Livrables (11) Report on the availability of cloud-based data analysis pipelines based on software developed in the project Report on the availability of cloudbased data analysis pipelines based on software developed in the project Report on data management practises Report on data management practises Optimized protocol for the enrichment and large-scale analysis of currently uncharacterized protein modifications Optimized protocol for the enrichment and largescale analysis of currently uncharacterized protein modifications Optimized protocol for high-sensitivity proteomics towards single cell analysis including loss-less sample preparation methods and LC-MS/MS acquisition parameters with proof-of-concept on FACS-sorted cell populations Optimized protocol for highsensitivity proteomics towards single cell analysis including lossless sample preparation methods and LCMSMS acquisition parameters with proofofconcept on FACSsorted cell populations Disseminate developed robust and high-throughput plasma proteomics technology to hospitals and research groups Disseminate developed robust and highthroughput plasma proteomics technology to hospitals and research groups Report on the integration of proteome organization data with functional protein association data Report on the integration of proteome organization data with functional protein association data Disseminate optimized and standardized protocol for the proteomic analysis of EVs in clinically relevant samples. Disseminate optimized and standardized protocol for the proteomic analysis of EVs in clinically relevant samples Report on the transfer of methods to study intact proteomes to the EPIC-XS access sites Report on the transfer of methods to study intact proteomes to the EPICXS access sites Disseminate protocols for enrichment and analysis of tissue leakage proteins from blood plasma and cell surface exposed proteins Disseminate protocols for enrichment and analysis of tissue leakage proteins from blood plasma and cell surface exposed proteins Report on the transfer of methods to study clinical proteomes to the EPIC-XS access sites Report on the transfer of methods to study clinical proteomes to the EPICXS access sites Optimized protocols for the preparation and analysis of protein assemblies using hybrid approaches in link with JRA4 Optimized protocols for the preparation and analysis of protein assemblies using hybrid approaches in link with JRA4 Documents, reports (30) Second progress report Second progress report Lightweight NDA between industrial platform and EPIC-XS Lightweight NDA between industrial platform and EPIC-XS Disseminate the clinical phosphoproteomics and histone PTM analysis technology within and outside EPIC-XS Disseminate the clinical phosphoproteomics and histone PTM analysis technology within and outside EPICXS Report on rigorous quality control approaches and software for mass spectrometry proteomics data from clinical samples Report on rigorous quality control approaches and software for mass spectrometry proteomics data from clinical samples Status report on publication performance resulting from TA Status report on publication performance resulting from TA Report on the transfer of methods to study proteome organization and structural and spatial proteomics to the EPIC-XS access sites Report on the transfer of methods to study proteome organization and structural and spatial proteomics to the EPICXS access sites Report on outreach activities Report on outreach activities Recruitment of a Project Manager Recruitment of a Project Manager Report on novel tools for the