Skip to main content
European Commission logo
English English
CORDIS - EU research results
CORDIS
CORDIS Web 30th anniversary CORDIS Web 30th anniversary

European Proteomics Infrastructure Consortium providing Access

Deliverables

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

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

DiagnoTop: A Computational Pipeline for Discriminating Bacterial Pathogens without Database Search

Author(s): Borges Lima D, Dupré M, Mariano Santos MD, Carvalho PC, Chamot-Rooke J.
Published in: J Am Soc Mass Spectrom, 2021, ISSN 1044-0305
Publisher: Elsevier BV
DOI: 10.1021/jasms.1c00014

Implementing the reuse of public DIA proteomics datasets: from the PRIDE database to Expression Atlas.

Author(s): 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. 
Published in: Scientific data, 2022, ISSN 2052-4463
Publisher: Nature Pub
DOI: 10.1038/s41597-022-01380-9

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

Author(s): Klykov, Oleg; Kopylov, Mykhailo; Carragher, Bridget; Heck, Albert J. R.; Noble, Alex J.; Scheltema, Richard A.
Published in: Mol. Cell, Issue 82/2, 2022, Page(s) 285-303, ISSN 1097-2765
Publisher: 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

Author(s): Walzer, Mathias; Jeong, Kyowon; Tabb, David L.; Vizcaino, Juan Antonio
Published in: Proteomics, 2023, ISSN 1615-9861
Publisher: WILEY
DOI: 10.1002/pmic.202200403

The biophysical, molecular, and anatomical landscape of pigeon CRY4: A candidate light-based quantal magnetosensor

Author(s): 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
Published in: Science Advances, Issue 6/33, 2020, Page(s) eabb9110, ISSN 2375-2548
Publisher: Amercian Assoc for the Advancement of Science
DOI: 10.1126/sciadv.abb9110

Investigating pathological epigenetic aberrations by epi-proteomics

Author(s): Robusti G, Vai A, Bonaldi T, Noberini R.
Published in: Clinical Epigenetics, 2022, ISSN 1868-7083
Publisher: BMC
DOI: 10.1186/s13148-022-01371-y

Neuroproteomics of the Synapse: Subcellular Quantification of Protein Networks and Signaling Dynamics

Author(s): Charlotte A.G.H. van Gelder, Maarten Altelaar
Published in: Molecular & Cellular Proteomics, Issue 20, 2021, Page(s) 100087, ISSN 1535-9476
Publisher: 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

Author(s): Bras, Ana Rita; Fernandes, Pedro; Moreira, Tiago; Morales-Sanfrutos, Julia; Sabido, Eduard; Antunes, Alexandra M. M.; Valente, Andreia; Preto, Ana
Published in: Pharmaceutics, Issue 15/6, 2023, Page(s) 1731, ISSN 1999-4923
Publisher: 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. 

Author(s): Fuertes-Perez S, Abele M, Ludwig C, Vogel RF, Hilgarth M.
Published in: Frontiers in Microbiology, 2022, ISSN 1664-302X
Publisher: Frontiers Media
DOI: 10.3389/fmicb.2022.866629

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

Author(s): Dhenin, Jonathan; Dupre, Mathieu; Druart, Karen; Krick, Alain; Mauriac, Christine; Chamot-Rooke, Julia
Published in: J. Mass Spectrom., Issue 58/3, 2023, Page(s) e4909, ISSN 1076-5174
Publisher: IM Publications
DOI: 10.1002/jms.4909

Protein Processing in Plant Mitochondria Compared to Yeast and Mammals

Author(s): Heidorn-Czarna M, Maziak A, Janska H
Published in: Front. Plant Sci., 2022, ISSN 1664-462X
Publisher: 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

Author(s): Jones AR, Deutsch EW, Vizcaíno JA. 
Published in: Proteomics, 2022, ISSN 1615-9861
Publisher: Wiley
DOI: 10.1002/pmic.202200014

Mimicked synthetic ribosomal protein complex for benchmarking crosslinking mass spectrometry workflows

Author(s): Matzinger M, Vasiu A, Madalinski M, Müller F, Stanek F, Mechtler K
Published in: Nature Communications, 2022, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-022-31701-w

