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PROTEOMICS4D SIGNED

Proteomics 4D: The proteome in context

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EC-Contrib. €

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 Outcomes and results

 PROTEOMICS4D project word cloud

Explore the words cloud of the PROTEOMICS4D project. It provides you a very rough idea of what is the project "PROTEOMICS4D" about.

comprehensively    linking    context    perturbations    array    mechanistic    functional    medicine    structure    transformation    transcriptomics    composition    tenants    structural    kinase    genomic    biology    single    integration    phenotypes    perturbed    data    seemingly    initially    protein    entity    chemical    molecular    topology    consisting    elusive    proteome    gwas    output    proteomics    base    modules    wgs    generate    4d    epigenetic    cross    tissue    variants    cancer    genetic    phosphoproteomic    elements    explores    notion    interactions    mutations    basic    probe    technologies    science    spectrometry    few    disease    hybrid    supporting    independent    mass    broad    generalize    proteomic    genetically    modular    catalyze    multiple    interacting    wild    quantitative    integrate    computational    biochemical    arise    cryoem    perturbation    disseminated    proteins    relate    powerful   

Project "PROTEOMICS4D" data sheet

The following table provides information about the project.

Coordinator		 EIDGENOESSISCHE TECHNISCHE HOCHSCHULE ZUERICH 

Organization address
address: Raemistrasse 101
city: ZUERICH
postcode: 8092
website: https://www.ethz.ch/de.html

contact info
title: n.a.
name: n.a.
surname: n.a.
function: n.a.
email: n.a.
telephone: n.a.
fax: n.a.
 Coordinator Country Switzerland [CH]
 Project website http://www.imsb.ethz.ch/research/aebersold.html
 Total cost 2˙208˙150 €
 EC max contribution 2˙208˙150 € (100%)
 Programme 1. H2020-EU.1.1. (EXCELLENT SCIENCE - European Research Council (ERC))
 Code Call ERC-2014-ADG
 Funding Scheme ERC-ADG
 Starting year 2015
 Duration (year-month-day) from 2015-09-01   to  2020-08-31

 Partnership

Take a look of project's partnership.

# participants  country  role  EC contrib. [€] 
1    EIDGENOESSISCHE TECHNISCHE HOCHSCHULE ZUERICH CH (ZUERICH) coordinator 2˙208˙150.00

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 Project objective

Elements operating in the context of a system generate results that are different from the simple addition of the results of each element. This notion is one of the basic tenants of systems science. In systems biology/medicine complex (disease) phenotypes arise from multiple interacting factors, specifically proteins. Yet, the biochemical and mechanistic base of complex phenotypes remain elusive. An array of powerful genomic technologies including GWAS, WGS, transcriptomics, epigenetic analyses and proteomics have identified numerous factors that contribute to complex phenotypes. It can be expected that over the next few years, genetic factors contributing to specific complex phenotypes will be comprehensively identified, while their interactions will remain elusive. The project “Proteomics 4D: The proteome in context “explores the concept, that complex phenotypes arise from the perturbation of modules of interacting proteins and that these modules integrate seemingly independent genomic variants into a single biochemical response. We will develop and apply a generic technology to directly measure the composition, topology and structure of wild type and genetically perturbed protein modules and relate structural changes to their functional output. This will be achieved by a the integration of quantitative proteomic and phosphoproteomic technologies determining molecular phenotypes, and hybrid structural methods consisting of chemical cross-linking and mass spectrometry, cryoEM and computational data integration to probe structural perturbations. The project will focus initially on the structural and functional effects of cancer associated mutations in protein kinase modules and then generalize to study perturbed modules in any tissue and disease state. The resources supporting this technology will be disseminated to catalyze a broad transformation of biology and molecular medicine towards the analysis of the proteome as a modular entity, the proteome in context.