identification and quantification of cross-linked peptides Report on novel tools for the identification and quantification of crosslinked peptides Report 2 on conferences and meetings with EPIC-XS representation Report on conferences and meetings with EPICXS representation Foresight White Paper Foresight White Paper Report 2 on outreach activities Report on outreach activities Management Guidelines Management Guidelines Status report on TA project evaluations and TA delivery Status report on TA project evaluations and TA delivery First report on the higher order organization of the plasma proteome First report on the higher order organization of the plasma proteome Midterm summary report on networking activities Midterm summary report on networking activities Report on conferences and meetings with EPIC-XS representation Report on conferences and meetings with EPIC-XS representation Status report 2 on publication performance resulting from TA Status report 2 on publication performance resulting from TA Status report 3 on TA project evaluations and TA delivery Status report 3 on TA project evaluations and TA delivery Standard protocol for intact protein analysis including sample preparation, LC-MS/MS and data analysis Standard protocol for intact protein analysis including sample preparation LCMSMS and data analysis Report on Coordination activities with ELIXIR Report on Coordination activities with ELIXIR First progress report First progress report Report on novel algorithms for top-down proteomics data Report on novel algorithms for topdown proteomics data Report on Machine Learning modules to predict fragmentation spectra for phosphorylated, ubiquitinylated and acylated peptides, and their implementation in performant DDA and DIA identification algorithms Report on Machine Learning modules to predict fragmentation spectra for phosphorylated ubiquitinylated and acylated peptides and their implementation in performant DDA and DIA identification algorithms Report on a novel fragmentation spectrum prediction algorithm for unmodified peptides, and its application in performant DDA and DIA identification algorithms Report on a novel fragmentation spectrum prediction algorithm for unmodified peptides, and its application in performant DDA and DIA identification algorithms Status report 2 on TA project evaluations and TA delivery Status report 2 on TA project evaluations and TA delivery Report on algorithms for the reliable, unbiased identification of modifications in proteomes Report on algorithms for the reliable unbiased identification of modifications in proteomes Library of synthetic cross-linked peptides and optimized workflows for XL-MS Library of synthetic crosslinked peptides and optimized workflows for XLMS Report on demands of the user community Report on demands of the user community Protocols for cooperation with ESFRI BMS RIs Protocols for cooperation with ESFRI BMS RIs Open Research Data Pilot (3) Report 2 on guidelines for data submission Report 2 on guidelines for data submission Report on guidelines for data submission (data management plan) Report on guidelines for data submission (data management plan) Report on open software practises Report on open software practises Publications Peer reviewed articles (175) DiagnoTop: A Computational Pipeline for Discriminating Bacterial Pathogens without Database Search Auteurs: Borges Lima D, Dupré M, Mariano Santos MD, Carvalho PC, Chamot-Rooke J. Publié dans: J Am Soc Mass Spectrom, 2021, ISSN 1044-0305 Éditeur: Elsevier BV DOI: 10.1021/jasms.1c00014 Implementing the reuse of public DIA proteomics