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European Proteomics Infrastructure Consortium providing Access

Livrables

Delivery of 375 days of access at UCPH
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 the organization of training workshops
Second progress report
Report 2 on Coordination activities with ELIXIR
Lightweight NDA between industrial platform and EPIC-XS
Delivery of 133 days of access at KTH
Status report 3 on publication performance resulting from TA
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

Delivery of 180 days of access at IP
Integrated structural characterization of target protein systems in vitro and in situ
Report on rigorous quality control approaches and software for mass spectrometry proteomics data from clinical samples
Report on the interaction with industrial parties
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

Delivery of 362 days of access at UU
Summary report on networking activities with industry
Delivery of 175 days of access at CRG
Draft Engagement Plan
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

Report on outreach activities
Dynamic structural and spatial proteome maps in response to perturbations or disease
Recruitment of a Project Manager
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 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

Report on the integration of proteome organization data with functional protein association data
Foresight White Paper
Report 2 on outreach activities

Report on outreach activities

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

Management Guidelines
Best practice DIA library-free and hybrid DIA workflows for comprehensive proteome analysis

Best practice DIA libraryfree and hybrid DIA workflows for comprehensive proteome analysis

Optimized LiP-MS and HDX protocols with enhanced sensitivity and in cell application
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

Status report on TA project evaluations and TA delivery
At least two articles for the general public
Delivery of 368 days of access at VIB
First report on the higher order organization of the plasma proteome
Delivery of 109 days of access at CNIO
Disseminate protocols for enrichment and analysis of tissue leakage proteins from blood plasma and cell surface exposed proteins
Midterm summary report on networking activities
Delivery of 345 days of access at ETH
Report on conferences and meetings with EPIC-XS representation
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

Status report 2 on publication performance resulting from TA
Report on the organization of annual user meetings
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
Delivery of 140 days of access at TUM
Delivery of 22 access projects at IEO
First progress report
Report on novel algorithms for top-down proteomics data

Report on novel algorithms for topdown proteomics data

Delivery of 40 days of access at MU
Delivery of 80 days of access at IMIC
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

Final report
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
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
Protocols for cooperation with ESFRI BMS RIs
Optimized protocols for the preparation and analysis of protein assemblies using hybrid approaches in link with JRA4

Publications

Integrated transcriptome and proteome analysis reveals posttranscriptional regulation of ribosomal genes in human brain organoids

Auteurs: Sidhaye, Jaydeep; Trepte, Philipp; Sepke, Natalie; Novatchkova, Maria; Schutzbier, Michael; Duernberger, Gerhard; Mechtler, Karl; Knoblich, Juergen A.
Publié dans: eLife, Numéro 12, 2023, Page(s) e85135, ISSN 2050-084X
Éditeur: eLife Sciences Publications
DOI: 10.7554/elife.85135

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

Label-free visual proteomics: Coupling MS- and EM-based approaches in structural biology

Auteurs: Klykov, Oleg; Kopylov, Mykhailo; Carragher, Bridget; Heck, Albert J. R.; Noble, Alex J.; Scheltema, Richard A.
Publié dans: Mol. Cell, Numéro 82/2, 2022, Page(s) 285-303, ISSN 1097-2765
Éditeur: Cell Press
DOI: 10.1016/j.molcel.2021.12.027

TopDownApp: An open and modular platform for analysis and visualisation of top-down proteomics data

Auteurs: Walzer, Mathias; Jeong, Kyowon; Tabb, David L.; Vizcaino, Juan Antonio
Publié dans: Proteomics, 2023, ISSN 1615-9861
Éditeur: WILEY
DOI: 10.1002/pmic.202200403

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, Numéro 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, Numéro 20, 2021, Page(s) 100087, ISSN 1535-9476
Éditeur: American Society for Biochemistry and Molecular Biology Inc.
DOI: 10.1016/j.mcpro.2021.100087

New Ruthenium-Cyclopentadienyl Complexes Affect Colorectal Cancer Hallmarks Showing High Therapeutic Potential

Auteurs: Bras, Ana Rita; Fernandes, Pedro; Moreira, Tiago; Morales-Sanfrutos, Julia; Sabido, Eduard; Antunes, Alexandra M. M.; Valente, Andreia; Preto, Ana
Publié dans: Pharmaceutics, Numéro 15/6, 2023, Page(s) 1731, ISSN 1999-4923
Éditeur: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/pharmaceutics15061731

 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

A multiparameter optimization in middle-down analysis of monoclonal antibodies by LC-MS/MS

Auteurs: Dhenin, Jonathan; Dupre, Mathieu; Druart, Karen; Krick, Alain; Mauriac, Christine; Chamot-Rooke, Julia
Publié dans: J. Mass Spectrom., Numéro 58/3, 2023, Page(s) e4909, ISSN 1076-5174
Éditeur: IM Publications
DOI: 10.1002/jms.4909

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, Numéro 181/6, 2020, Page(s) 1291-1306.e19, ISSN 0092-8674
Éditeur: Cell Press
DOI: 10.1016/j.cell.2020.04.036

Complementary omics strategies to dissect p53 signaling networks under nutrient stress

Auteurs: Galhuber, Markus; Michenthaler, Helene; Heininger, Christoph; Reinisch, Isabel; Noessing, Christoph; Krstic, Jelena; Kupper, Nadja; Moyschewitz, Elisabeth; Auer, Martina; Heitzer, Ellen; Ulz, Peter; Birner-Gruenberger, Ruth; Liesinger, Laura; Lenihan-Geels, Georgia Ngawai; Oster, Moritz; Spreitzer, Emil; Chiozzi, Riccardo Zenezini; Schulz, Tim J.; Schupp, Michael; Madl, Tobias; Heck, Albert J. R.;
Publié dans: Cell. Mol. Life Sci., Numéro 79/6, 2022, Page(s) 326, ISSN 1420-682X
Éditeur: Birkhauser Verlag
DOI: 10.1007/s00018-022-04345-8

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, Numéro 93/9, 2021, Page(s) 4166-4174, ISSN 0003-2700
Éditeur: American Chemical Society
DOI: 10.1021/acs.analchem.0c04430

Proteomics contributions to epigenetic drug discovery

Auteurs: Noberini, Roberta; Bonaldi, Tiziana
Publié dans: Proteomics, 2023, ISSN 1615-9853
Éditeur: John Wiley & Sons Ltd.
DOI: 10.1002/pmic.202200435

Selective ribosome profiling reveals a role for SecB in the co-translational inner membrane protein biogenesis

Auteurs: Eismann, Lena; Fijalkowski, Igor; Galmozzi, Carla Veronica; Koubek, Jiri; Tippmann, Frank; Van Damme, Petra; Kramer, Guenter
Publié dans: Cell Reports, Numéro 41/10, 2022, Page(s) 111776, ISSN 2211-1247
Éditeur: Cell Press
DOI: 10.1016/j.celrep.2022.111776

Loss of CRMP2 O-GlcNAcylation leads to reduced novel object recognition performance in mice

Auteurs: Muha, Villo; Williamson, Ritchie; Hills, Rachel; McNeilly, Alison D.; McWilliams, Thomas G.; Alonso, Jana; Schimpl, Marianne; Leney, Aneika C.; Heck, Albert J. R.; Sutherland, Calum; Read, Kevin D.; McCrimmon, Rory J.; Brooks, Simon P.; van Aalten, Daan M. F.
Publié dans: Open Biol, Numéro 9/11, 2019, Page(s) 190192, ISSN 2046-2441
Éditeur: Royal Society Publishing
DOI: 10.1098/rsob.190192

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

Allosteric Communication in the Multifunctional and Redox NQO1 Protein Studied by Cavity-Making Mutations

Auteurs: Pacheco-Garcia, Juan Luis; Loginov, Dmitry S.; Anoz-Carbonell, Ernesto; Vankova, Pavla; Palomino-Morales, Rogelio; Salido, Eduardo; Man, Petr; Medina, Milagros; Naganathan, Athi N.; Pey, Angel L.
Publié dans: Antioxidants, Numéro 11/6, 2022, ISSN 2076-3921
Éditeur: MDPI
DOI: 10.3390/antiox11061110

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, Numéro 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

Malignant tissues produce divergent antibody glycosylation of relevance for cancer gene therapy effectiveness

Auteurs: Brucher, Dominik; Franc, Vojtech; Smith, Sheena N.; Heck, Albert J. R.; Pluckthun, Andreas
Publié dans: mAbs, Numéro 12/1, 2020, Page(s) 1792084, ISSN 1942-0862
Éditeur: TAYLOR & FRANCIS INC
DOI: 10.1080/19420862.2020.1792084

Experimental characterization of de novo proteins and their unevolved random-sequence counterparts

Auteurs: Heames, Brennen; Buchel, Filip; Aubel, Margaux; Tretyachenko, Vyacheslav; Loginov, Dmitry; Novak, Petr; Lange, Andreas; Bornberg-Bauer, Erich; Hlouchova, Klara
Publié dans: Nat. Ecol. Evol., Numéro 7/4, 2023, Page(s) 570, ISSN 2397-334X
Éditeur: NATURE PORTFOLIO
DOI: 10.1038/s41559-023-02010-2

Updated MS2PIP web server delivers fast and accurate MS2 peak intensity prediction for multiple fragmentation methods, instruments and labeling techniques

Auteurs: Gabriels, Ralf; Martens, Lennart; Degroeve, Sven
Publié dans: Nucleic Acids Res., Numéro 47/W1, 2019, Page(s) W295-W299, ISSN 0305-1048
Éditeur: Oxford University Press
DOI: 10.1093/nar/gkz299

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, Numéro 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, Numéro 22/6, 2021, ISSN 1469-221X
Éditeur: Nature Publishing Group
DOI: 10.15252/embr.202152626

Changes in Medicago truncatula seed proteome along the rehydration-dehydration cycle highlight new players in the genotoxic stress response

Auteurs: Pagano, Andrea; Kunz, Laura; Dittmann, Antje; Araujo, Susana De Sousa; Macovei, Anca; Shridhar Gaonkar, Shraddha; Sincinelli, Federico; Wazeer, Hisham; Balestrazzi, Alma
Publié dans: Front. Plant Sci., Numéro 14, 2023, Page(s) 1188546, ISSN 1664-462X
Éditeur: Frontiers Media S. A.
DOI: 10.3389/fpls.2023.1188546

Transient suppression of SUMOylation in embryonic stem cells generates embryo-like structures