 Publications

year authors and title journal last update
List of publications.
2018 Saikat Chowdhury, Chinatsu Otomo, Alexander Leitner, Kazuto Ohashi, Ruedi Aebersold, Gabriel C. Lander, Takanori Otomo
Insights into autophagosome biogenesis from structural and biochemical analyses of the ATG2A-WIPI4 complex
published pages: E9792-E9801, ISSN: 0027-8424, DOI: 10.1073/pnas.1811874115 		Proceedings of the National Academy of Sciences 115/42 2020-04-15
2019 Helleboid, Pierre-Yves; Heusel, Moritz; Duc, Julien; Piot, Cecile; Thorball, Christian W.; Coluccio, Andrea; Pontis, Julien; Turelli, Priscilla; Aebersold, Ruedi; Trono, Didier
The interactome of KRAB zinc finger proteins reveals the evolutionary history of their functional diversification
published pages: , ISSN: 0261-4189, DOI: 10.3929/ethz-b-000360670 		The EMBO Journal, 38 (18) 2 2020-04-15
2019 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.
Quantitative Proteome Landscape of the NCI-60 Cancer Cell Lines
published pages: , ISSN: 1538-8514, DOI: 10.3929/ethz-b-000378057 		iScience, 21 5 2020-04-15
2018 Yi Zhu, Jiang Zhu, Cong Lu, Qiushi Zhang, Wei Xie, Ping Sun, Xiaochuan Dong, Liang Yue, Yaoting Sun, Xiao Yi, Tiansheng Zhu, Guan Ruan, Ruedi Aebersold, Shi\'ang Huang, Tiannan Guo
Identification of Protein Abundance Changes in Hepatocellular Carcinoma Tissues Using PCT–SWATH
published pages: 1700179, ISSN: 1862-8346, DOI: 10.1002/prca.201700179 		PROTEOMICS – Clinical Applications 13/1 2020-04-15
2019 Natalie Romanov, Michael Kuhn, Ruedi Aebersold, Alessandro Ori, Martin Beck, Peer Bork
Disentangling Genetic and Environmental Effects on the Proteotypes of Individuals
published pages: 1308-1318.e10, ISSN: 0092-8674, DOI: 10.1016/j.cell.2019.03.015 		Cell 177/5 2020-04-15
2019 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
Comparative analysis of mRNA and protein degradation in prostate tissues indicates high stability of proteins
published pages: , ISSN: 2041-1723, DOI: 10.5167/uzh-171764 		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 8 2020-04-15
2020 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
A Conserved Mito-Cytosolic Translational Balance Links Two Longevity Pathways
published pages: 549-563.e7, ISSN: 1550-4131, DOI: 10.1016/j.cmet.2020.01.011 		Cell Metabolism 31/3 2020-04-15
2020 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
ChromID identifies the protein interactome at chromatin marks
published pages: , ISSN: 1087-0156, DOI: 10.1038/s41587-020-0434-2 		Nature Biotechnology 2020-04-15
2019 Daniel Gestaut, Soung Hun Roh, Boxue Ma, Grigore Pintilie, Lukasz A. Joachimiak, Alexander Leitner, Thomas Walzthoeni, Ruedi Aebersold, Wah Chiu, Judith Frydman
The Chaperonin TRiC/CCT Associates with Prefoldin through a Conserved Electrostatic Interface Essential for Cellular Proteostasis
published pages: 751-765.e15, ISSN: 0092-8674, DOI: 10.1016/j.cell.2019.03.012 		Cell 177/3 2020-04-15
2019 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
Multi-omic measurements of heterogeneity in HeLa cells across laboratories
published pages: 314-322, ISSN: 1087-0156, DOI: 10.1038/s41587-019-0037-y 		Nature Biotechnology 37/3 2020-04-15
2019 Peter Blattmann, Vivienne Stutz, Giulia Lizzo, Joy Richard, Philipp Gut, Ruedi Aebersold
Generation of a zebrafish SWATH-MS spectral library to quantify 10,000 proteins
published pages: , ISSN: 2052-4463, DOI: 10.1038/sdata.2019.11 		Scientific Data 6/1 2020-04-15
2019 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
Quantitative Interactomics in Primary T Cells Provides a Rationale for Concomitant PD-1 and BTLA Coinhibitor Blockade in Cancer Immunotherapy
published pages: 3315-3330.e7, ISSN: 2211-1247, DOI: 10.1016/j.celrep.2019.05.041 		Cell Reports 27/11 2020-04-15
2019 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
Breast Cancer Classification Based on Proteotypes Obtained by SWATH Mass Spectrometry