datasets: from the PRIDE database to Expression Atlas. Auteurs: Walzer M, García-Seisdedos D, Prakash A, Brack P, Crowther P, Graham RL, George N, Mohammed S, Moreno P, Papatheodorou I, Hubbard SJ, Vizcaíno JA. Publié dans: Scientific data, 2022, ISSN 2052-4463 Éditeur: Nature Pub DOI: 10.1038/s41597-022-01380-9 The biophysical, molecular, and anatomical landscape of pigeon CRY4: A candidate light-based quantal magnetosensor Auteurs: Tobias Hochstoeger, Tarek Al Said, Dante Maestre, Florian Walter, Alexandra Vilceanu, Miriam Pedron, Thomas D. Cushion, William Snider, Simon Nimpf, Gregory Charles Nordmann, Lukas Landler, Nathaniel Edelman, Lennard Kruppa, Gerhard Dürnberger, Karl Mechtler, Stefan Schuechner, Egon Ogris, E. Pascal Malkemper, Stefan Weber, Erik Schleicher, David A. Keays Publié dans: Science Advances, Issue 6/33, 2020, Page(s) eabb9110, ISSN 2375-2548 Éditeur: Amercian Assoc for the Advancement of Science DOI: 10.1126/sciadv.abb9110 Investigating pathological epigenetic aberrations by epi-proteomics Auteurs: Robusti G, Vai A, Bonaldi T, Noberini R. Publié dans: Clinical Epigenetics, 2022, ISSN 1868-7083 Éditeur: BMC DOI: 10.1186/s13148-022-01371-y Neuroproteomics of the Synapse: Subcellular Quantification of Protein Networks and Signaling Dynamics Auteurs: Charlotte A.G.H. van Gelder, Maarten Altelaar Publié dans: Molecular & Cellular Proteomics, Issue 20, 2021, Page(s) 100087, ISSN 1535-9476 Éditeur: American Society for Biochemistry and Molecular Biology Inc. DOI: 10.1016/j.mcpro.2021.100087 Impact of Modified Atmospheres on Growth and Metabolism of Meat-Spoilage Relevant Photobacterium spp. as Predicted by Comparative Proteomics. Auteurs: Fuertes-Perez S, Abele M, Ludwig C, Vogel RF, Hilgarth M. Publié dans: Frontiers in Microbiology, 2022, ISSN 1664-302X Éditeur: Frontiers Media DOI: 10.3389/fmicb.2022.866629 Protein Processing in Plant Mitochondria Compared to Yeast and Mammals Auteurs: Heidorn-Czarna M, Maziak A, Janska H Publié dans: Front. Plant Sci., 2022, ISSN 1664-462X Éditeur: Frontiers Media S. A. DOI: 10.3389/fpls.2022.824080 Is DIA proteomics data FAIR? Current data sharing practices, available bioinformatics infrastructure and recommendations for the future Auteurs: Jones AR, Deutsch EW, Vizcaíno JA. Publié dans: Proteomics, 2022, ISSN 1615-9861 Éditeur: Wiley DOI: 10.1002/pmic.202200014 Mimicked synthetic ribosomal protein complex for benchmarking crosslinking mass spectrometry workflows Auteurs: Matzinger M, Vasiu A, Madalinski M, Müller F, Stanek F, Mechtler K Publié dans: Nature Communications, 2022, ISSN 2041-1723 Éditeur: Nature Publishing Group DOI: 10.1038/s41467-022-31701-w High-Resolution mRNA and Secretome Atlas of Human Enteroendocrine Cells Auteurs: Joep Beumer, Jens Puschhof, Julia Bauzá-Martinez, Adriana Martínez-Silgado, Rasa Elmentaite, Kylie R. James, Alexander Ross, Delilah Hendriks, Benedetta Artegiani, Georg A. Busslinger, Bas Ponsioen, Amanda Andersson-Rolf, Aurelia Saftien, Charelle Boot, Kai Kretzschmar, Maarten H. Geurts, Yotam E. Bar-Ephraim, Cayetano Pleguezuelos-Manzano, Yorick Post, Harry Begthel, Franka van der Linden, Carm Publié dans: Cell, Issue 181/6, 2020, Page(s) 1291-1306.e19, ISSN 0092-8674 Éditeur: Cell Press DOI: 10.1016/j.cell.2020.04.036 Advanced In Vivo Cross-Linking Mass Spectrometry Platform to Characterize Proteome-Wide Protein Interactions Auteurs: Martial Rey, Jonathan Dhenin, Youxin Kong, Lucienne Nouchikian, Isaac Filella, Magalie Duchateau, Mathieu Dupré, Riccardo Pellarin, Guillaume Duménil, Julia Chamot-Rooke Publié dans: Analytical Chemistry, Issue 93/9, 