Auteurs: Cossec, Jack-Christophe; Traboulsi, Tatiana; Sart, Sebastien; Loe-Mie, Yann; Guthmann, Manuel; Hendriks, Ivo A.; Theurillat, Ilan; Nielsen, Michael L.; Torres-Padilla, Maria-Elena; Baroud, Charles N.; Dejean, Anne
Publié dans: Cell Reports, Numéro 42/4, 2023, Page(s) 112380, ISSN 2211-1247
Éditeur: Cell Press
DOI: 10.1016/j.celrep.2023.112380

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

Peroxiredoxin 2 is required for the redox mediated adaptation to exercise

Auteurs: Xia, Qin; Casas-Martinez, Jose C.; Zarzuela, Eduardo; Munoz, Javier; Miranda-Vizuete, Antonio; Goljanek-Whysall, Katarzyna; McDonagh, Brian
Publié dans: Redox Biol., Numéro 60, 2023, Page(s) 102631, ISSN 2213-2317
Éditeur: Elsevier BV
DOI: 10.1016/j.redox.2023.102631

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, Numéro 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, Numéro 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, Numéro 6/15, 2021, Page(s) 10352-10361, ISSN 2470-1343
Éditeur: AMER CHEMICAL SOC
DOI: 10.1021/acsomega.1c00732

PepGM: a probabilistic graphical model for taxonomic inference of viral proteome samples with associated confidence scores

Auteurs: Holstein, Tanja; Kistner, Franziska; Martens, Lennart; Muth, Thilo
Publié dans: Bioinformatics, Numéro 39/5, 2023, Page(s) btad289, ISSN 1367-4803
Éditeur: Oxford University Press
DOI: 10.1093/bioinformatics/btad289

Machine Learning on Large-Scale Proteomics Data Identifies Tissue and Cell-Type Specific Proteins

Auteurs: Claeys, Tine; Menu, Maxime; Bouwmeester, Robbin; Gevaert, Kris; Martens, Lennart
Publié dans: J. Proteome Res., Numéro 22/4, 2023, Page(s) 1181-1192, ISSN 1535-3893
Éditeur: American Chemical Society
DOI: 10.1021/acs.jproteome.2c00644

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

Small molecule-induced epigenomic reprogramming of APL blasts leading to antiviral-like response and c-MYC downregulation

Auteurs: Amatori, Stefano; Persico, Giuseppe; Cantatore, Francesco; Rusin, Martina; Formica, Mauro; Giorgi, Luca; Macedi, Eleonora; Casciaro, Francesca; Provenzano, Alfredo Errico; Gambardella, Stefano; Noberini, Roberta; Bonaldi, Tiziana; Fusi, Vieri; Giorgio, Marco; Fanelli, Mirco
Publié dans: Cancer Gene Ther., Numéro 30/5, 2023, Page(s) 671-682, ISSN 0929-1903
Éditeur: Nature Publishing Group
DOI: 10.1038/s41417-022-00576-w

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

Characterising the RNA-binding protein atlas of the mammalian brain uncovers RBM5 misregulation in mouse models of Huntington's disease

Auteurs: Mullari, Meeli; Fossat, Nicolas; Skotte, Niels H.; Asenjo-Martinez, Andrea; Humphreys, David T.; Bukh, Jens; Kirkeby, Agnete; Scheel, Troels K. H.; Nielsen, Michael L.
Publié dans: Nat. Commun., Numéro 14/1, 2023, ISSN 2041-1723
Éditeur: Nature Publishing Group
DOI: 10.1038/s41467-023-39936-x

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, Numéro 17/5, 2021, ISSN 1744-4292
Éditeur: Nature Publishing Group
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Chaperoning of the histone octamer by the acidic domain of DNA repair factor APLF

Auteurs: Corbeski, Ivan; Guo, Xiaohu; Eckhardt, Bruna, V; Fasci, Domenico; Wiegant, Wouter; Graewert, Melissa A.; Vreeken, Kees; Wienk, Hans; Svergun, Dmitri, I; Heck, Albert J. R.; van Attikum, Haico; Boelens, Rolf; Sixma, Titia K.; Mattiroli, Francesca; van Ingen, Hugo
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The rise of single-cell proteomics

Auteurs: Ctortecka, Claudia; Mechtler, Karl
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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
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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
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Beneficial Effects of Mifepristone Treatment in Patients with Breast Cancer Selected by the Progesterone Receptor Isoform Ratio: Results from the MIPRA Trial

Auteurs: Elia, Andres; Saldain, Leo; Vanzulli, Silvia I.; Helguero, Luisa A.; Lamb, Caroline A.; Fabris, Victoria; Pataccini, Gabriela; Martinez-Vazquez, Paula; Burruchaga, Javier; Caillet-Bois, Ines; Spengler, Eunice; Haab, Gabriela Acosta; Liguori, Marcos; Castets, Alejandra; Lovisi, Silvia; Abascal, Maria F.; Novaro, Virginia; Sanchez, Jana; Munoz, Javier; Belizan, Jose M.; Abba, Martin C.; Gass, Hugo;
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Volatilome and proteome responses to Colletotrichum lindemuthianum infection in a moderately resistant and a susceptible bean genotype

Auteurs: Monti, Maurilia M.; Mancini, Ilaria; Gualtieri, Liberata; Domingo, Guido; Beccaccioli, Marzia; Bossa, Rosanna; Bracale, Marcella; Loreto, Francesco; Ruocco, Michelina
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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.
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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
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Quality Control for the Target Decoy Approach for Peptide Identification

Auteurs: Debrie, Elke; Malfait, Milan; Gabriels, Ralf; Declerq, Arthur; Sticker, Adriaan; Martens, Lennart; Clement, Lieven
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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
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DAXX adds a de novo H3.3K9me3 deposition pathway to the histone chaperone network

Auteurs: Carraro, Massimo; Hendriks, Ivo A.; Hammond, Colin M.; Solis-Mezarino, Victor; Volker-Albert, Moritz; Elsborg, Jonas D.; Weisser, Melanie B.; Spanos, Christos; Montoya, Guillermo; Rappsilber, Juri; Imhof, Axel; Nielsen, Michael L.; Groth, Anja
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Quantitative Accuracy and Precision in Multiplexed Single-Cell Proteomics. 

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Utilization of Fast Photochemical Oxidation of Proteins and Both Bottom-up and Top-down Mass Spectrometry for Structural Characterization of a Transcription Factor-dsDNA Complex

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Prosit Transformer: A transformer for Prediction of MS2 Spectrum Intensities

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Loss of N-terminal acetyltransferase A activity induces thermally unstable ribosomal proteins and increases their turnover in Saccharomyces cerevisiae

Auteurs: Guzman, Ulises H. H.; Aksnes, Henriette; Ree, Rasmus; Krogh, Nicolai; Jakobsson, Magnus E. E.; Jensen, Lars J. J.; Arnesen, Thomas; Olsen, Jesper V. V.
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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.
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lesSDRF is more: maximizing the value of proteomics data through streamlined metadata annotation

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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
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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
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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. 
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CAF-1 deposits newly synthesized histones during DNA replication using distinct mechanisms on the leading and lagging strands

Auteurs: Rouillon, Clement; Eckhardt, Bruna, V; Kollenstart, Leonie; Gruss, Fabian; Verkennis, Alexander E. E.; Rondeel, Inge; Krijger, Peter H. L.; Ricci, Giulia; Biran, Alva; van Laar, Theo; de Fenffe, Charlotte M. Delvaux; Luppens, Georgiana; Albanese, Pascal; Sato, Koichi; Scheltema, Richard A.; de Laat, Wouter; Knipscheer, Puck; Dekker, Nynke H.; Groth, Anja; Mattiroli, Francesca
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Merits of Diazirine Photo-Immobilization for Target Profiling of Natural Products and Cofactors

Auteurs: Prokofeva, Polina; Hoefer, Stefanie; Hornisch, Maximilian; Abele, Miriam; Kuster, Bernhard; Medard, Guillaume
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MRPS36 provides a structural link in the eukaryotic 2-oxoglutarate dehydrogenase complex

Auteurs: Hevler, Johannes F.; Albanese, Pascal; Cabrera-Orefice, Alfredo; Potter, Alisa; Jankevics, Andris; Misic, Jelena; Scheltema, Richard A.; Brandt, Ulrich; Arnold, Susanne; Heck, Albert J. R.
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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
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Robust and Easy-to-Use One-Pot Workflow for Label-Free Single-Cell Proteomics

Auteurs: Matzinger, Manuel; Mueller, Elisabeth; Duernberger, Gerhard; Pichler, Peter; Mechtler, Karl
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Subcellular Transcriptomics and Proteomics: A Comparative Methods Review

Auteurs: Christopher JA, Geladaki A, Dawson CS, Vennard OL, Lilley KS.
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A universal GlycoDesign for lysosomal replacement enzymes to improve circulation time and biodistribution

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Site‐specific ubiquitination of the E3 ligase HOIP regulates apoptosis and immune signaling

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DNAJC9 integrates heat shock molecular chaperones into the histone chaperone network

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Structure of the human signal peptidase complex reveals the determinants for signal peptide cleavage

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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
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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
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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
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Identification of Protein Complexes by Integrating Protein Abundance and Interaction Features Using a Deep Learning Strategy

Auteurs: Li, Bohui; Altelaar, Maarten; van Breukelen, Bas
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Monitoring mAb proteoforms in mouse plasma using an automated immunocapture combined with top-down and middle-down mass spectrometry

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Data, Reagents, Assays and Merits of Proteomics for SARS-CoV-2 Research and Testing

Auteurs: Zecha, Jana; Lee, Chien-Yun; Bayer, Florian P.; Meng, Chen; Grass, Vincent; Zerweck, Johannes; Schnatbaum, Karsten; Michler, Thomas; Pichlmair, Andreas; Ludwig, Christina; Kuster, Bernhard
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Fasting improves therapeutic response in hepatocellular carcinoma through p53-dependent metabolic synergism

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Deep learning boosts sensitivity of mass spectrometry-based immunopeptidomics

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Reversible amyloids of pyruvate kinase couple cell metabolism and stress granule assembly

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MassIVE.quant: a community resource of quantitative mass spectrometry–based proteomics datasets

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Bap-Independent Biofilm Formation in Staphylococcus xylosus

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Domestic animal proteomics in the 21st century: A global retrospective and viewpoint analysis

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Structure of the inner kinetochore CCAN complex assembled onto a centromeric nucleosome

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Proteome Dynamics of Persulfidation in Leaf Tissue under Light/Dark Conditions and Carbon Deprivation

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Comparative Analysis of Antibodies and Heavily Glycosylated Macromolecular Immune Complexes by Size-Exclusion Chromatography Multi-Angle Light Scattering, Native Charge Detection Mass Spectrometry, and Mass Photometry

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Regulation of Rad52-dependent replication fork recovery through serine ADP-ribosylation of PolD3

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The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences

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Fast Fluoroalkylation of Proteins Uncovers the Structure and Dynamics of Biological Macromolecules

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Decoding protein methylation function with thermal stability analysis

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Spatial epi-proteomics enabled by histone post-translational modification analysis from low-abundance clinical samples

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azyx-1 is a new gene that overlaps with zyxin and affects its translation in C. elegans, impacting muscular integrity and locomotion

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Pharmacological inhibition of LSD1 triggers myeloid differentiation by targeting GSE1 oncogenic functions in AML. 