published pages: 832-843.e7, ISSN: 2211-1247, DOI: 10.1016/j.celrep.2019.06.046 		Cell Reports 28/3 2020-04-15
2020 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
A Global Screen for Assembly State Changes of the Mitotic Proteome by SEC-SWATH-MS
published pages: 133-155.e6, ISSN: 2405-4712, DOI: 10.1016/j.cels.2020.01.001 		Cell Systems 10/2 2020-04-15
2019 Alexander Schäfer, Enio Gjerga, Richard WD Welford, Imke Renz, Francois Lehembre, Peter MA Groenen, Julio Saez‐Rodriguez, Ruedi Aebersold, Matthias Gstaiger
Elucidating essential kinases of endothelin signalling by logic modelling of phosphoproteomics data
published pages: , ISSN: 1744-4292, DOI: 10.15252/msb.20198828 		Molecular Systems Biology 15/8 2020-04-15
2019 Sabine Amon, Fabienne Meier-Abt, Ludovic C. Gillet, Slavica Dimitrieva, Alexandre P. A. Theocharides, Markus G. Manz, Ruedi Aebersold
Sensitive Quantitative Proteomics of Human Hematopoietic Stem and Progenitor Cells by Data-independent Acquisition Mass Spectrometry
published pages: 1454-1467, ISSN: 1535-9476, DOI: 10.1074/mcp.TIR119.001431 		Molecular & Cellular Proteomics 18/7 2020-04-15
2019 Ruedi Aebersold, Peter Blattmann
Mass Spectrometric Exploration of the Biochemical Basis of Living Systems
published pages: 540-548, ISSN: 0009-4293, DOI: 10.2533/chimia.2019.540 		CHIMIA International Journal for Chemistry 73/7 2020-04-15
2019 Moritz Heusel, Isabell Bludau, George Rosenberger, Robin Hafen, Max Frank, Amir Banaei‐Esfahani, Audrey Drogen, Ben C Collins, Matthias Gstaiger, Ruedi Aebersold
Complex‐centric proteome profiling by SEC ‐ SWATH ‐ MS
published pages: , ISSN: 1744-4292, DOI: 10.15252/msb.20188438 		Molecular Systems Biology 15/1 2020-04-15
2019 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
The MLL1 trimeric catalytic complex is a dynamic conformational ensemble stabilized by multiple weak interactions
published pages: , ISSN: 0305-1048, DOI: 10.1093/nar/gkz697 		Nucleic Acids Research 2020-04-15
2016 Hirokazu Okada, H. Alexander Ebhardt, Sibylle Chantal Vonesch, Ruedi Aebersold, Ernst Hafen
Proteome-wide association studies identify biochemical modules associated with a wing-size phenotype in Drosophila melanogaster
published pages: 12649, ISSN: 2041-1723, DOI: 10.1038/ncomms12649 		Nature Communications 7 2019-07-05
2016 Yansheng Liu, Andreas Beyer, Ruedi Aebersold
On the Dependency of Cellular Protein Levels on mRNA Abundance
published pages: 535-550, ISSN: 0092-8674, DOI: 10.1016/j.cell.2016.03.014 		Cell 165/3 2019-07-05
2016 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
Human SRMAtlas: A Resource of Targeted Assays to Quantify the Complete Human Proteome
published pages: 766-778, ISSN: 0092-8674, DOI: 10.1016/j.cell.2016.06.041 		Cell 166/3 2019-07-05
2016 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
TRIC: an automated alignment strategy for reproducible protein quantification in targeted proteomics
published pages: 777-783, ISSN: 1548-7091, DOI: 10.1038/nmeth.3954 		Nature Methods 13/9 2019-07-05
2017 Blattmann, Peter; Henriques, David; Zimmermann, Michael; Frommelt, Fabian; Sauer, Uwe; Saez-Rodriguez, Julio; Aebersold, Ruedi
Systems Pharmacology Dissection of Cholesterol Regulation Reveals Determinants of Large Pharmacodynamic Variability between Cell Lines
published pages: , ISSN: 2405-4712, DOI: 10.3929/ethz-b-000228208 		Cell Systems 11 2019-07-05
2016 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
Systems proteomics of liver mitochondria function
published pages: aad0189-aad0189, ISSN: 0036-8075, DOI: 10.1126/science.aad0189 		Science 352/6291 2019-07-05
2018 Buljan, Marija; Blattmann, Peter; Aebersold, Ruedi; Boutros, Michael
Systematic characterization of pan‐cancer mutation clusters
published pages: , ISSN: 1744-4292, DOI: 10.3929/ethz-b-000256182 		Molecular Systems Biology 1 2019-07-05
2017 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