2021, Page(s) 4166-4174, ISSN 0003-2700 Éditeur: American Chemical Society DOI: 10.1021/acs.analchem.0c04430 The emerging landscape of spatial profiling technologie Auteurs: Moffitt JR, Lundberg E, Heyn H. Publié dans: Nature Reviews Genetics, 2022, ISSN 1471-0056 Éditeur: Nature Publishing Group DOI: 10.1038/s41576-022-00515-3 The Human Proteoform Project: Defining the human proteome Auteurs: Smith LM, Agar J, Chamot-Rooke J, Danis P, Ge Y, Loo J, Pasa-Tolic L, Tsybin YO, Kelleher N. Publié dans: Science Advances, 2021, ISSN 2375-2548 Éditeur: Amercian Assoc for the Advancement of Science DOI: 10.1126/sciadv.abk0734 How paired PSII–LHCII supercomplexes mediate the stacking of plant thylakoid membranes unveiled by structural mass-spectrometry Auteurs: Pascal Albanese, Sem Tamara, Guido Saracco, Richard A. Scheltema, Cristina Pagliano Publié dans: Nature Communications, Issue 11/1, 2020, ISSN 2041-1723 Éditeur: Nature Publishing Group DOI: 10.1038/s41467-020-15184-1 Panoramic Perspective on Human Phosphosites Auteurs: Ramasamy P, Vandermarliere E, Vranken WF, Martens L. Publié dans: J. Proteome Research, 2022, ISSN 1535-3893 Éditeur: American Chemical Society DOI: 10.1021/acs.jproteome.2c00164 A wealth of genotype-specific proteoforms fine-tunes hemoglobin scavenging by haptoglobin Auteurs: Sem Tamara, Vojtech Franc, Albert J. R. Heck Publié dans: Proceedings of the National Academy of Sciences, Issue 117/27, 2020, Page(s) 15554-15564, ISSN 0027-8424 Éditeur: National Academy of Sciences DOI: 10.1073/pnas.2002483117 Quality standards in proteomics research facilities Auteurs: Cristina Chiva, Teresa Mendes Maia, Christian Panse, Karel Stejskal, Thibaut Douché, Mariette Matondo, Damarys Loew, Dominic Helm, Mandy Rettel, Karl Mechtler, Francis Impens, Paolo Nanni, Anna Shevchenko, Eduard Sabidó Publié dans: EMBO reports, Issue 22/6, 2021, ISSN 1469-221X Éditeur: Nature Publishing Group DOI: 10.15252/embr.202152626 Spatial-proteomics reveals phospho-signaling dynamics at subcellular resolution Auteurs: Martinez-Val A, Bekker-Jensen DB, Steigerwald S, Koenig C, Østergaard O, Mehta A, Tran T, Sikorski K, Torres-Vega E, Kwasniewicz E, Brynjólfsdóttir SH, Frankel LB, Kjøbsted R, Krogh N, Lundby A, Bekker-Jensen S, Lund-Johansen F, Olsen JV. Publié dans: Nature Communications, 2021, ISSN 2041-1723 Éditeur: Nature Publishing Group DOI: 10.1038/s41467-021-27398-y Sensitivity towards HDAC inhibition is associated with RTK/MAPK pathway activation in gastric cancer Auteurs: Seidlitz T, Schmäche T, Garcίa F, Lee JH, Qin N, Kochall S, Fohgrub J, Pauck D, Rothe A, Koo BK, Weitz J, Remke M, Muñoz J, Stange DE. Publié dans: EMBO Molecular Medicine, 2022, ISSN 1757-4676 Éditeur: John Wiley & Sons Ltd. DOI: 10.15252/emmm.202215705 Dynamic 3D proteomes reveal protein functional alterations at high resolution in situ Auteurs: Valentina Cappelletti, Thomas Hauser, Ilaria Piazza, Monika Pepelnjak, Liliana Malinovska, Tobias Fuhrer, Yaozong Li, Christian Dörig, Paul Boersema, Ludovic Gillet, Jan Grossbach, Aurelien Dugourd, Julio Saez-Rodriguez, Andreas Beyer, Nicola Zamboni, Amedeo Caflisch, Natalie de Souza, Paola Picotti Publié dans: Cell, Issue 184/2, 2021, Page(s) 545-559.e22, ISSN 0092-8674 Éditeur: Cell Press DOI: 10.1016/j.cell.2020.12.021 Critical Assessment of MetaProteome Investigation (CAMPI): a multi-laboratory comparison of established workflows Auteurs: Van Den Bossche T, Kunath BJ, Schallert K, Schäpe SS, Abraham PE, Armengaud J, Arntzen MØ, Bassignani A, Benndorf D, Fuchs S, Giannone RJ, Griffin TJ, Hagen LH, Halder R, Henry C, Hettich RL, Heyer R, Jagtap P, Jehmlich