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An Integrative Structural Biology Analysis of Von Willebrand Factor Binding and Processing by ADAMTS-13 in Solution

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Global analysis of protein-RNA interactions in SARS-CoV-2-infected cells reveals key regulators of infection

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Pout2Prot:AnEfficient Tool to Create Protein (Sub)groups from Percolator Output Files

Auteurs: Schallert, Kay; Verschaffelt, Pieter; Mesuere, Bart; Benndorf, Dirk; Martens, Lennart; Van den Bossche, Tim
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Deep (phospho)proteomics profiling of pre- treatment needle biopsies identifies signatures of treatment resistance in HER2+breast cancer

Auteurs: Debets, Donna O.; Stecker, Kelly E.; Piskopou, Anastasia; Liefaard, Marte C.; Wesseling, Jelle; Sonke, Gabe S.; Lips, Esther H.; Altelaar, Maarten
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Deep Single-Shot NanoLC-MS Proteome Profiling with a 1500 Bar UHPLC System, Long Fully Porous Columns, and HRAM MS

Auteurs: Zheng R, Stejskal K, Pynn C, Mechtler K, Boychenko A
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Precursor deconvolution error estimation: The missing puzzle piece in false discovery rate in top-down proteomics

Auteurs: Jeong, Kyowon; Kaulich, Philipp T.; Jung, Wonhyeuk; Kim, Jihyung; Tholey, Andreas; Kohlbacher, Oliver
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The histone code of the fungal genus Aspergillus uncovered by evolutionary and proteomic analyses

Auteurs: Zhang X, Noberini R, Bonaldi T, Collemare J, Seidl MF. 
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ANGEL2 is a member of the CCR4 family of deadenylases with 2′,3′-cyclic phosphatase activity

Auteurs: Pinto, Paola H.; Kroupova, Alena; Schleiffer, Alexander; Mechtler, Karl; Jinek, Martin; Weitzer, Stefan; Martinez, Javier
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Éditeur: American Association for the Advancement of Science
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Generalized Calibration Across Liquid Chromatography Setups for Generic Prediction of Small-Molecule Retention Times

Auteurs: Bouwmeester, Robbin; Martens, Lennart; Degroeve, Sven
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Éditeur: American Chemical Society
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Similarities and differences in the structures and proteoform profiles of the complement proteins C6 and C7

Auteurs: Marie V. Lukassen, Vojtech Franc, Johannes F. Hevler, Albert J.R. Heck
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Lipid nanoparticles allow efficient and harmless ex vivo gene editing of human hematopoietic cells

Auteurs: Vavassori, Valentina; Ferrari, Samuele; Beretta, Stefano; Asperti, Claudia; Albano, Luisa; Annoni, Andrea; Gaddoni, Chiara; Varesi, Angelica; Soldi, Monica; Cuomo, Alessandro; Bonaldi, Tiziana; Radrizzani, Marina; Merelli, Ivan; Naldini, Luigi
Publié dans: Blood, Numéro 142/9, 2023, Page(s) 812-826, ISSN 0006-4971
Éditeur: American Society of Hematology
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Zebrafish Ski7 tunes RNA levels during the oocyte-to-embryo transition

Auteurs: Luis Enrique Cabrera-Quio, Alexander Schleiffer, Karl Mechtler, Andrea Pauli
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Mass Spectrometry-Driven Discovery of Neuropeptides Mediating Nictation Behavior of Nematodes

Auteurs: Cockx, Bram; Van Bael, Sven; Boelen, Rose; Vandewyer, Elke; Yang, Heeseung; Le, Tuan Anh; Dalzell, Johnathan J.; Beets, Isabel; Ludwig, Christina; Lee, Junho; Temmerman, Liesbet
Publié dans: Mol. Cell. Proteomics, Numéro 22/2, 2023, Page(s) 100479, ISSN 1535-9476
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AKIRIN2 controls the nuclear import of proteasomes in vertebrates

Auteurs: Melanie de Almeida, Matthias Hinterndorfer, Hanna Brunner, Irina Grishkovskaya, Kashish Singh, Alexander Schleiffer, Julian Jude, Sumit Deswal, Robert Kalis, Milica Vunjak, Thomas Lendl, Richard Imre, Elisabeth Roitinger, Tobias Neumann, Susanne Kandolf, Michael Schutzbier, Karl Mechtler, Gijs A. Versteeg, David Haselbach, Johannes Zuber
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In Vitro Evolution Reveals Noncationic Protein-RNA Interaction Mediated by Metal Ions

Auteurs: Giacobelli VG, Fujishima K, Lepšík M, Tretyachenko V, Kadavá T, Makarov M, Bednárová L, Novák P, Hlouchová K
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Éditeur: Oxford University Press
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Benefits of Collisional Cross Section Assisted Precursor Selection (caps-PASEF) for Cross-linking Mass Spectrometry

Auteurs: Barbara Steigenberger, Henk W. P. van den Toorn, Emiel Bijl, Jean-François Greisch, Oliver Räther, Markus Lubeck, Roland J. Pieters, Albert J. R. Heck, Richard A. Scheltema
Publié dans: Molecular & Cellular Proteomics, Numéro 19/10, 2020, Page(s) 1677-1687, ISSN 1535-9476
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Decrypting drug actions and protein modifications by dose- and time-resolved proteomics

Auteurs: Zecha, Jana; Bayer, Florian P.; Wiechmann, Svenja; Woortman, Julia; Berner, Nicola; Mueller, Julian; Schneider, Annika; Kramer, Karl; Abril-Gil, Mar; Hopf, Thomas; Reichart, Leonie; Chen, Lin; Hansen, Fynn M.; Lechner, Severin; Samaras, Patroklos; Eckert, Stephan; Lautenbacher, Ludwig; Reinecke, Maria; Hamood, Firas; Prokofeva, Polina; Vornholz, Larsen; Falcomata, Chiara; Dorsch, Madeleine; Schroe
Publié dans: Science, Numéro 380/6640, 2023, ISSN 0036-8075
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A combination of molecular and clinical parameters provides a new strategy for high-grade serous ovarian cancer patient management

Auteurs: Bradbury, Melissa; Borras, Eva; Vilar, Marta; Castellvi, Josep; Luis Sanchez-Iglesias, Jose; Perez-Benavente, Assumpcio; Gil-Moreno, Antonio; Santamaria, Anna; Sabido, Eduard
Publié dans: J. Transl. Med., Numéro 20/1, 2022, Page(s) 611, ISSN 1479-5876
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Scop3P: A Comprehensive Resource of Human Phosphosites within Their Full Context

Auteurs: Ramasamy, Pathmanaban; Turan, Demet; Tichshenko, Natalia; Hulstaert, Niels; Vandermarliere, Elien; Vranken, Wim; Martens, Lennart
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Label-Free Mass Spectrometry-Based Quantification of Linker Histone H1 Variants in Clinical Samples

Auteurs: Roberta Noberini, Cristina Morales Torres, Evelyn Oliva Savoia, Stefania Brandini, Maria Giovanna Jodice, Giovanni Bertalot, Giuseppina Bonizzi, Maria Capra, Giuseppe Diaferia, Paola Scaffidi, Tiziana Bonaldi
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Chromatin-Bound Proteome Profiling by Genome Capture

Auteurs: Sergi Aranda, Eva Borràs, Eduard Sabidó, Luciano Di Croce
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Comparing Top-Down Proteoform Identification: Deconvolution, PrSM Overlap, and PTM Detection

Auteurs: Tabb, David L.; Jeong, Kyowon; Druart, Karen; Gant, Megan S.; Brown, Kyle A.; Nicora, Carrie; Zhou, Mowei; Couvillion, Sneha; Nakayasu, Ernesto; Williams, Janet E.; Peterson, Haley K.; McGuire, Michelle K.; McGuire, Mark A.; Metz, Thomas O.; Chamot-Rooke, Julia
Publié dans: J. Proteome Res., Numéro 22/7, 2023, Page(s) 2199-2217, ISSN 1535-3893
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Hybrid-DIA: intelligent data acquisition integrates targeted and discovery proteomics to analyze phospho-signaling in single spheroids

Auteurs: Martinez-Val, Ana; Fort, Kyle; Koenig, Claire; van der Hoeven, Leander; Franciosa, Giulia; Moehring, Thomas; Ishihama, Yasushi; Chen, Yu-ju; Makarov, Alexander; Xuan, Yue; Olsen, Jesper V.
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Feature-based molecular networking in the GNPS analysis environment

Auteurs: Louis-Félix Nothias, Daniel Petras, Robin Schmid, Kai Dührkop, Johannes Rainer, Abinesh Sarvepalli, Ivan Protsyuk, Madeleine Ernst, Hiroshi Tsugawa, Markus Fleischauer, Fabian Aicheler, Alexander A. Aksenov, Oliver Alka, Pierre-Marie Allard, Aiko Barsch, Xavier Cachet, Andres Mauricio Caraballo-Rodriguez, Ricardo R. Da Silva, Tam Dang, Neha Garg, Julia M. Gauglitz, Alexey Gurevich, Giorgis Isaac
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Combining CRISPRi and metabolomics for functional annotation of compound libraries

Auteurs: Anglada-Girotto M, Handschin G, Ortmayr K, Campos AI, Gillet L, Manfredi P, Mulholland CV, Berney M, Jenal U, Picotti P, Zampieri M.
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Integrated Proteomics Unveils Nuclear PDE3A2 as a Regulator of Cardiac Myocyte Hypertrophy

Auteurs: Subramaniam, Gunasekaran; Schleicher, Katharina; Kovanich, Duangnapa; Zerio, Anna; Folkmanaite, Milda; Chao, Ying-Chi; Surdo, Nicoletta C.; Koschinski, Andreas; Hu, Jianshu; Scholten, Arjen; Heck, Albert J. R.; Ercu, Maria; Sholokh, Anastasiia; Park, Kyung Chan; Klussmann, Enno; Meraviglia, Viviana; Bellin, Milena; Zanivan, Sara; Hester, Svenja; Mohammed, Shabaz; Zaccolo, Manuela
Publié dans: Circ.Res., Numéro 132/7, 2023, Page(s) 828-848, ISSN 0009-7330
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N-terminal acetylation shields proteins from degradation and promotes age-dependent motility and longevity

