Author(s): Ben C. Collins, Christie L. Hunter, Yansheng Liu, Birgit Schilling, George Rosenberger, Samuel L. Bader, Daniel W. Chan, Bradford W. Gibson, Anne-Claude Gingras, Jason M. Held, Mio Hirayama-Kurogi, Guixue Hou, Christoph Krisp, Brett Larsen, Liang Lin, Siqi Liu, Mark P. Molloy, Robert L. Moritz, Sumio Ohtsuki, Ralph Schlapbach, Nathalie Selevsek, Stefani N. Thomas, Shin-Cheng Tzeng, Hui Zhang, Rued
Published in: Nature Communications, Issue 8/1, 2017, ISSN 2041-1723
DOI: 10.1038/s41467-017-00249-5

Precise Temporal Profiling of Signaling Complexes in Primary Cells Using SWATH Mass Spectrometry

Author(s): Etienne Caron, Romain Roncagalli, Takeshi Hase, Witold E. Wolski, Meena Choi, Marisa G. Menoita, Stephane Durand, Antonio García-Blesa, Ivo Fierro-Monti, Tatjana Sajic, Moritz Heusel, Tobias Weiss, Marie Malissen, Ralph Schlapbach, Ben C. Collins, Samik Ghosh, Hiroaki Kitano, Ruedi Aebersold, Bernard Malissen, Matthias Gstaiger
Published in: Cell Reports, Issue 18/13, 2017, Page(s) 3219-3226, ISSN 2211-1247
DOI: 10.1016/j.celrep.2017.03.019

Structural modeling of protein–RNA complexes using crosslinking of segmentally isotope-labeled RNA and MS/MS

Author(s): Georg Dorn, Alexander Leitner, Julien Boudet, Sébastien Campagne, Christine von Schroetter, Ahmed Moursy, Ruedi Aebersold, Frédéric H-T Allain
Published in: Nature Methods, Issue 14/5, 2017, Page(s) 487-490, ISSN 1548-7091
DOI: 10.1038/NMETH.4235

Building ProteomeTools based on a complete synthetic human proteome

Author(s): Daniel P Zolg, Mathias Wilhelm, Karsten Schnatbaum, Johannes Zerweck, Tobias Knaute, Bernard Delanghe, Derek J Bailey, Siegfried Gessulat, Hans-Christian Ehrlich, Maximilian Weininger, Peng Yu, Judith Schlegl, Karl Kramer, Tobias Schmidt, Ulrike Kusebauch, Eric W Deutsch, Ruedi Aebersold, Robert L Moritz, Holger Wenschuh, Thomas Moehring, Stephan Aiche, Andreas Huhmer, Ulf Reimer, Bernhard Kuster
Published in: Nature Methods, Issue 14/3, 2017, Page(s) 259-262, ISSN 1548-7091
DOI: 10.1038/NMETH.4153

On the Dependency of Cellular Protein Levels on mRNA Abundance

Author(s): Yansheng Liu, Andreas Beyer, Ruedi Aebersold
Published in: Cell, Issue 165/3, 2016, Page(s) 535-550, ISSN 0092-8674
DOI: 10.1016/j.cell.2016.03.014

A multicenter study benchmarks software tools for label-free proteome quantification

Author(s): Pedro Navarro, Jörg Kuharev, Ludovic C Gillet, Oliver M Bernhardt, Brendan MacLean, Hannes L Röst, Stephen A Tate, Chih-Chiang Tsou, Lukas Reiter, Ute Distler, George Rosenberger, Yasset Perez-Riverol, Alexey I Nesvizhskii, Ruedi Aebersold, Stefan Tenzer
Published in: Nature Biotechnology, Issue 34/11, 2016, Page(s) 1130-1136, ISSN 1087-0156
DOI: 10.1038/nbt.3685

Systems proteomics of liver mitochondria function

Author(s): E. G. Williams, Y. Wu, P. Jha, S. Dubuis, P. Blattmann, C. A. Argmann, S. M. Houten, T. Amariuta, W. Wolski, N. Zamboni, R. Aebersold, J. Auwerx
Published in: Science, Issue 352/6291, 2016, Page(s) aad0189-aad0189, ISSN 0036-8075
DOI: 10.1126/science.aad0189