N, Jensen M, Juste C, Kleiner M, Langella O, Lehmann T, Leith E, May P, Mesuere B, Miotello G, Peters SL, Pible O, Queiros PT, Reichl U, Renard BY, Schiebenhoefer H, Sczyrba A, T Publié dans: Nature Publishing Group, 2021, ISSN 2041-1723 Éditeur: Nature Publishing Group DOI: 10.1038/s41467-021-27542-8 Motif orientation matters: Structural characterization of TEAD1 recognition of genomic DNA Auteurs: Růžena Filandrová, Karel Vališ, Jiří Černý, Josef Chmelík, Lukáš Slavata, Jan Fiala, Michal Rosůlek, Daniel Kavan, Petr Man, Tomáš Chum, Marek Cebecauer, Daniele Fabris, Petr Novák Publié dans: Structure, Issue 29/4, 2021, Page(s) 345-356.e8, ISSN 0969-2126 Éditeur: Cell Press DOI: 10.1016/j.str.2020.11.018 SPIN enables high throughput species identification of archaeological bone by proteomics. Auteurs: Rüther PL, Husic IM, Bangsgaard P, Gregersen KM, Pantmann P, Carvalho M, Godinho RM, Friedl L, Cascalheira J, Taurozzi AJ, Jørkov MLS, Benedetti MM, Haws J, Bicho N, Welker F, Cappellini E, Olsen JV Publié dans: Nat Commun, 2022, ISSN 2041-1723 Éditeur: Nature Publishing Group DOI: 10.1038/s41467-022-30097-x Benefits of Ion Mobility Separation and Parallel Accumulation–Serial Fragmentation Technology on timsTOF Pro for the Needs of Fast Photochemical Oxidation of Protein Analysis Auteurs: Dmitry S. Loginov, Jan Fiala, Josef Chmelik, Peter Brechlin, Gary Kruppa, Petr Novak Publié dans: ACS Omega, Issue 6/15, 2021, Page(s) 10352-10361, ISSN 2470-1343 Éditeur: AMER CHEMICAL SOC DOI: 10.1021/acsomega.1c00732 An interactive mass spectrometry atlas of histone posttranslational modifications in T-cell acute leukemia Auteurs: Provez L, Van Puyvelde B, Corveleyn L, Demeulemeester N, Verhelst S, Lintermans B, Daled S, Roels J, Clement L, Martens L, Deforce D, Van Vlierberghe P, Dhaenens M. Publié dans: Science Data, 2022, ISSN 2052-4463 Éditeur: Nature Portfolio DOI: 10.1038/s41597-022-01736-1 Goat Milk Exosomes As Natural Nanoparticles for Detecting Inflammatory Processes By Optical Imaging Auteurs: Ana Santos-Coquillat,María Isabel González,Agustín Clemente-Moragón,Mario González-Arjona,Virginia Albaladejo-García,Héctor Peinado,Javier Muñoz,Pilar Ximénez Embún,Borja Ibañez,Eduardo Oliver, Manuel Desco, Beatriz Salinas Publié dans: Small, 2021, ISSN 1613-6810 Éditeur: Wiley - V C H Verlag GmbbH & Co. DOI: 10.1002/smll.202105421 Automated High-Throughput Method for the Fast, Robust, and Reproducible Enrichment of Newly Synthesized Proteins Auteurs: Vargas-Diaz D, Altelaar M Publié dans: J Proteome Res, 2022, ISSN 1535-3893 Éditeur: American Chemical Society DOI: 10.1021/acs.jproteome.1c00743 From coarse to fine: the absolute Escherichia coli proteome under diverse growth conditions Auteurs: Matteo Mori, Zhongge Zhang, Amir Banaei‐Esfahani, Jean‐Benoît Lalanne, Hiroyuki Okano, Ben C Collins, Alexander Schmidt, Olga T Schubert, Deok‐Sun Lee, Gene‐Wei Li, Ruedi Aebersold, Terence Hwa, Christina Ludwig Publié dans: Molecular Systems Biology, Issue 17/5, 2021, ISSN 1744-4292 Éditeur: Nature Publishing Group DOI: 10.15252/msb.20209536 Meta-heterogeneity: Evaluating and Describing the Diversity in Glycosylation Between Sites on the Same Glycoprotein Auteurs: Tomislav Čaval, Albert J.R. Heck, Karli R. Reiding Publié dans: Molecular & Cellular Proteomics, Issue 20, 2021, Page(s) 100010, ISSN 1535-9476 Éditeur: American Society for Biochemistry and Molecular Biology Inc. DOI: 10.1074/mcp.r120.002093 Phosphorylation-Dependent Interactome of Ryanodine Receptor Type 2 in the Heart Auteurs: David Y. Chiang, Satadru Lahiri, Guoliang Wang, Jason Karch, Meng C. Wang, Sung