Auteurs: Varland, Sylvia; Silva, Rui Duarte; Kjosas, Ine; Faustino, Alexandra; Bogaert, Annelies; Billmann, Maximilian; Boukhatmi, Hadi; Kellen, Barbara; Costanzo, Michael; Drazic, Adrian; Osberg, Camilla; Chan, Katherine; Zhang, Xiang; Tong, Amy Hin Yan; Andreazza, Simonetta; Lee, Juliette J.; Nedyalkova, Lyudmila; Usaj, Matej; Whitworth, Alexander J.; Andrews, Brenda J.; Moffat, Jason; Myers, Chad L.; Ge
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The Role of Pseudo-Orthocaspase (SyOC) of Synechocystis sp. PCC 6803 in Attenuating the Effect of Oxidative Stress

Auteurs: Saul Lema A, Marina Klemenčič, Franziska Völlmy, Maarten Altelaar, Christiane Funk
Publié dans: Frontiers in Microbiology, Numéro 12, 2021, ISSN 1664-302X
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Optineurin links Hace1-dependent Rac ubiquitylation to integrin-mediated mechanotransduction to control bacterial invasion and cell division

Auteurs: Petracchini S, Hamaoui D, Doye A, Asnacios A, Fage F, Vitiello E, Balland M, Janel S, Lafont F, Gupta M, Ladoux B, Gilleron J, Maia TM, Impens F, Gagnoux-Palacios L, Daugaard M, Sorensen PH, Lemichez E, Mettouchi A.
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Spatiotemporal proteomic profiling of the pro-inflammatory response to lipopolysaccharide in the THP-1 human leukaemia cell line

Auteurs: Claire M. Mulvey, Lisa M. Breckels, Oliver M. Crook, David J. Sanders, Andre L. R. Ribeiro, Aikaterini Geladaki, Andy Christoforou, Nina Kočevar Britovšek, Tracey Hurrell, Michael J. Deery, Laurent Gatto, Andrew M. Smith, Kathryn S. Lilley
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Serine ADP-ribosylation in Drosophila provides insights into the evolution of reversible ADP-ribosylation signalling

Auteurs: Fontana, Pietro; Buch-Larsen, Sara C.; Suyari, Osamu; Smith, Rebecca; Suskiewicz, Marcin J.; Schutzenhofer, Kira; Ariza, Antonio; Rack, Johannes Gregor Matthias; Nielsen, Michael L.; Ahel, Ivan
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Connecting MetaProteomeAnalyzer and PeptideShaker to Unipept for Seamless End-to-End Metaproteomics Data Analysis

Auteurs: Van den Bossche, Tim; Verschaffelt, Pieter; Schallert, Kay; Barsnes, Harald; Dawyndt, Peter; Benndorf, Dirk; Renard, Bernhard Y.; Mesuere, Bart; Martens, Lennart; Muth, Thilo
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Data Management of Sensitive Human Proteomics Data: Current Practices, Recommendations, and Perspectives for the Future

Auteurs: Nuno Bandeira, Eric W. Deutsch, Oliver Kohlbacher, Lennart Martens, Juan Antonio Vizcaíno
Publié dans: Molecular & Cellular Proteomics, Numéro 20, 2021, Page(s) 100071, ISSN 1535-9476
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A machine learning-based chemoproteomic approach to identify drug targets and binding sites in complex proteomes

Auteurs: Ilaria Piazza, Nigel Beaton, Roland Bruderer, Thomas Knobloch, Crystel Barbisan, Lucie Chandat, Alexander Sudau, Isabella Siepe, Oliver Rinner, Natalie de Souza, Paola Picotti, Lukas Reiter
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Urinary Collectrin (TMEM27) as Novel Marker for Acute Kidney Injury

Auteurs: Pajenda S, Wagner L, Gerges D, Herkner H, Tevdoradze T, Mechtler K, Schmidt A, Winnicki W. 
Publié dans: Life, 2022, ISSN 2075-1729
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Accurate peptide fragmentation predictions allow data driven approaches to replace and improve upon proteomics search engine scoring functions

Auteurs: C Silva AS, Bouwmeester R, Martens L, Degroeve S
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Neutrophil azurophilic granule glycoproteins are distinctively decorated by atypical pauci- and phosphomannose glycans

Auteurs: Karli R. Reiding, Yu-Hsien Lin, Floris P. J. van Alphen, Alexander B. Meijer, Albert J. R. Heck
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High Resolution Proteomic Analysis of Subcellular Fractionated Boar Spermatozoa Provides Comprehensive Insights Into Perinuclear Theca-Residing Proteins

Auteurs: Zhang M, Chiozzi RZ, Skerrett-Byrne DA, Veenendaal T, Klumperman J, Heck AJR, Nixon B, Helms JB, Gadella BM, Bromfield EG
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Proteomic investigation of Cbl and Cbl-b in neuroblastoma cell differentiation highlights roles for SHP-2 and CDK16

Auteurs: Anna-Kathrine Pedersen, Anamarija Pfeiffer, Gopal Karemore, Vyacheslav Akimov, Dorte B. Bekker-Jensen, Blagoy Blagoev, Chiara Francavilla, Jesper V. Olsen
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A serum proteome signature to predict mortality in severe COVID-19 patients

Auteurs: Franziska Völlmy, Henk van den Toorn, Riccardo Zenezini Chiozzi, Ottavio Zucchetti, Alberto Papi, Carlo Alberto Volta, Luisa Marracino, Francesco Vieceli Dalla Sega, Francesca Fortini, Vadim Demichev, Pinkus Tober-Lau, Gianluca Campo, Marco Contoli, Markus Ralser, Florian Kurth, Savino Spadaro, Paola Rizzo, Albert JR Heck
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BRCA1 mutations in high-grade serous ovarian cancer are associated with proteomic changes in DNA repair, splicing, transcription regulation and signaling

Auteurs: Bradbury M, Borràs E, Castellví J, Méndez O, Sánchez-Iglesias JL, Pérez-Benavente A, Gil-Moreno A, Sabidó E, Santamaria A.
Publié dans: Scientific Reports, 2022, ISSN 2045-2322
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Expression of NORAD correlates with breast cancer aggressiveness and protects breast cancer cells from chemotherapy

Auteurs: Alves-Vale, Catarina; Capela, Ana Maria; Tavares-Marcos, Carlota; Domingues-Silva, Beatriz; Pereira, Bruno; Santos, Francisco; Gomes, Carla Pereira; Espadas, Guadalupe; Vitorino, Rui; Sabido, Eduard; Borralho, Paula; Nobrega-Pereira, Sandrina; de Jesuse, Bruno Bernardes
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Waves of sumoylation support transcription dynamics during adipocyte differentiation

Auteurs: Zhao X, Hendriks IA, Le Gras S, Ye T, Ramos-Alonso L, Nguéa P A, Lien GF, Ghasemi F, Klungland A, Jost B, Enserink JM, Nielsen ML
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Comparative Proteome Signatures of Trace Samples by Multiplexed Data-Independent Acquisition

Auteurs: Ctortecka C, Krššáková G, Stejskal K, Penninger JM, Mendjan S, Mechtler K, Stadlmann J.
Publié dans: Mol Cell Proteomics, 2022, ISSN 1535-9484
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MS Annika 2.0 Identifies Cross-Linked Peptides in MS2-MS3-Based Workflows at High Sensitivity and Specificity

Auteurs: Birklbauer, Micha J. J.; Matzinger, Manuel; Mueller, Fraenze; Mechtler, Karl; Dorfer, Viktoria
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Cross-ID: Analysis and Visualization of Complex XL–MS-Driven Protein Interaction Networks

Auteurs: Sebastiaan C. de Graaf, Oleg Klykov, Henk van den Toorn, Richard A. Scheltema
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PhoX: An IMAC-Enrichable Cross-Linking Reagent

Auteurs: Barbara Steigenberger, Roland J. Pieters, Albert J. R. Heck, Richard A. Scheltema
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Binding of eIF3 in complex with eIF5 and eIF1 to the 40S ribosomal subunit is accompanied by dramatic structural changes

Auteurs: Jakub Zeman, Yuzuru Itoh, Zdeněk Kukačka, Michal Rosůlek, Daniel Kavan, Tomáš Kouba, Myrte E Jansen, Mahabub P Mohammad, Petr Novák, Leoš S Valášek
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Quantifying the impact of public omics data

Auteurs: Yasset Perez-Riverol, Andrey Zorin, Gaurhari Dass, Manh-Tu Vu, Pan Xu, Mihai Glont, Juan Antonio Vizcaíno, Andrew F. Jarnuczak, Robert Petryszak, Peipei Ping, Henning Hermjakob
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N-terminal β-strand underpins biochemical specialization of an ATG8 isoform

Auteurs: Erin K. Zess, Cassandra Jensen, Neftaly Cruz-Mireles, Juan Carlos De la Concepcion, Jan Sklenar, Madlen Stephani, Richard Imre, Elisabeth Roitinger, Richard Hughes, Khaoula Belhaj, Karl Mechtler, Frank L. H. Menke, Tolga Bozkurt, Mark J. Banfield, Sophien Kamoun, Abbas Maqbool, Yasin F. Dagdas
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A Colorful Pallet of B-Phycoerythrin Proteoforms Exposed by a Multimodal Mass Spectrometry Approach

Auteurs: Sem Tamara, Max Hoek, Richard A. Scheltema, Aneika C. Leney, Albert J.R. Heck
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Isotopologue Multipoint Calibration for Proteomics Biomarker Quantification in Clinical Practice

Auteurs: Cristina Chiva, Olga Pastor, Lucía Trilla-Fuertes, Angelo Gámez-Pozo, Juan Ángel Fresno Vara, Eduard Sabidó
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Phosphopeptide Fragmentation and Site Localization by Mass Spectrometry: An Update

Auteurs: Clement M. Potel, Simone Lemeer, Albert J. R. Heck
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MS-Based Approaches Enable the Structural Characterization of Transcription Factor/DNA Response Element Complex

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Improved Sensitivity in Low-Input Proteomics Using Micropillar Array-Based Chromatography

Auteurs: Johannes Stadlmann, Otto Hudecz, Gabriela Krššáková, Claudia Ctortecka, Geert Van Raemdonck, Jeff Op De Beeck, Gert Desmet, Josef M. Penninger, Paul Jacobs, Karl Mechtler
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Absolute quantification of cohesin, CTCF and their regulators in human cells