Proteome-wide association studies identify biochemical modules associated with a wing-size phenotype in Drosophila melanogaster

Author(s): Hirokazu Okada, H. Alexander Ebhardt, Sibylle Chantal Vonesch, Ruedi Aebersold, Ernst Hafen
Published in: Nature Communications, Issue 7, 2016, Page(s) 12649, ISSN 2041-1723
DOI: 10.1038/ncomms12649

Human SRMAtlas: A Resource of Targeted Assays to Quantify the Complete Human Proteome

Author(s): Ulrike Kusebauch, David S. Campbell, Eric W. Deutsch, Caroline S. Chu, Douglas A. Spicer, Mi-Youn Brusniak, Joseph Slagel, Zhi Sun, Jeffrey Stevens, Barbara Grimes, David Shteynberg, Michael R. Hoopmann, Peter Blattmann, Alexander V. Ratushny, Oliver Rinner, Paola Picotti, Christine Carapito, Chung-Ying Huang, Meghan Kapousouz, Henry Lam, Tommy Tran, Emek Demir, John D. Aitchison, Chris Sander, Le
Published in: Cell, Issue 166/3, 2016, Page(s) 766-778, ISSN 0092-8674
DOI: 10.1016/j.cell.2016.06.041

TRIC: an automated alignment strategy for reproducible protein quantification in targeted proteomics

Author(s): Hannes L Röst, Yansheng Liu, Giuseppe D'Agostino, Matteo Zanella, Pedro Navarro, George Rosenberger, Ben C Collins, Ludovic Gillet, Giuseppe Testa, Lars Malmström, Ruedi Aebersold
Published in: Nature Methods, Issue 13/9, 2016, Page(s) 777-783, ISSN 1548-7091
DOI: 10.1038/nmeth.3954

Breast Cancer Classification Based on Proteotypes Obtained by SWATH Mass Spectrometry

Author(s): Pavel Bouchal, Olga T. Schubert, Jakub Faktor, Lenka Capkova, Hana Imrichova, Karolina Zoufalova, Vendula Paralova, Roman Hrstka, Yansheng Liu, Holger Alexander Ebhardt, Eva Budinska, Rudolf Nenutil, Ruedi Aebersold
Published in: Cell Reports, Issue 28/3, 2019, Page(s) 832-843.e7, ISSN 2211-1247
DOI: 10.1016/j.celrep.2019.06.046

Complex‐centric proteome profiling by SEC ‐ SWATH ‐ MS

Author(s): Moritz Heusel, Isabell Bludau, George Rosenberger, Robin Hafen, Max Frank, Amir Banaei‐Esfahani, Audrey Drogen, Ben C Collins, Matthias Gstaiger, Ruedi Aebersold
Published in: Molecular Systems Biology, Issue 15/1, 2019, ISSN 1744-4292
DOI: 10.15252/msb.20188438

Mass Spectrometric Exploration of the Biochemical Basis of Living Systems

Author(s): Ruedi Aebersold, Peter Blattmann
Published in: CHIMIA International Journal for Chemistry, Issue 73/7, 2019, Page(s) 540-548, ISSN 0009-4293
DOI: 10.2533/chimia.2019.540

Elucidating essential kinases of endothelin signalling by logic modelling of phosphoproteomics data

Author(s): Alexander Schäfer, Enio Gjerga, Richard WD Welford, Imke Renz, Francois Lehembre, Peter MA Groenen, Julio Saez‐Rodriguez, Ruedi Aebersold, Matthias Gstaiger
Published in: Molecular Systems Biology, Issue 15/8, 2019, ISSN 1744-4292
DOI: 10.15252/msb.20198828

Comparative analysis of mRNA and protein degradation in prostate tissues indicates high stability of proteins