Y. Jung, Albert J. R. Heck, Arjen Scholten, Xander H. T. Wehrens Publié dans: Proteomes, Issue 9/2, 2021, Page(s) 27, ISSN 2227-7382 Éditeur: MDPI DOI: 10.3390/proteomes9020027 The Key Role of Metal Adducts in the Differentiation of Phosphopeptide from Sulfopeptide Sequences by High-Resolution Mass Spectrometry. Auteurs: Piovesana S, Capriotti AL, Cavaliere C, Cerrato A, Montone CM, Zenezini Chiozzi R, Laganà A. Publié dans: Anal Chem, 2022, ISSN 0003-2700 Éditeur: American Chemical Society DOI: 10.1021/acs.analchem.1c05621 Molecular characterization of a complex of apoptosis-inducing factor 1 with cytochrome c oxidase of the mitochondrial respiratory chain Auteurs: Johannes F. Hevler, Riccardo Zenezeni Chiozzi, Alfredo Cabrera-Orefice, Ulrich Brandt, Susanne Arnold, Albert J. R. Heck Publié dans: Proceedings of the National Academy of Sciences, Issue 118/39, 2021, Page(s) e2106950118, ISSN 0027-8424 Éditeur: National Academy of Sciences DOI: 10.1073/pnas.2106950118 MegaGO: A Fast Yet Powerful Approach to Assess Functional Gene Ontology Similarity across Meta-Omics Data Sets Auteurs: Pieter Verschaffelt, Tim Van Den Bossche, Wassim Gabriel, Michał Burdukiewicz, Alessio Soggiu, Lennart Martens, Bernhard Y. Renard, Henning Schiebenhoefer, Bart Mesuere Publié dans: Journal of Proteome Research, Issue 20/4, 2021, Page(s) 2083-2088, ISSN 1535-3893 Éditeur: American Chemical Society DOI: 10.1021/acs.jproteome.0c00926 Quantitative Accuracy and Precision in Multiplexed Single-Cell Proteomics. Auteurs: Ctortecka C, Stejskal K, Krššáková G, Mendjan S, Mechtler K Publié dans: Anal Chem, 2022, ISSN 0002-7863 Éditeur: American Chemical Society DOI: 10.1021/acs.analchem.1c04174 Prosit Transformer: A transformer for Prediction of MS2 Spectrum Intensities Auteurs: Ekvall M, Truong P, Gabriel W, Wilhelm M, Käll L. Publié dans: J. Proteome Research, 2022, ISSN 1535-3893 Éditeur: American Chemical Society DOI: 10.1021/acs.jproteome.1c00870 Huntingtin structure is orchestrated by HAP40 and shows a polyglutamine expansion-specific interaction with exon 1 Auteurs: Harding, R.J., Deme, J.C., Hevler, J.F. et al. Publié dans: Nat Cell Biol., 2021, ISSN 1465-7392 Éditeur: Nature Publishing Group DOI: 10.1038/s42003-021-02895-4 The Q-junction and the inflammatory response are critical pathological and therapeutic factors in CoQ deficiency Auteurs: González-García P, Díaz-Casado ME, Hidalgo-Gutiérrez A, Jiménez-Sánchez L, Bakkali M, Barriocanal-Casado E, Escames G, Chiozzi RZ, Völlmy F, Zaal EA, Berkers CR, Heck AJR, López LC Publié dans: Redox Biology, 2022, ISSN 2213-2317 Éditeur: Elsevier BV DOI: 10.1016/j.redox.2022.102403 A Sample Preparation Protocol for High Throughput Immunofluorescence of Suspension Cells on an Adherent Surface Auteurs: Anna Bäckström, Laura Kugel, Christian Gnann, Hao Xu, Joseph E. Aslan, Emma Lundberg, Charlotte Stadler Publié dans: Journal of Histochemistry & Cytochemistry, Issue 68/7, 2020, Page(s) 473-489, ISSN 0022-1554 Éditeur: Histochemical Society DOI: 10.1369/0022155420935403 Coronary Artery Disease and Aortic Valve Stenosis: A Urine Proteomics Study Auteurs: Perpétuo L, Barros AS, Dalsuco J, Nogueira-Ferreira R, Resende-Gonçalves P, Falcão-Pires I, Ferreira R, Leite-Moreira A, Trindade F, Vitorino R. Publié dans: International Journal of Molecular Sciences, 2022, ISSN 1422-0067 Éditeur: Multidisciplinary Digital Publishing Institute (MDPI) DOI: 10.3390/ijms232113579 Label-Free Quantitative Proteomic Analysis of Nitrogen Starvation in Arabidopsis Root Reveals New Aspects of H2S Signaling by Protein Persulfidation Auteurs: Ana Jurado-Flores, Luis