Auteurs: Johann Holzmann, Antonio Z Politi, Kota Nagasaka, Merle Hantsche-Grininger, Nike Walther, Birgit Koch, Johannes Fuchs, Gerhard Dürnberger, Wen Tang, Rene Ladurner, Roman R Stocsits, Georg A Busslinger, Béla Novák, Karl Mechtler, Iain Finley Davidson, Jan Ellenberg, Jan-Michael Peters
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Proteases Immobilization for In Situ Time-Limited Proteolysis on MALDI Chips

Auteurs: Rosulek, Darebna, Pompach, Slavata, Novak
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Oncogenic Mutations Rewire Signaling Pathways by Switching Protein Recruitment to Phosphotyrosine Sites

Auteurs: Alicia Lundby, Giulia Franciosa, Kristina B. Emdal, Jan C. Refsgaard, Sebastian P. Gnosa, Dorte B. Bekker-Jensen, Anna Secher, Svetlana R. Maurya, Indranil Paul, Blanca L. Mendez, Christian D. Kelstrup, Chiara Francavilla, Marie Kveiborg, Guillermo Montoya, Lars J. Jensen, Jesper V. Olsen
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Missing regions within the molecular architecture of human fibrin clots structurally resolved by XL-MS and integrative structural modeling

Auteurs: Oleg Klykov, Carmen van der Zwaan, Albert J. R. Heck, Alexander B. Meijer, Richard A. Scheltema
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Targeting proline in (phospho)proteomics

Auteurs: Saar A. M. Laarse, Charlotte A. G. H. Gelder, Marshall Bern, Michiel Akeroyd, Maurien M. A. Olsthoorn, Albert J. R. Heck
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Accurate peptide fragmentation predictions allow data driven approaches to replace and improve upon proteomics search engine scoring functions

Auteurs: Ana S C. Silva, Robbin Bouwmeester, Lennart Martens, Sven Degroeve
Publié dans: Bioinformatics, Numéro 35/24, 2019, Page(s) 5243-5248, ISSN 1367-4803
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Rapid and site-specific deep phosphoproteome profiling by data-independent acquisition without the need for spectral libraries

Auteurs: 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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EPIFANY: A Method for Efficient High-Confidence Protein Inference

Auteurs: Julianus Pfeuffer, Timo Sachsenberg, Tjeerd M. H. Dijkstra, Oliver Serang, Knut Reinert, Oliver Kohlbacher
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Enrichment of histones from patient samples for mass spectrometry-based analysis of post-translational modifications

Auteurs: Roberta Noberini, Camilla Restellini, Evelyn Oliva Savoia, Tiziana Bonaldi
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ThermoRawFileParser: Modular, Scalable, and Cross-Platform RAW File Conversion

Auteurs: Niels Hulstaert, Jim Shofstahl, Timo Sachsenberg, Mathias Walzer, Harald Barsnes, Lennart Martens, Yasset Perez-Riverol
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The Human Immunopeptidome Project: A Roadmap to Predict and Treat Immune Diseases

Auteurs: Juan Antonio Vizcaíno, Peter Kubiniok, Kevin A. Kovalchik, Qing Ma, Jérôme D. Duquette, Ian Mongrain, Eric W. Deutsch, Bjoern Peters, Alessandro Sette, Isabelle Sirois, Etienne Caron
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ESCO1 and CTCF enable formation of long chromatin loops by protecting cohesinSTAG1 from WAPL

Auteurs: Gordana Wutz, Rene Ladurner, Brian Glenn St Hilaire, Roman R Stocsits, Kota Nagasaka, Benoit Pignard, Adrian Sanborn, Wen Tang, Csilla Várnai, Miroslav P Ivanov, Stefan Schoenfelder, Petra van der Lelij, Xingfan Huang, Gerhard Dürnberger, Elisabeth Roitinger, Karl Mechtler, Iain Finley Davidson, Peter Fraser, Erez Lieberman-Aiden, Jan-Michael Peters
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Generating high quality libraries for DIA MS with empirically corrected peptide predictions

Auteurs: Brian C. Searle, Kristian E. Swearingen, Christopher A. Barnes, Tobias Schmidt, Siegfried Gessulat, Bernhard Küster, Mathias Wilhelm
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The omics discovery REST interface

Auteurs: Gaurhari Dass, Manh-Tu Vu, Pan Xu, Enrique Audain, Marc-Phillip Hitz, Björn A Grüning, Henning Hermjakob, Yasset Perez-Riverol
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FLASHDeconv: Ultrafast, High-Quality Feature Deconvolution for Top-Down Proteomics

Auteurs: Kyowon Jeong, Jihyung Kim, Manasi Gaikwad, Siti Nurul Hidayah, Laura Heikaus, Hartmut Schlüter, Oliver Kohlbacher
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Removing the Hidden Data Dependency of DIA with Predicted Spectral Libraries

Auteurs: Bart Van Puyvelde, Sander Willems, Ralf Gabriels, Simon Daled, Laura De Clerck, Sofie Vande Casteele, An Staes, Francis Impens, Dieter Deforce, Lennart Martens, Sven Degroeve, Maarten Dhaenens
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To Cleave or Not To Cleave in XL-MS?

Auteurs: B. Steigenberger, P. Albanese, A. J. R. Heck, R. A. Scheltema
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Resolving heterogeneous macromolecular assemblies by Orbitrap-based single-particle charge detection mass spectrometry

Auteurs: Tobias P. Wörner, Joost Snijder, Antonette Bennett, Mavis Agbandje-McKenna, Alexander A. Makarov, Albert J. R. Heck
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Simple Peptide Quantification Approach for MS-Based Proteomics Quality Control

Auteurs: Teresa Mendes Maia, An Staes, Kim Plasman, Jarne Pauwels, Katie Boucher, Andrea Argentini, Lennart Martens, Tony Montoye, Kris Gevaert, Francis Impens
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N-Terminal Proteoforms in Human Disease

Auteurs: Annelies Bogaert, Esperanza Fernandez, Kris Gevaert
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The ProteomeXchange consortium in 2020: enabling ‘big data’ approaches in proteomics

Auteurs: Eric W Deutsch, Nuno Bandeira, Vagisha Sharma, Yasset Perez-Riverol, Jeremy J Carver, Deepti J Kundu, David García-Seisdedos, Andrew F Jarnuczak, Suresh Hewapathirana, Benjamin S Pullman, Julie Wertz, Zhi Sun, Shin Kawano, Shujiro Okuda, Yu Watanabe, Henning Hermjakob, Brendan MacLean, Michael J MacCoss, Yunping Zhu, Yasushi Ishihama, Juan A Vizcaíno
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Influence of cross-linker polarity on selectivity towards lysine side chains

Auteurs: Jan Fiala, Zdeněk Kukačka, Petr Novák
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COSS: A fast and user-friendly tool for spectral library searching

Auteurs: Genet Abay Shiferaw, Elien Vandermarliere, Niels Hulstaert, Ralf Gabriels, Lennart Martens, Pieter-Jan Volders
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Fast and Highly Efficient Affinity Enrichment of Azide-A-DSBSO Cross-Linked Peptides

Auteurs: Manuel Matzinger, Wolfgang Kandioller, Philipp Doppler, Elke H. Heiss, Karl Mechtler
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Fishing for newly synthesized proteins with phosphonate-handles

Auteurs: Fleur Kleinpenning, Barbara Steigenberger, Wei Wu, Albert J. R. Heck
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A synthetic peptide library for benchmarking crosslinking-mass spectrometry search engines for proteins and protein complexes

Auteurs: Rebecca Beveridge, Johannes Stadlmann, Josef M. Penninger, Karl Mechtler
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The Age of Data‐Driven Proteomics: How Machine Learning Enables Novel Workflows

Auteurs: Robbin Bouwmeester, Ralf Gabriels, Tim Van Den Bossche, Lennart Martens, Sven Degroeve
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Connecting MetaProteomeAnalyzer and PeptideShaker to Unipept for Seamless End-to-End Metaproteomics Data Analysis

Auteurs: Tim Van Den Bossche, Pieter Verschaffelt, Kay Schallert, Harald Barsnes, Peter Dawyndt, Dirk Benndorf, Bernhard Y. Renard, Bart Mesuere, Lennart Martens, Thilo Muth
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Robust Summarization and Inference in Proteome-wide Label-free Quantification

Auteurs: Adriaan Sticker, Ludger Goeminne, Lennart Martens, Lieven Clement
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Generalized Calibration Across Liquid Chromatography Setups for Generic Prediction of Small-Molecule Retention Times

Auteurs: Robbin Bouwmeester, Lennart Martens, Sven Degroeve
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Scop3P: A Comprehensive Resource of Human Phosphosites within Their Full Context

Auteurs: Pathmanaban Ramasamy, Demet Turan, Natalia Tichshenko, Niels Hulstaert, Elien Vandermarliere, Wim Vranken, Lennart Martens
Publié dans: Journal of Proteome Research, 2020, ISSN 1535-3893
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Updated MS²PIP web server delivers fast and accurate MS² peak intensity prediction for multiple fragmentation methods, instruments and labeling techniques

Auteurs: Ralf Gabriels, Lennart Martens, Sven Degroeve
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New findings on the action of hypericin in hypoxic cancer cells with a focus on the modulation of side population cells

Auteurs: Bukova, Viktoria; Vargova, Jana; Babincak, Marian; Jendzelovsky, Rastislav; Zdrahal, Zbynek; Roudnicky, Pavel; Kosuth, Jan; Fedorocko, Peter
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Notch–Jagged signaling complex defined by an interaction mosaic

Auteurs: Matthieu R. Zeronian, Oleg Klykov, Júlia Portell i de Montserrat, Maria J. Konijnenberg, Anamika Gaur, Richard A. Scheltema, Bert J. C. Janssen
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MSstats Version 4.0: Statistical Analyses of Quantitative Mass Spectrometry-Based Proteomic Experiments with Chromatography-Based Quantification at Scale

Auteurs: Kohler, Devon; Staniak, Mateusz; Tsai, Tsung-Heng; Huang, Ting; Shulman, Nicholas; Bernhardt, Oliver M.; MacLean, Brendan X.; Nesvizhskii, Alexey I.; Reiter, Lukas; Sabido, Eduard; Choi, Meena; Vitek, Olga
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psm_utils: A High-Level Python API for Parsing and Handling Peptide-Spectrum Matches and Proteomics Search Results

Auteurs: Gabriels, Ralf; Declercq, Arthur; Bouwmeester, Robbin; Degroeve, Sven; Martens, Lennart
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Mass spectrometry‐based characterization of histones in clinical samples: applications, progresses, and challenges

Auteurs: Roberta Noberini, Giulia Robusti, Tiziana Bonaldi
Publié dans: The FEBS Journal, 2021, ISSN 1742-464X
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The LncRNA LENOX Interacts with RAP2C to Regulate Metabolism and Promote Resistance to MAPK Inhibition in Melanoma