High-Resolution mRNA and Secretome Atlas of Human Enteroendocrine Cells

Author(s): 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
Published in: Cell, Issue 181/6, 2020, Page(s) 1291-1306.e19, ISSN 0092-8674
Publisher: Cell Press
DOI: 10.1016/j.cell.2020.04.036

Complementary omics strategies to dissect p53 signaling networks under nutrient stress

Author(s): 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.;
Published in: Cell. Mol. Life Sci., Issue 79/6, 2022, Page(s) 326, ISSN 1420-682X
Publisher: Birkhauser Verlag
DOI: 10.1007/s00018-022-04345-8

Advanced In Vivo Cross-Linking Mass Spectrometry Platform to Characterize Proteome-Wide Protein Interactions

Author(s): Martial Rey, Jonathan Dhenin, Youxin Kong, Lucienne Nouchikian, Isaac Filella, Magalie Duchateau, Mathieu Dupré, Riccardo Pellarin, Guillaume Duménil, Julia Chamot-Rooke
Published in: Analytical Chemistry, Issue 93/9, 2021, Page(s) 4166-4174, ISSN 0003-2700
Publisher: American Chemical Society
DOI: 10.1021/acs.analchem.0c04430

Proteomics contributions to epigenetic drug discovery

Author(s): Noberini, Roberta; Bonaldi, Tiziana
Published in: Proteomics, 2023, ISSN 1615-9853
Publisher: 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

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

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

Author(s): 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.
Published in: Open Biol, Issue 9/11, 2019, Page(s) 190192, ISSN 2046-2441
Publisher: Royal Society Publishing
DOI: 10.1098/rsob.190192

The emerging landscape of spatial profiling technologie

Author(s): Moffitt JR, Lundberg E, Heyn H. 
Published in: Nature Reviews Genetics, 2022, ISSN 1471-0056
Publisher: Nature Publishing Group
DOI: 10.1038/s41576-022-00515-3

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

Author(s): 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.
Published in: Antioxidants, Issue 11/6, 2022, ISSN 2076-3921
Publisher: MDPI
DOI: 10.3390/antiox11061110

The Human Proteoform Project: Defining the human proteome

Author(s): Smith LM, Agar J, Chamot-Rooke J, Danis P, Ge Y, Loo J, Pasa-Tolic L, Tsybin YO, Kelleher N.
Published in: Science Advances, 2021, ISSN 2375-2548
Publisher: 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

Author(s): Pascal Albanese, Sem Tamara, Guido Saracco, Richard A. Scheltema, Cristina Pagliano
Published in: Nature Communications, Issue 11/1, 2020, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-020-15184-1

Panoramic Perspective on Human Phosphosites

Author(s): Ramasamy P, Vandermarliere E, Vranken WF, Martens L.
Published in: J. Proteome Research, 2022, ISSN 1535-3893
Publisher: American Chemical Society
DOI: 10.1021/acs.jproteome.2c00164

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

Author(s): Brucher, Dominik; Franc, Vojtech; Smith, Sheena N.; Heck, Albert J. R.; Pluckthun, Andreas
Published in: mAbs, Issue 12/1, 2020, Page(s) 1792084, ISSN 1942-0862
Publisher: TAYLOR & FRANCIS INC
DOI: 10.1080/19420862.2020.1792084

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

Author(s): Heames, Brennen; Buchel, Filip; Aubel, Margaux; Tretyachenko, Vyacheslav; Loginov, Dmitry; Novak, Petr; Lange, Andreas; Bornberg-Bauer, Erich; Hlouchova, Klara
Published in: Nat. Ecol. Evol., Issue 7/4, 2023, Page(s) 570, ISSN 2397-334X
Publisher: 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

Author(s): Gabriels, Ralf; Martens, Lennart; Degroeve, Sven
Published in: Nucleic Acids Res., Issue 47/W1, 2019, Page(s) W295-W299, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkz299

A wealth of genotype-specific proteoforms fine-tunes hemoglobin scavenging by haptoglobin

Author(s): Sem Tamara, Vojtech Franc, Albert J. R. Heck
Published in: Proceedings of the National Academy of Sciences, Issue 117/27, 2020, Page(s) 15554-15564, ISSN 0027-8424
Publisher: National Academy of Sciences
DOI: 10.1073/pnas.2002483117

Quality standards in proteomics research facilities

Author(s): 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
Published in: EMBO reports, Issue 22/6, 2021, ISSN 1469-221X
Publisher: 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