C. Romero, Cecilia Gotor Publié dans: Antioxidants, Issue 10/4, 2021, Page(s) 508, ISSN 2076-3921 Éditeur: MDPI DOI: 10.3390/antiox10040508 Subcellular Transcriptomics and Proteomics: A Comparative Methods Review Auteurs: Christopher JA, Geladaki A, Dawson CS, Vennard OL, Lilley KS. Publié dans: Mol Cell Proteomics, 2022, ISSN 1535-9484 Éditeur: Elsiver DOI: 10.1016/j.mcpro.2021.100186 Site‐specific ubiquitination of the E3 ligase HOIP regulates apoptosis and immune signaling Auteurs: Lilian M Fennell, Carlos Gomez Diaz, Luiza Deszcz, Anoop Kavirayani, David Hoffmann, Kota Yanagitani, Alexander Schleiffer, Karl Mechtler, Astrid Hagelkruys, Josef Penninger, Fumiyo Ikeda Publié dans: The EMBO Journal, Issue 39/24, 2020, ISSN 0261-4189 Éditeur: Nature Publishing Group DOI: 10.15252/embj.2019103303 DNAJC9 integrates heat shock molecular chaperones into the histone chaperone network Auteurs: Colin M. Hammond, Hongyu Bao, Ivo A. Hendriks, Massimo Carraro, Alberto García-Nieto, Yanhong Liu, Nazaret Reverón-Gómez, Christos Spanos, Liu Chen, Juri Rappsilber, Michael L. Nielsen, Dinshaw J. Patel, Hongda Huang, Anja Groth Publié dans: Molecular Cell, Issue 81/12, 2021, Page(s) 2533-2548.e9, ISSN 1097-2765 Éditeur: Cell Press DOI: 10.1016/j.molcel.2021.03.041 Structure of the human signal peptidase complex reveals the determinants for signal peptide cleavage Auteurs: A. Manuel Liaci, Barbara Steigenberger, Paulo Cesar Telles de Souza, Sem Tamara, Mariska Gröllers-Mulderij, Patrick Ogrissek, Siewert J. Marrink, Richard A. Scheltema, Friedrich Förster Publié dans: Molecular Cell, Issue 81/19, 2021, Page(s) 3934-3948.e11, ISSN 1097-2765 Éditeur: Cell Press DOI: 10.1016/j.molcel.2021.07.031 Subcellular proteomics Auteurs: Josie A. Christopher, Charlotte Stadler, Claire E. Martin, Marcel Morgenstern, Yanbo Pan, Cora N. Betsinger, David G. Rattray, Diana Mahdessian, Anne-Claude Gingras, Bettina Warscheid, Janne Lehtiö, Ileana M. Cristea, Leonard J. Foster, Andrew Emili, Kathryn S. Lilley Publié dans: Nature Reviews Methods Primers, Issue 1/1, 2021, ISSN 2662-8449 Éditeur: Springer Nature DOI: 10.1038/s43586-021-00029-y Top-Down Detection of Oxidative Protein Footprinting by Collision-Induced Dissociation, Electron-Transfer Dissociation, and Electron-Capture Dissociation Auteurs: Yassaghi G, Kukačka Z, Fiala J, Kavan D, Halada P, Volný M, Novák P Publié dans: Analytical Chemistry, 2022, ISSN 0003-2700 Éditeur: American Chemical Society DOI: 10.1021/acs.analchem.1c05476 Deciphering the signaling network of breast cancer improves drug sensitivity prediction Auteurs: Marco Tognetti, Attila Gabor, Mi Yang, Valentina Cappelletti, Jonas Windhager, Oscar M. Rueda, Konstantina Charmpi, Elham Esmaeilishirazifard, Alejandra Bruna, Natalie de Souza, Carlos Caldas, Andreas Beyer, Paola Picotti, Julio Saez-Rodriguez, Bernd Bodenmiller Publié dans: Cell Systems, Issue 12/5, 2021, Page(s) 401-418.e12, ISSN 2405-4712 Éditeur: CELL PRESS DOI: 10.1016/j.cels.2021.04.002 Fasting improves therapeutic response in hepatocellular carcinoma through p53-dependent metabolic synergism Auteurs: Krstic J, Reinisch I, Schindlmaier K, Galhuber M, Riahi Z, Berger N, Kupper N, Moyschewitz E, Auer M, Michenthaler H, Nössing C, Depaoli MR, Ramadani-Muja J, Usluer S, Stryeck S, Pichler M, Rinner B, Deutsch AJA, Reinisch A, Madl T, Chiozzi RZ, Heck AJR, Huch M, Malli R, Prokesch A. Publié dans: Science Advances, 2022, ISSN 2375-2548 Éditeur: Am soc for the advancement of Science DOI: 10.1126/sciadv.abh2635 Deep learning boosts sensitivity of mass spectrometry-based immunopeptidomics Auteurs: Mathias