Auteurs: Gambi, Giovanni; Mengus, Gabrielle; Davidson, Guillaume; Demesmaeker, Ewout; Cuomo, Alessandro; Bonaldi, Tiziana; Katopodi, Vicky; Malouf, Gabriel G.; Leucci, Eleonora; Davidson, Irwin
Publié dans: Cancer Res., Numéro 82/24, 2022, Page(s) 4555-4570, ISSN 0008-5472
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β-RA Targets Mitochondrial Metabolism and Adipogenesis, Leading to Therapeutic Benefits against CoQ Deficiency and Age-Related Overweight

Auteurs: Agustín Hidalgo-Gutiérrez, Eliana Barriocanal-Casado, María Elena Díaz-Casado, Pilar González-García, Riccardo Zenezini Chiozzi, Darío Acuña-Castroviejo, Luis Carlos López
Publié dans: Biomedicines, Numéro 9/10, 2021, Page(s) 1457, ISSN 2227-9059
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Optimization of a Top-Down Proteomics Platform for Closely Related Pathogenic Bacterial Discrimination

Auteurs: Mathieu Dupré, Magalie Duchateau, Christian Malosse, Diogo Borges-Lima, Valeria Calvaresi, Isabelle Podglajen, Dominique Clermont, Martial Rey, Julia Chamot-Rooke
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DUX4-r exerts a neomorphic activity that depends on GTF2I in acute lymphoblastic leukemia

Auteurs: Campolungo, Daniele; Salome, Mara; Biferali, Beatrice; Tascini, Anna Sofia; Gabellini, Davide
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Deciphering of benzothiadiazole (BTH)-induced response of tomato (Solanum lycopersicum L.) and its effect on early response to virus infection through the multi-omics approach

Auteurs: Frackowiak, Patryk; Wrzesinska, Barbara; Wieczorek, Przemyslaw; Sanchez-Bel, Paloma; Kunz, Laura; Dittmann, Antje; Obrepalska-Steplowska, Aleksandra
Publié dans: Plant Soil, Numéro 481/1-2, 2022, Page(s) 511-534, ISSN 0032-079X
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Detection and quantification of the histone code in the fungal genus Aspergillus

Auteurs: Zhang, Xin; Noberini, Roberta; Vai, Alessandro; Bonaldi, Tiziana; Seidl, Michael F.; Collemare, Jerome
Publié dans: Fungal Genet. Biol., Numéro 167, 2023, Page(s) 103800, ISSN 1087-1845
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 Predicting fragment intensities and retention time of iTRAQ- and TMTPro-labeled peptides with Prosit-TMT

Auteurs: Gabriel W, Giurcoiu V, Lautenbacher L, Wilhelm M.
Publié dans: Proteomics, 2022, ISSN 1615-9853
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Extending Native Top-Down Electron Capture Dissociation to MDa Immunoglobulin Complexes Provides Useful Sequence Tags Covering Their Critical Variable Complementarity-Determining Regions

Auteurs: Greisch, Jean-Francois; den Boer, Maurits A.; Lai, Szu-Hsueh; Gallagher, Kelly; Bondt, Albert; Commandeur, Jan; Heck, Albert J. R.
Publié dans: Anal. Chem., Numéro 93/48, 2021, Page(s) 16068-16075, ISSN 0003-2700
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Enzyme expression kinetics by Escherichia coli during transition from rich to minimal media depends on proteome reserves

Auteurs: Wu, Chenhao; Mori, Matteo; Abele, Miriam; Banaei-Esfahani, Amir; Zhang, Zhongge; Okano, Hiroyuki; Aebersold, Ruedi; Ludwig, Christina; Hwa, Terence
Publié dans: NAT. MICROBIOL, Numéro 8/2, 2023, Page(s) 347, ISSN 2058-5276
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Cleavable Cross-Linkers and Mass Spectrometry for the Ultimate Task of Profiling Protein–Protein Interaction Networks in Vivo

Auteurs: Manuel Matzinger, Karl Mechtler
Publié dans: Journal of Proteome Research, Numéro 20/1, 2021, Page(s) 78-93, ISSN 1535-3893
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Human plasma IgG1 repertoires are simple, unique, and dynamic

Auteurs: Bondt, Albert; Hoek, Max; Tamara, Sem; Bastiaan de Graaf; Peng, Weiwei; Schulte, Douwe; van Rijswijck, Danique M. H.; den Boer, Maurits A.; Greisch, Jean-Francois; Varkila, Meri R. J.; Snijder, Joost; Cremer, Olaf L.; Bonten, Marc J. M.; Heck, Albert J. R.
Publié dans: Cell Syst., Numéro 12/12, 2021, Page(s) 1131, ISSN 2405-4712
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Ultrasensitive NanoLC-MS of Subnanogram Protein Samples Using Second Generation Micropillar Array LC Technology with Orbitrap Exploris 480 and FAIMS PRO

Auteurs: Karel Stejskal, Jeff Op de Beeck, Gerhard Dürnberger, Paul Jacobs, Karl Mechtler
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Molecular principles of Piwi-mediated cotranscriptional silencing through the dimeric SFiNX complex

Auteurs: Jakob Schnabl, Juncheng Wang, Ulrich Hohmann, Maja Gehre, Julia Batki, Veselin I. Andreev, Kim Purkhauser, Nina Fasching, Peter Duchek, Maria Novatchkova, Karl Mechtler, Clemens Plaschka, Dinshaw J. Patel, Julius Brennecke
Publié dans: Genes & Development, Numéro 35/5-6, 2021, Page(s) 392-409, ISSN 0890-9369
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Repurposing the antipsychotic drug amisulpride for targeting synovial fibroblast activation in arthritis

Auteurs: Papadopoulou, Dimitra; Roumelioti, Fani; Tzaferis, Christos; Chouvardas, Panagiotis; Pedersen, Anna-Kathrine; Charalampous, Filippos; Christodoulou-Vafeiadou, Eleni; Ntari, Lydia; Karagianni, Niki; Denis, Maria C.; V. Olsen, Jesper V.; Matralis, Alexios N.; Kollias, George
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Identification of Carcinogenesis and Tumor Progression Processes in Pancreatic Ductal Adenocarcinoma Using High-Throughput Proteomics

Auteurs: Trilla-Fuertes L, Gámez-Pozo A, Lumbreras-Herrera MI, López-Vacas R, Heredia-Soto V, Ghanem I, López-Camacho E, Zapater-Moros A, Miguel M, Peña-Burgos EM, Palacios E, De Uribe M, Guerra L, Dittmann A, Mendiola M, Fresno Vara JÁ, Feliu J
Publié dans: Cancers, 2022, ISSN 2072-6694
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Quantifying Positional Isomers (QPI) by Top-Down Mass Spectrometry

Auteurs: Andrea M. Brunner, Philip Lössl, Paul P. Geurink, Huib Ovaa, P. Albanese, A.F. Maarten Altelaar, Albert J.R. Heck, Richard A. Scheltema
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FLASHIda enables intelligent data acquisition for top-down proteomics to boost proteoform identification counts

Auteurs: Jeong, Kyowon; Babovic, Masa; Gorshkov, Vladimir; Kim, Jihyung; Jensen, Ole N.; Kohlbacher, Oliver
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Systemic LRG1 Expression in Melanoma is Associated with Disease Progression and Recurrence

Auteurs: Hoefsmit, Esmee P.; Vollmy, Franziska; Rozeman, Elisa A.; Reijers, Irene L. M.; Versluis, Judith M.; Hoekman, Liesbeth; van Akkooi, Alexander C. J.; Long, Georgina, V; Schadendorf, Dirk; Dummer, Reinhard; Altelaar, Maarten; Blank, Christian U.
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Nse5/6 inhibits the Smc5/6 ATPase and modulates DNA substrate binding

Auteurs: Michael Taschner, Jérôme Basquin, Barbara Steigenberger, Ingmar B Schäfer, Young‐Min Soh, Claire Basquin, Esben Lorentzen, Markus Räschle, Richard A Scheltema, Stephan Gruber
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Single-cell derived tumor organoids display diversity in HLA class I peptide presentation

Auteurs: Laura C. Demmers, Kai Kretzschmar, Arne Van Hoeck, Yotam E. Bar-Epraïm, Henk W. P. van den Toorn, Mandy Koomen, Gijs van Son, Joost van Gorp, Apollo Pronk, Niels Smakman, Edwin Cuppen, Hans Clevers, Albert J. R. Heck, Wei Wu
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Quantitative Longitudinal Inventory of the N -Glycoproteome of Human Milk from a Single Donor Reveals the Highly Variable Repertoire and Dynamic Site-Specific Changes

Auteurs: Jing Zhu, Yu-Hsien Lin, Kelly A. Dingess, Marko Mank, Bernd Stahl, Albert J. R. Heck
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Staphylococcal protein A inhibits complement activation by interfering with IgG hexamer formation

Auteurs: Ana Rita Cruz, Maurits A. den Boer, Jürgen Strasser, Seline A. Zwarthoff, Frank J. Beurskens, Carla J. C. de Haas, Piet C. Aerts, Guanbo Wang, Rob N. de Jong, Fabio Bagnoli, Jos A. G. van Strijp, Kok P. M. van Kessel, Janine Schuurman, Johannes Preiner, Albert J. R. Heck, Suzan H. M. Rooijakkers
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Cov-MS: A Community-Based Template Assay for Mass-Spectrometry-Based Protein Detection in SARS-CoV-2 Patients

Auteurs: Bart Van Puyvelde, Katleen Van Uytfanghe, Olivier Tytgat, Laurence Van Oudenhove, Ralf Gabriels, Robbin Bouwmeester, Simon Daled, Tim Van Den Bossche, Pathmanaban Ramasamy, Sigrid Verhelst, Laura De Clerck, Laura Corveleyn, Sander Willems, Nathan Debunne, Evelien Wynendaele, Bart De Spiegeleer, Peter Judak, Kris Roels, Laurie De Wilde, Peter Van Eenoo, Tim Reyns, Marc Cherlet, Emmie Dumont, Griet
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ProteomicsML: An Online Platform for Community-Curated Data sets and Tutorials for Machine Learning in Proteomics

Auteurs: Rehfeldt, Tobias G.; Gabriels, Ralf; Bouwmeester, Robbin; Gessulat, Siegfried; Neely, Benjamin A.; Palmblad, Magnus; Perez-Riverol, Yasset; Schmidt, Tobias; Vizcaino, Juan Antonio; Deutsch, Eric W.
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Label-free single cell proteomics utilizing ultrafast LC and MS instrumentation: A valuable complementary technique to multiplexing