Author(s): Shao, Wenguang; Guo, Tiannan; Toussaint, Nora C.; Xue, Peng; Wagner, Ulrich; Li, Li; Charmpi, Konstantina; Zhu, Yi; Wu, Jianmin; Buljan, Marija; Sun, Rui; Rutishauser, Dorothea; Hermanns, Thomas; Fankhauser, Christian Daniel; Poyet, Cedric; Ljubicic, Jelena; Rupp, Niels; Rüschoff, Jan H.; Zhong, Qing; Beyer, Andreas; Ji, Jiafu; Collins, Ben C.; Liu, Yansheng; Rätsch, Gunnar; Wild, Peter J.; Aebe
Published in: Shao, Wenguang <javascript:contributorCitation( 'Shao, Wenguang' );>; Guo, Tiannan <javascript:contributorCitation( 'Guo, Tiannan' );>; Toussaint, Nora C <javascript:contributorCitation( 'Toussaint, Nora C' );>; Xue, Peng <javascript:contributorCitation( 'Xue, Peng' );>; Wagner, Ulrich <javascript:contributorCitation( 'Wagner, Ulrich' );>; Li, Li <javascript:contri, Issue 8, 2019, ISSN 2041-1723
DOI: 10.5167/uzh-171764

Disentangling Genetic and Environmental Effects on the Proteotypes of Individuals

Author(s): Natalie Romanov, Michael Kuhn, Ruedi Aebersold, Alessandro Ori, Martin Beck, Peer Bork
Published in: Cell, Issue 177/5, 2019, Page(s) 1308-1318.e10, ISSN 0092-8674
DOI: 10.1016/j.cell.2019.03.015

The interactome of KRAB zinc finger proteins reveals the evolutionary history of their functional diversification

Author(s): Helleboid, Pierre-Yves; Heusel, Moritz; Duc, Julien; Piot, Cecile; Thorball, Christian W.; Coluccio, Andrea; Pontis, Julien; Turelli, Priscilla; Aebersold, Ruedi; Trono, Didier
Published in: The EMBO Journal, 38 (18), Issue 2, 2019, ISSN 0261-4189
DOI: 10.3929/ethz-b-000360670

Quantitative Proteome Landscape of the NCI-60 Cancer Cell Lines

Author(s): Guo, T.; Luna, A.; Rajapakse, V.N.; Koh, C.C.; Wu, Z.; Liu, W.; Sun, Y.; Gao, H.; Menden, M.P.; Xu, C.; Calzone, L.; Martignetti, L.; Auwerx, C.; Buljan, M.; Banaei-Esfahani, A.; Ori, A.; Iskar, M.; Gillet, L.; Bi, R.; Zhang, J.; Zhang, H.; Yu, C.; Zhong, Q.; Varma, S.; Schmitt, U.; Qiu, P.; Zhang, Q.; Zhu, Y.; Wild, P.J.; Garnett, M.J.; Bork, P.; Beck, M.; Liu, K.; Saez-Rodriguez, J.; Elloumi, F.
Published in: iScience, 21, Issue 5, 2019, ISSN 1538-8514
DOI: 10.3929/ethz-b-000378057

Insights into autophagosome biogenesis from structural and biochemical analyses of the ATG2A-WIPI4 complex

Author(s): Saikat Chowdhury, Chinatsu Otomo, Alexander Leitner, Kazuto Ohashi, Ruedi Aebersold, Gabriel C. Lander, Takanori Otomo
Published in: Proceedings of the National Academy of Sciences, Issue 115/42, 2018, Page(s) E9792-E9801, ISSN 0027-8424
DOI: 10.1073/pnas.1811874115

Generation of a zebrafish SWATH-MS spectral library to quantify 10,000 proteins

Author(s): Peter Blattmann, Vivienne Stutz, Giulia Lizzo, Joy Richard, Philipp Gut, Ruedi Aebersold
Published in: Scientific Data, Issue 6/1, 2019, ISSN 2052-4463
DOI: 10.1038/sdata.2019.11

Multi-omic measurements of heterogeneity in HeLa cells across laboratories

Author(s): Yansheng Liu, Yang Mi, Torsten Mueller, Saskia Kreibich, Evan G. Williams, Audrey Van Drogen, Christelle Borel, Max Frank, Pierre-Luc Germain, Isabell Bludau, Martin Mehnert, Michael Seifert, Mario Emmenlauer, Isabel Sorg, Fedor Bezrukov, Frederique Sloan Bena, Hu Zhou, Christoph Dehio, Giuseppe Testa, Julio Saez-Rodriguez, Stylianos E. Antonarakis, Wolf-Dietrich Hardt, Ruedi Aebersold
Published in: Nature Biotechnology, Issue 37/3, 2019, Page(s) 314-322, ISSN 1087-0156
DOI: 10.1038/s41587-019-0037-y