Wilhelm, Daniel P. Zolg, Michael Graber, Siegfried Gessulat, Tobias Schmidt, Karsten Schnatbaum, Celina Schwencke-Westphal, Philipp Seifert, Niklas de Andrade Krätzig, Johannes Zerweck, Tobias Knaute, Eva Bräunlein, Patroklos Samaras, Ludwig Lautenbacher, Susan Klaeger, Holger Wenschuh, Roland Rad, Bernard Delanghe, Andreas Huhmer, Steven A. Carr, Karl R. Clauser, Angela M. Krackhardt, U Publié dans: Nature Communications, Issue 12/1, 2021, ISSN 2041-1723 Éditeur: Nature Publishing Group DOI: 10.1038/s41467-021-23713-9 Reversible amyloids of pyruvate kinase couple cell metabolism and stress granule assembly Auteurs: Cereghetti G, Wilson-Zbinden C, Kissling VM, Diether M, Arm A, Yoo H, Piazza I, Saad S, Picotti P, Drummond DA, Sauer U, Dechant R, Peter M Publié dans: Nature Cell Biology, 2021, ISSN 1465-7392 Éditeur: Nature Publishing Group DOI: 10.1038/s41556-021-00760-4 MassIVE.quant: a community resource of quantitative mass spectrometry–based proteomics datasets Auteurs: Meena Choi, Jeremy Carver, Cristina Chiva, Manuel Tzouros, Ting Huang, Tsung-Heng Tsai, Benjamin Pullman, Oliver M. Bernhardt, Ruth Hüttenhain, Guo Ci Teo, Yasset Perez-Riverol, Jan Muntel, Maik Müller, Sandra Goetze, Maria Pavlou, Erik Verschueren, Bernd Wollscheid, Alexey I. 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Publié dans: Nature Methods, 2021, ISSN 1548-7091 Éditeur: Nature Publishing Group DOI: 10.1038/s41592-021-01301-5 Systems approach reveals distinct and shared signaling networks of the four PGE 2 receptors in T cells Auteurs: Anna M. Lone, Piero Giansanti, Marthe Jøntvedt Jørgensen, Enio Gjerga, Aurelien Dugourd, Arjen Scholten, Julio Saez-Rodriguez, Albert J. R. Heck, Kjetil Taskén Publié dans: Science Signaling, Issue 14/703, 2021, ISSN 1937-9145 Éditeur: American Association for the Advancement of Science DOI: 10.1126/scisignal.abc8579 Universal Spectrum Explorer: A Standalone (Web-)Application for Cross-Resource Spectrum Comparison Auteurs: Tobias Schmidt, Patroklos Samaras, Viktoria Dorfer, Christian Panse, Tobias Kockmann, Leon Bichmann, Bart van Puyvelde, Yasset Perez-Riverol, Eric W. Deutsch, Bernhard Kuster, Mathias Wilhelm Publié dans: Journal of Proteome Research, Issue 20/6, 2021, Page(s) 3388-3394, ISSN 1535-3893 Éditeur: American Chemical Society DOI: 10.1021/acs.jproteome.1c00096 TDFragMapper: a visualization tool for evaluating experimental parameters in top-down proteomics Auteurs: Dhenin J, Borges Lima D, Dupré M, Chamot-Rooke J. Publié dans: Bioinformatics, 2021, ISSN 1367-4803 Éditeur: Oxford University Press DOI: 10.1093/bioinformatics/btab784 Book chapters (1) Postlymphadenectomy Analysis of Exosomes from Lymphatic Exudate/Exudative Seroma of Melanoma Patients Auteurs: Susana García-Silva, Pilar Ximénez-Embún, Javier Muñoz, Héctor Peinado Publié dans: Melanoma - Methods and Protocols, Issue 2265, 2021, Page(s) 345-359, ISBN 978-1-0716-1204-0 Éditeur: Springer US DOI: 10.1007/978-1-0716-1205-7_25 Non-peer reviewed articles (1) A Compact Quadrupole-Orbitrap Mass Spectrometer with FAIMS Interface Improves Proteome Coverage in Short LC Gradients Auteurs: Dorte B. Bekker-Jensen, Ana Martínez-Val, Sophia Steigerwald, Patrick Rüther, Kyle L. Fort, Tabiwang N. Arrey, Alexander Harder, Alexander Makarov, Jesper V. Olsen Publié dans: Molecular & Cellular Proteomics, Issue 19/4, 2020, Page(s) 716-729, ISSN 1535-9476 Éditeur: American Society for Biochemistry and Molecular Biology Inc. DOI: 10.1074/mcp.tir119.001906 Recherche de données OpenAIRE... Une erreur s’est produite lors de la recherche de données OpenAIRE Aucun résultat disponible