Auteurs: Matzinger, Manuel; Mayer, Rupert L.; Mechtler, Karl
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Crosstalk between H2A variant-specific modifications impacts vital cell functions

Auteurs: Anna Schmücker, Bingkun Lei, Zdravko J. Lorković, Matías Capella, Sigurd Braun, Pierre Bourguet, Olivier Mathieu, Karl Mechtler, Frédéric Berger
Publié dans: PLOS Genetics, Numéro 17/6, 2021, Page(s) e1009601, ISSN 1553-7404
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Spatial proteomics defines the content of trafficking vesicles captured by golgin tethers

Auteurs: John J. H. Shin, Oliver M. Crook, Alicia C. Borgeaud, Jérôme Cattin-Ortolá, Sew Y. Peak-Chew, Lisa M. Breckels, Alison K. Gillingham, Jessica Chadwick, Kathryn S. Lilley, Sean Munro
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Mapping Physiological ADP-Ribosylation Using Activated Ion Electron Transfer Dissociation

Auteurs: Sara C. Buch-Larsen, Ivo A. Hendriks, Jean M. Lodge, Martin Rykær, Benjamin Furtwängler, Evgenia Shishkova, Michael S. Westphall, Joshua J. Coon, Michael L. Nielsen
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MS(2)Rescore: Data-Driven Rescoring Dramatically Boosts Immunopeptide Identification Rates

Auteurs: Declercq A, Bouwmeester R, Hirschler A, Carapito C, Degroeve S, Martens L, Gabriels R.
Publié dans: Mol Cell Proteomics, 2022, ISSN 1535-9476
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Sensitive and Specific Spectral Library Searching with CompOmics Spectral Library Searching Tool and Percolator

Auteurs: Shiferaw, Genet Abay; Gabriels, Ralf; Bouwmeester, Robbin; Van den Bossche, Tim; Vandermarliere, Elien; Martens, Lennart; Volders, Pieter-Jan
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MaxQuant.Live Enables Enhanced Selectivity and Identification of Peptides Modified by Endogenous SUMO and Ubiquitin

Auteurs: Ivo A. Hendriks, Vyacheslav Akimov, Blagoy Blagoev, Michael L. Nielsen
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MS Annika: A New Cross-Linking Search Engine

Auteurs: Georg J. Pirklbauer, Christian E. Stieger, Manuel Matzinger, Stephan Winkler, Karl Mechtler, Viktoria Dorfer
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LFQ-Based Peptide and Protein Intensity Differential Expression Analysis

Auteurs: Bai, Mingze; Deng, Jingwen; Dai, Chengxin; Pfeuffer, Julianus; Sachsenberg, Timo; Perez-Riverol, Yasset
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Optimal analytical strategies for sensitive and quantitative phosphoproteomics using TMT-based multiplexing

Auteurs: Koenig C, Martinez-Val A, Franciosa G, Olsen JV.
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"Response to ""BAP1 Germline Mutation Associated with Bilateral Primary Uveal Melanoma"

Auteurs: Herwig-Carl MC, Sharma A, Melzer C, Holz FG, Loeffler KU.
Publié dans: Ocular Oncology and Pathlogy, 2021, ISSN 2296-4681
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Protocol for high-throughput semi-automated label-free- or TMT-based phosphoproteome profiling

Auteurs: Koenig, Claire; Martinez-Val, Ana; Naicker, Previn; Stoychev, Stoyan; Jordaan, Justin; Oslen, Jesper, V
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PDBe-KB: collaboratively defining the biological context of structural data,

Auteurs: PDBe-KB consortium
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Obtaining Complete Human Proteomes

Auteurs: Martinez-Val, Ana; Guzman, Ulises H.; Olsen, Jesper, V
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Robust Summarization and Inference in Proteome-wide Label-free Quantification

Auteurs: Sticker, Adriaan; Goeminne, Ludger; Martens, Lennart; Clement, Lieven
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Widespread amyloidogenicity potential of multiple myeloma patient-derived immunoglobulin light chains

Auteurs: Sternke-Hoffmann, Rebecca; Pauly, Thomas; Norrild, Rasmus K.; Hansen, Jan; Tucholski, Florian; Hoie, Magnus Haraldson; Marcatili, Paolo; Dupre, Mathieu; Duchateau, Magalie; Rey, Martial; Malosse, Christian; Metzger, Sabine; Boquoi, Amelie; Platten, Florian; Egelhaaf, Stefan U.; Chamot-Rooke, Julia; Fenk, Roland; Nagel-Steger, Luitgard; Haas, Rainer; Buell, Alexander K.
Publié dans: BMC Biol., Numéro 21/1, 2023, Page(s) 21, ISSN 1741-7007
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Oktoberfest: Open-source spectral library generation and rescoring pipeline based on Prosit

Auteurs: Picciani, Mario; Gabriel, Wassim; Giurcoiu, Victor-George; Shouman, Omar; Hamood, Firas; Lautenbacher, Ludwig; Jensen, Cecilia Bang; Mueller, Julian; Kalhor, Mostafa; Soleymaniniya, Armin; Kuster, Bernhard; The, Matthew; Wilhelm, Mathias
Publié dans: Proteomics, 2023, ISSN 1615-9853
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The regulatory landscape of the human HPF1- and ARH3-dependent ADP-ribosylome

Auteurs: Ivo A. Hendriks, Sara C. Buch-Larsen, Evgeniia Prokhorova, Jonas D. Elsborg, Alexandra K.L.F.S. Rebak, Kang Zhu, Dragana Ahel, Claudia Lukas, Ivan Ahel, Michael L. Nielsen
Publié dans: Nature Communications, Numéro 12/1, 2021, ISSN 2041-1723
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Secretome Screening of BRAFV600E-Mutated Colon Cancer Cells Resistant to Vemurafenib

Auteurs: Car, Iris; Dittmann, Antje; Klobucar, Marko; Grbcic, Petra; Pavelic, Sandra Kraljevic; Sedic, Mirela
Publié dans: Biology, Numéro 12/4, 2023, Page(s) 608, ISSN 2079-7737
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De Novo Sequencing of Antibody Light Chain Proteoforms from Patients with Multiple Myeloma

Auteurs: Mathieu Dupré, Magalie Duchateau, Rebecca Sternke-Hoffmann, Amelie Boquoi, Christian Malosse, Roland Fenk, Rainer Haas, Alexander K. Buell, Martial Rey, Julia Chamot-Rooke
Publié dans: Analytical Chemistry, Numéro 93/30, 2021, Page(s) 10627-10634, ISSN 0003-2700
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System-wide analysis of RNA and protein subcellular localization dynamics

Auteurs: Villanueva, Eneko; Smith, Tom; Pizzinga, Mariavittoria; Elzek, Mohamed; Queiroz, Rayner M. L.; Harvey, Robert F.; Breckels, Lisa M.; Crook, Oliver M.; Monti, Mie; Dezi, Veronica; Willis, Anne E.; Lilley, Kathryn S.
Publié dans: Nat. Methods, 2023, ISSN 1548-7091
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Oxonium Ion-Guided Optimization of Ion Mobility-Assisted Glycoproteomics on the timsTOF Pro

Auteurs: Mukherjee, Soumya; Jankevics, Andris; Busch, Florian; Lubeck, Markus; Zou, Yang; Kruppa, Gary; Heck, Albert J. R.; Scheltema, Richard A.; Reiding, Karli R.
Publié dans: Mol. Cell. Proteomics, Numéro 22/2, 2023, Page(s) 100486, ISSN 1535-9476
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Real-Time Spectral Library Matching for Sample Multiplexed Quantitative Proteomics

Auteurs: McGann, Chris D.; Barshop, William D.; Canterbury, Jesse D.; Lin, Chuwei; Gabriel, Wassim; Huang, Jingjing; Bergen, David; Zabrouskov, Vlad; Melani, Rafael D.; Wilhelm, Mathias; McAlister, Graeme C.; Schweppe, Devin K.
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Juxtaposition of Bub1 and Cdc20 on phosphorylated Mad1 during catalytic mitotic checkpoint complex assembly

Auteurs: Fischer ES, Yu CWH, Hevler JF, McLaughlin SH, Maslen SL, Heck AJR, Freund SMV, Barford D. 
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Hydroxyl radical footprinting analysis of a human haptoglobin-hemoglobin complex.

Auteurs: Loginov DS, Fiala J, Brechlin P, Kruppa G, Novak P.
Publié dans: Biochemica et Biophysica Acta, 2021, ISSN 1570-9639
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Bacterial-type ferroxidase tunes iron-dependent phosphate sensing during Arabidopsis root development. 

Auteurs: Naumann C, Heisters M, Brandt W, Janitza P, Alfs C, Tang N, Toto Nienguesso A, Ziegler J, Imre R, Mechtler K, Dagdas Y, Hoehenwarter W, Sawers G, Quint M, Abel S.
Publié dans: Current Biology, 2022, ISSN 0960-9822
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Updated MS2PIP web server supports cutting-edge proteomics applications

Auteurs: Declercq, Arthur; Bouwmeester, Robbin; Chiva, Cristina; Sabido, Eduard; Hirschler, Aurelie; Carapito, Christine; Martens, Lennart; Degroeve, Sven; Gabriels, Ralf
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Selectivity over coverage in de novo sequencing of IgGs

Auteurs: den Boer, Maurits A.; Greisch, Jean-Francois; Tamara, Sem; Bondt, Albert; Heck, Albert J. R.
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Optimized Suspension Trapping Method for Phosphoproteomics Sample Preparation

Auteurs: Wang, Fujia; Veth, Tim; Kuipers, Marije; Altelaar, Maarten; Stecker, Kelly E.
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Temporal and Site-Specific ADP-Ribosylation Dynamics upon Different Genotoxic Stresses

Auteurs: Sara C. Buch-Larsen, Alexandra K.L.F.S.rebak, Ivo. A. Hendriks and Michael L. Nielsen
Publié dans: Cells, 2021, ISSN 2073-4409
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Use of Linear Ion Traps in Data-Independent Acquisition Methods Benefits Low-Input Proteomics

Auteurs: Eva Borràs, Olga Pastor, Eduard Sabidó
Publié dans: Analytical Chemistry, Numéro 93/34, 2021, Page(s) 11649-11653, ISSN 0003-2700
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MS Amanda 2.0: Advancements in the standalone implementation

Auteurs: Viktoria Dorfer, Marina Strobl, Stephan Winkler, Karl Mechtler
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Profiling of the Helicobacter pylori redox switch HP1021 regulon using a multi-omics approach