Inference and quantification of peptidoforms in large sample cohorts by SWATH-MS
published pages: 781-788, ISSN: 1087-0156, DOI: 10.1038/nbt.3908 		Nature Biotechnology 35/8 2019-07-05
2016 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
A multicenter study benchmarks software tools for label-free proteome quantification
published pages: 1130-1136, ISSN: 1087-0156, DOI: 10.1038/nbt.3685 		Nature Biotechnology 34/11 2019-07-05
2017 Xiaorong Wang, Peter Cimermancic, Clinton Yu, Andreas Schweitzer, Nikita Chopra, James L. Engel, Charles H Greenberg, Alexander S Huszagh, Florian Beck, Eri Sakata, Yingying Yang, Eric J Novitsky, Alexander Leitner, Paolo Nanni, Abdullah Kahraman, Xing Guo, Jack E Dixon, Scott D Rychnovsky, Ruedi Aebersold, Wolfgang Baumeister, Andrej Sali, Lan Huang
Molecular Details Underlying Dynamic Structures and Regulation of the Human 26S Proteasome
published pages: mcp.M116.065326, ISSN: 1535-9476, DOI: 10.1074/mcp.M116.065326 		Molecular & Cellular Proteomics 2019-07-05
2017 Yansheng Liu, Mar Gonzàlez-Porta, Sergio Santos, Alvis Brazma, John C. Marioni, Ruedi Aebersold, Ashok R. Venkitaraman, Vihandha O. Wickramasinghe
Impact of Alternative Splicing on the Human Proteome
published pages: 1229-1241, ISSN: 2211-1247, DOI: 10.1016/j.celrep.2017.07.025 		Cell Reports 20/5 2019-04-18
2017 Olga T Schubert, Hannes L Röst, Ben C Collins, George Rosenberger, Ruedi Aebersold
Quantitative proteomics: challenges and opportunities in basic and applied research
published pages: 1289-1294, ISSN: 1754-2189, DOI: 10.1038/nprot.2017.040 		Nature Protocols 12/7 2019-04-18
2018 Sabina Schütz, Erich Michel, Fred F. Damberger, Michaela Oplová, Cohue Peña, Alexander Leitner, Ruedi Aebersold, Frederic H.-T. Allain, Vikram Govind Panse
Molecular basis for disassembly of an importin:ribosomal protein complex by the escortin Tsr2
published pages: , ISSN: 2041-1723, DOI: 10.1038/s41467-018-06160-x 		Nature Communications 9/1 2019-04-18
2016 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
Epigenetic stress responses induce muscle stem-cell ageing by Hoxa9 developmental signals
published pages: 428-432, ISSN: 0028-0836, DOI: 10.1038/nature20603 		Nature 540/7633 2019-04-18
2017 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
Building ProteomeTools based on a complete synthetic human proteome
published pages: 259-262, ISSN: 1548-7091, DOI: 10.1038/NMETH.4153 		Nature Methods 14/3 2019-04-18
2018 Vignesh Kasinath, Marco Faini, Simon Poepsel, Dvir Reif, Xinyu Ashlee Feng, Goran Stjepanovic, Ruedi Aebersold, Eva Nogales
Structures of human PRC2 with its cofactors AEBP2 and JARID2
published pages: 940-944, ISSN: 0036-8075, DOI: 10.1126/science.aar5700 		Science 359/6378 2019-04-18
2016 Terfve C, Sabidó E, Wu Y, Gonçalves E, Choi M, Vaga S, Vitek O, Saez-Rodriguez J, Aebersold R.
System-wide quantitative proteomics of the metabolic syndrome in mice: genotypic and dietary effects
published pages: , ISSN: 1535-3893, DOI: 		Journal of Proteome Research 2019-04-18
2018 Christina Ludwig, Ludovic Gillet, George Rosenberger, Sabine Amon, Ben C Collins, Ruedi Aebersold
Data‐independent acquisition‐based SWATH‐MS for quantitative proteomics: a tutorial
published pages: e8126, ISSN: 1744-4292, DOI: 10.15252/msb.20178126 		Molecular Systems Biology 14/8 2019-04-18
2017 Marcello Clerici, Marco Faini, Ruedi Aebersold, Martin Jinek
Structural insights into the assembly and polyA signal recognition mechanism of the human CPSF complex
published pages: , ISSN: 2050-084X, DOI: 10.7554/eLife.33111 		eLife 6 2019-04-18
2017 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
Precise Temporal Profiling of Signaling Complexes in Primary Cells Using SWATH Mass Spectrometry
published pages: 3219-3226, ISSN: 2211-1247, DOI: 10.1016/j.celrep.2017.03.019 		Cell Reports 18/13 2019-04-18