The Chaperonin TRiC/CCT Associates with Prefoldin through a Conserved Electrostatic Interface Essential for Cellular Proteostasis

Author(s): Daniel Gestaut, Soung Hun Roh, Boxue Ma, Grigore Pintilie, Lukasz A. Joachimiak, Alexander Leitner, Thomas Walzthoeni, Ruedi Aebersold, Wah Chiu, Judith Frydman
Published in: Cell, Issue 177/3, 2019, Page(s) 751-765.e15, ISSN 0092-8674
DOI: 10.1016/j.cell.2019.03.012

The MLL1 trimeric catalytic complex is a dynamic conformational ensemble stabilized by multiple weak interactions

Author(s): Lilia Kaustov, Alexander Lemak, Hong Wu, Marco Faini, Lixin Fan, Xianyang Fang, Hong Zeng, Shili Duan, Abdellah Allali-Hassani, Fengling Li, Yong Wei, Masoud Vedadi, Ruedi Aebersold, Yunxing Wang, Scott Houliston, Cheryl H Arrowsmith
Published in: Nucleic Acids Research, 2019, ISSN 0305-1048
DOI: 10.1093/nar/gkz697

Quantitative Interactomics in Primary T Cells Provides a Rationale for Concomitant PD-1 and BTLA Coinhibitor Blockade in Cancer Immunotherapy

Author(s): Javier Celis-Gutierrez, Peter Blattmann, Yunhao Zhai, Nicolas Jarmuzynski, Kilian Ruminski, Claude Grégoire, Youcef Ounoughene, Frédéric Fiore, Ruedi Aebersold, Romain Roncagalli, Matthias Gstaiger, Bernard Malissen
Published in: Cell Reports, Issue 27/11, 2019, Page(s) 3315-3330.e7, ISSN 2211-1247
DOI: 10.1016/j.celrep.2019.05.041

A Global Screen for Assembly State Changes of the Mitotic Proteome by SEC-SWATH-MS

Author(s): Moritz Heusel, Max Frank, Mario Köhler, Sabine Amon, Fabian Frommelt, George Rosenberger, Isabell Bludau, Simran Aulakh, Monika I. Linder, Yansheng Liu, Ben C. Collins, Matthias Gstaiger, Ulrike Kutay, Ruedi Aebersold
Published in: Cell Systems, Issue 10/2, 2020, Page(s) 133-155.e6, ISSN 2405-4712
DOI: 10.1016/j.cels.2020.01.001

ChromID identifies the protein interactome at chromatin marks

Author(s): Rodrigo Villaseñor, Ramon Pfaendler, Christina Ambrosi, Stefan Butz, Sara Giuliani, Elana Bryan, Thomas W. Sheahan, Annika L. Gable, Nina Schmolka, Massimiliano Manzo, Joël Wirz, Christian Feller, Christian von Mering, Ruedi Aebersold, Philipp Voigt, Tuncay Baubec
Published in: Nature Biotechnology, 2020, ISSN 1087-0156
DOI: 10.1038/s41587-020-0434-2

A Conserved Mito-Cytosolic Translational Balance Links Two Longevity Pathways

Author(s): Marte Molenaars, Georges E. Janssens, Evan G. Williams, Aldo Jongejan, Jiayi Lan, Sylvie Rabot, Fatima Joly, Perry D. Moerland, Bauke V. Schomakers, Marco Lezzerini, Yasmine J. Liu, Mark A. McCormick, Brian K. Kennedy, Michel van Weeghel, Antoine H.C. van Kampen, Ruedi Aebersold, Alyson W. MacInnes, Riekelt H. Houtkooper
Published in: Cell Metabolism, Issue 31/3, 2020, Page(s) 549-563.e7, ISSN 1550-4131
DOI: 10.1016/j.cmet.2020.01.011

Automated SWATH Data Analysis Using Targeted Extraction of Ion Chromatograms

Author(s): Hannes L. Röst, Ruedi Aebersold, Olga T. Schubert
Published in: Proteomics: Methods and Protocols, 2017, Page(s) 289-307
DOI: 10.1007/978-1-4939-6747-6_20