Auteurs: Noszka, Mateusz; Strzalka, Agnieszka; Muraszko, Jakub; Kolenda, Rafal; Meng, Chen; Ludwig, Christina; Stingl, Kerstin; Zawilak-Pawlik, Anna
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Platelet factor 4 is a biomarker for lymphatic-promoted disorders

Auteurs: Wanshu Ma, Hyea Jin Gil, Noelia Escobedo, Alberto Benito-Martín, Pilar Ximénez-Embún, Javier Muñoz, Héctor Peinado, Stanley G. Rockson, Guillermo Oliver
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A deeper look at carrier proteome effects for single-cell proteomics

Auteurs: Ye Z, Batth TS, Rüther P, Olsen JV
Publié dans: Commun Biol, 2022, ISSN 2399-3642
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Glycoproteoform Profiles of Individual Patients’ Plasma Alpha-1-Antichymotrypsin are Unique and Extensively Remodeled Following a Septic Episode

Auteurs: Tomislav Čaval, Yu-Hsien Lin, Meri Varkila, Karli R. Reiding, Marc J. M. Bonten, Olaf L. Cremer, Vojtech Franc, Albert J. R. Heck
Publié dans: Frontiers in Immunology, Numéro 11, 2021, ISSN 1664-3224
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Spectral Prediction Features as a Solution for the Search Space Size Problem in Proteogenomics

Auteurs: Steven Verbruggen, Siegfried Gessulat, Ralf Gabriels, Anna Matsaroki, Hendrik Van de Voorde, Bernhard Kuster, Sven Degroeve, Lennart Martens, Wim Van Criekinge, Mathias Wilhelm, Gerben Menschaert
Publié dans: Molecular & Cellular Proteomics, Numéro 20, 2021, Page(s) 100076, ISSN 1535-9476
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The ProteomeXchange consortium at 10 years: 2023 update

Auteurs: Deutsch, Eric W.; Bandeira, Nuno; Perez-Riverol, Yasset; Sharma, Vagisha; Carver, Jeremy J.; Mendoza, Luis; Kundu, Deepti J.; Wang, Shengbo; Bandla, Chakradhar; Kamatchinathan, Selvakumar; Hewapathirana, Suresh; Pullman, Benjamin S.; Wertz, Julie; Sun, Zhi; Kawano, Shin; Okuda, Shujiro; Watanabe, Yu; MacLean, Brendan; MacCoss, Michael J.; Zhu, Yunping; Ishihama, Yasushi; Vizcaino, Juan Antonio
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Serum proteomics profiling identifies a preliminary signature for the diagnosis of early-stage lung cancer

Auteurs: Gasparri, Roberto; Noberini, Roberta; Cuomo, Alessandro; Yadav, Avinash; Tricarico, Davide; Salvetto, Carola; Maisonneuve, Patrick; Caminiti, Valentina; Sedda, Giulia; Sabalic, Angela; Bonaldi, Tiziana; Spaggiari, Lorenzo
Publié dans: Proteom. Clin. Appl., 2023, ISSN 1862-8346
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Foresight in clinical proteomics: current status, ethical considerations, and future perspectives

Auteurs: Mundt F, Albrechtsen NJW, Mann SP, Treit P, Ghodgaonkar-Steger M, O'Flaherty M, Raijmakers R, Vizcaíno JA, Heck AJR, Mann M
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A cyclin-dependent kinase-mediated phosphorylation switch of disordered protein condensation

Auteurs: Valverde, Juan Manuel; Dubra, Geronimo; Phillips, Michael; Haider, Austin; Elena-Real, Carlos; Fournet, Aurelie; Alghoul, Emile; Chahar, Dhanvantri; Andres-Sanchez, Nuria; Paloni, Matteo; Bernado, Pau; van Mierlo, Guido; Vermeulen, Michiel; van den Toorn, Henk; Heck, Albert J. R.; Constantinou, Angelos; Barducci, Alessandro; Ghosh, Kingshuk; Sibille, Nathalie; Knipscheer, Puck; Krasinska, Liliana;
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Cells Responding to Closely Related Cholesterol-Dependent Cytolysins Release Extracellular Vesicles with a Common Proteomic Content Including Membrane Repair Proteins

Auteurs: Alves, Sara; Pereira, Joana M.; Mayer, Rupert L.; Goncalves, Alexandre D. A.; Impens, Francis; Cabanes, Didier; Sousa, Sandra
Publié dans: Toxins, Numéro 15/1, 2023, Page(s) 4, ISSN 2072-6651
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Selective cross‐linking of coinciding protein assemblies by in‐gel cross‐linking mass spectrometry

Auteurs: Johannes F Hevler, Marie V Lukassen, Alfredo Cabrera‐Orefice, Susanne Arnold, Matti F Pronker, Vojtech Franc, Albert J R Heck
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A novel dynamic proteomics approach for the measurement of broiler chicken protein fractional synthesis rate

Auteurs: Peinado-Izaguerri, Jorge; Zarzuela, Eduardo; McLaughlin, Mark; Small, Alexandra C.; Riva, Francesca; McKeegan, Dorothy E. F.; Bain, Maureen; Munoz, Javier; Bhide, Mangesh; Preston, Tom
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BioContainers Registry: Searching Bioinformatics and Proteomics Tools, Packages, and Containers

Auteurs: Jingwen Bai, Chakradhar Bandla, Jiaxin Guo, Roberto Vera Alvarez, Mingze Bai, Juan Antonio Vizcaíno, Pablo Moreno, Björn Grüning, Olivier Sallou, Yasset Perez-Riverol
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QCloud2: An Improved Cloud-based Quality-Control System for Mass-Spectrometry-based Proteomics Laboratories

Auteurs: Roger Olivella, Cristina Chiva, Marc Serret, Daniel Mancera, Luca Cozzuto, Antoni Hermoso, Eva Borràs, Guadalupe Espadas, Julia Morales, Olga Pastor, Amanda Solé, Julia Ponomarenko, Eduard Sabidó
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Operation of a TCA cycle subnetwork in the mammalian nucleus

Auteurs: Kafkia, Eleni; Andres-Pons, Amparo; Ganter, Kerstin; Seiler, Markus; Smith, Tom S.; Andrejeva, Anna; Jouhten, Paula; Pereira, Filipa; Franco, Catarina; Kuroshchenkova, Anna; Leone, Sergio; Sawarkar, Ritwick; Boston, Rebecca; Thaventhiran, James; Zaugg, Judith B.; Lilley, Kathryn S.; Lancrin, Christophe; Beck, Martin; Patil, Kiran Raosaheb
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Phosphoproteomics of primary AML patient samples reveals rationale for AKT combination therapy and p53 context to overcome selinexor resistance

Auteurs: Emdal KB, Palacio-Escat N, Wigerup C, Eguchi A, Nilsson H, Bekker-Jensen DB, Rönnstrand L, Kazi JU, Puissant A, Itzykson R, Saez-Rodriguez J, Masson K, Blume-Jensen P, Olsen JV.
Publié dans: Cell Reports, 2022, ISSN 2211-1247
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Proteomics of resistance to Notch1 inhibition in acute lymphoblastic leukemia reveals targetable kinase signatures

Auteurs: Giulia Franciosa, Jos G. A. Smits, Sonia Minuzzo, Ana Martinez-Val, Stefano Indraccolo, Jesper V. Olsen
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Clinico-pathological correlation of lacrimal caruncle tumors: a retrospective analysis over 22 years at the University Eye Hospital Bonn

Auteurs: Clemens, A. C.; Loeffler, K. U.; Holz, F. G.; Herwig-Carl, M. C.
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Complete and cooperative in vitro assembly of computationally designed self-assembling protein nanomaterials

Auteurs: Adam J. Wargacki, Tobias P. Wörner, Michiel van de Waterbeemd, Daniel Ellis, Albert J. R. Heck, Neil P. King
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Structural basis of soluble membrane attack complex packaging for clearance

Auteurs: Anaïs Menny, Marie V. Lukassen, Emma C. Couves, Vojtech Franc, Albert J. R. Heck, Doryen Bubeck
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Molecular characterization of triple negative breast cancer formaldehyde‐fixed paraffin‐embedded samples by data‐independent acquisition proteomics

Auteurs: Silvia García‐Adrián, Lucía Trilla‐Fuertes, Angelo Gámez‐Pozo, Cristina Chiva, Rocío López‐Vacas, Elena López‐Camacho, Andrea Zapater‐Moros, María I. Lumbreras‐Herrera, David Hardisson, Laura Yébenes, Pilar Zamora, Eduard Sabidó, Juan Ángel Fresno Vara, Enrique Espinosa
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Utility of CYP2D6 copy number variants as prognostic biomarker in localized anal squamous cell carcinoma

Auteurs: Trilla-Fuertes, Lucia; Gamez-Pozo, Angelo; Nogue, Miguel; Busquier, Isabel; Arias, Fernando; Lopez-Campos, Fernando; Fernandez-Montes, Ana; Ruiz, Ana; Velazquez, Concepcion; Martin-Bravo, Celia; Perez-Ruiz, Elisabeth; Asensio, Elena; Hernandez-Yague, Xavier; Rodrigues, Aline; Ghanem, Ismael; Lopez-Vacas, Rocio; Hafez, Ahmed; Arias, Pedro; Dapia, Irene; Solis, Mario; Dittmann, Antje; Ramos, Ricardo
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Éditeur: John Wiley & Sons Inc.
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DeepLC can predict retention times for peptides that carry as-yet unseen modifications

Auteurs: Bouwmeester, R., Gabriels, R., Hulstaert, N. et al.
Publié dans: Nature Methods, 2021, ISSN 1548-7091
Éditeur: Nature Publishing Group
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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, Numéro 14/703, 2021, ISSN 1937-9145
Éditeur: American Association for the Advancement of Science
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Proteomics Standards Initiative's ProForma 2.0: Unifying the Encoding of Proteoforms and Peptidoforms

Auteurs: LeDuc, Richard D.; Deutsch, Eric W.; Binz, Pierre-Alain; Fellers, Ryan T.; Cesnik, Anthony J.; Klein, Joshua A.; Van den Bossche, Tim; Gabriels, Ralf; Yalavarthi, Arshika; Perez-Riverol, Yasset; Carver, Jeremy; Bittremieux, Wout; Kawano, Shin; Pullman, Benjamin; Bandeira, Nuno; Kelleher, Neil L.; Thomas, Paul M.; Vizcaino, Juan Antonio
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Éditeur: American Chemical Society
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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
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Éditeur: American Chemical Society
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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
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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, Numéro 2265, 2021, Page(s) 345-359, ISBN 978-1-0716-1204-0
Éditeur: Springer US
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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, Numéro 19/4, 2020, Page(s) 716-729, ISSN 1535-9476
Éditeur: American Society for Biochemistry and Molecular Biology Inc.
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