2018 Julia Hülsmann, Bojana Kravic, Matthias Weith, Matthias Gstaiger, Ruedi Aebersold, Ben C. Collins, Hemmo Meyer
AP-SWATH Reveals Direct Involvement of VCP/p97 in Integrated Stress Response Signaling Through Facilitating CReP/PPP1R15B Degradation
published pages: 1295-1307, ISSN: 1535-9476, DOI: 10.1074/mcp.RA117.000471 		Molecular & Cellular Proteomics 17/7 2019-04-18
2017 Wenguang Shao, Henry Lam
Tandem mass spectral libraries of peptides and their roles in proteomics research
published pages: 634-648, ISSN: 0277-7037, DOI: 10.1002/mas.21512 		Mass Spectrometry Reviews 36/5 2019-04-18
2017 Hannes L. Röst, Ruedi Aebersold, Olga T. Schubert
Automated SWATH Data Analysis Using Targeted Extraction of Ion Chromatograms
published pages: 289-307, ISSN: , DOI: 10.1007/978-1-4939-6747-6_20 		Proteomics: Methods and Protocols 2019-04-18
2018 Christian Feller, Ruedi Aebersold
A Proteomic Connectivity Map
published pages: 403-405, ISSN: 2405-4712, DOI: 10.1016/j.cels.2018.04.007 		Cell Systems 6/4 2019-04-18
2018 Jungmin Yoon, Seung Joong Kim, Sojin An, Saehyun Cho, Alexander Leitner, Taeyang Jung, Ruedi Aebersold, Hans Hebert, Uhn-Soo Cho, Ji-Joon Song
Integrative Structural Investigation on the Architecture of Human Importin4_Histone H3/H4_Asf1a Complex and Its Histone H3 Tail Binding
published pages: 822-841, ISSN: 0022-2836, DOI: 10.1016/j.jmb.2018.01.015 		Journal of Molecular Biology 430/6 2019-04-18
2018 Evan G. Williams, Yibo Wu, Witold Wolski, Jun Yong Kim, Jiayi Lan, Moaraj Hasan, Christian Halter, Pooja Jha, Dongryeol Ryu, Johan Auwerx, Ruedi Aebersold
Quantifying and Localizing the Mitochondrial Proteome Across Five Tissues in A Mouse Population
published pages: 1766-1777, ISSN: 1535-9476, DOI: 10.1074/mcp.RA118.000554 		Molecular & Cellular Proteomics 17/9 2019-04-18
2017 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
Systematic proteome and proteostasis profiling in human Trisomy 21 fibroblast cells
published pages: , ISSN: 2041-1723, DOI: 10.1038/s41467-017-01422-6 		Nature Communications 8/1 2019-04-18
2018 Boris Eliseev, Lahari Yeramala, Alexander Leitner, Manikandan Karuppasamy, Etienne Raimondeau, Karine Huard, Elena Alkalaeva, Ruedi Aebersold, Christiane Schaffitzel
Structure of a human cap-dependent 48S translation pre-initiation complex
published pages: 2678-2689, ISSN: 0305-1048, DOI: 10.1093/nar/gky054 		Nucleic Acids Research 46/5 2019-04-18
2017 Neha Patel, Florian Stengel, Ruedi Aebersold, Matthew G. Gold
Molecular basis of AKAP79 regulation by calmodulin
published pages: , ISSN: 2041-1723, DOI: 10.1038/s41467-017-01715-w 		Nature Communications 8/1 2019-04-18
2017 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
Statistical control of peptide and protein error rates in large-scale targeted data-independent acquisition analyses
published pages: 921-927, ISSN: 1548-7091, DOI: 10.1038/NMETH.4398 		Nature Methods 14/9 2019-04-18
2017 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, Ruedi Aebersold
Multi-laboratory assessment of reproducibility, qualitative and quantitative performance of SWATH-mass spectrometry
published pages: , ISSN: 2041-1723, DOI: 10.1038/s41467-017-00249-5 		Nature Communications 8/1 2019-04-18
2018 Marcello Clerici, Marco Faini, Lena M. Muckenfuss, Ruedi Aebersold, Martin Jinek
Author Correction: Structural basis of AAUAAA polyadenylation signal recognition by the human CPSF complex
published pages: 355-355, ISSN: 1545-9993, DOI: 10.1038/s41594-018-0044-6 		Nature Structural & Molecular Biology 25/4 2019-04-18
2017 Georg Dorn, Alexander Leitner, Julien Boudet, Sébastien Campagne, Christine von Schroetter, Ahmed Moursy, Ruedi Aebersold, Frédéric H-T Allain
Structural modeling of protein–RNA complexes using crosslinking of segmentally isotope-labeled RNA and MS/MS
published pages: 487-490, ISSN: 1548-7091, DOI: 10.1038/NMETH.4235 		Nature Methods 14/5 2019-04-18

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