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

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

Author(s): 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
Published in: Cell Reports, Issue 42/4, 2023, Page(s) 112380, ISSN 2211-1247
Publisher: Cell Press
DOI: 10.1016/j.celrep.2023.112380

Spatial-proteomics reveals phospho-signaling dynamics at subcellular resolution

Author(s): 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.
Published in: Nature Communications, 2021, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-021-27398-y

Sensitivity towards HDAC inhibition is associated with RTK/MAPK pathway activation in gastric cancer

Author(s): 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. 
Published in: EMBO Molecular Medicine, 2022, ISSN 1757-4676
Publisher: John Wiley & Sons Ltd.
DOI: 10.15252/emmm.202215705

Peroxiredoxin 2 is required for the redox mediated adaptation to exercise

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

Dynamic 3D proteomes reveal protein functional alterations at high resolution in situ

Author(s): 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
Published in: Cell, Issue 184/2, 2021, Page(s) 545-559.e22, ISSN 0092-8674
Publisher: Cell Press
DOI: 10.1016/j.cell.2020.12.021

Critical Assessment of MetaProteome Investigation (CAMPI): a multi-laboratory comparison of established workflows

Author(s): 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
Published in: Nature Publishing Group, 2021, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-021-27542-8

Motif orientation matters: Structural characterization of TEAD1 recognition of genomic DNA

Author(s): 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
Published in: Structure, Issue 29/4, 2021, Page(s) 345-356.e8, ISSN 0969-2126
Publisher: Cell Press
DOI: 10.1016/j.str.2020.11.018

 SPIN enables high throughput species identification of archaeological bone by proteomics.

Author(s): 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
Published in: Nat Commun, 2022, ISSN 2041-1723
Publisher: 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

Author(s): Dmitry S. Loginov, Jan Fiala, Josef Chmelik, Peter Brechlin, Gary Kruppa, Petr Novak
Published in: ACS Omega, Issue 6/15, 2021, Page(s) 10352-10361, ISSN 2470-1343
Publisher: AMER CHEMICAL SOC
DOI: 10.1021/acsomega.1c00732

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

Author(s): Holstein, Tanja; Kistner, Franziska; Martens, Lennart; Muth, Thilo
Published in: Bioinformatics, Issue 39/5, 2023, Page(s) btad289, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btad289

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

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

An interactive mass spectrometry atlas of histone posttranslational modifications in T-cell acute leukemia

Author(s): 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.
Published in: Science Data, 2022, ISSN 2052-4463
Publisher: 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

Author(s): 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
Published in: Cancer Gene Ther., Issue 30/5, 2023, Page(s) 671-682, ISSN 0929-1903
Publisher: Nature Publishing Group
DOI: 10.1038/s41417-022-00576-w

Goat Milk Exosomes As Natural Nanoparticles for Detecting Inflammatory Processes By Optical Imaging

Author(s): 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
Published in: Small, 2021, ISSN 1613-6810
Publisher: 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

Author(s): Mullari, Meeli; Fossat, Nicolas; Skotte, Niels H.; Asenjo-Martinez, Andrea; Humphreys, David T.; Bukh, Jens; Kirkeby, Agnete; Scheel, Troels K. H.; Nielsen, Michael L.
Published in: Nat. Commun., Issue 14/1, 2023, ISSN 2041-1723
Publisher: 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

Author(s): Vargas-Diaz D, Altelaar M
Published in: J Proteome Res, 2022, ISSN 1535-3893
Publisher: American Chemical Society
DOI: 10.1021/acs.jproteome.1c00743

From coarse to fine: the absolute Escherichia coli proteome under diverse growth conditions

Author(s): 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
Published in: Molecular Systems Biology, Issue 17/5, 2021, ISSN 1744-4292
Publisher: Nature Publishing Group
DOI: 10.15252/msb.20209536

Chaperoning of the histone octamer by the acidic domain of DNA repair factor APLF

Author(s): 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
Published in: Sci. Adv., Issue 8/30, 2022, Page(s) eabo0517, ISSN 2375-2548
Publisher: AMER ASSOC ADVANCEMENT SCIENCE
DOI: 10.1126/sciadv.abo0517

The rise of single-cell proteomics

Author(s): Ctortecka, Claudia; Mechtler, Karl
Published in: Anal. Sci. Adv., Issue 2/3-4, 2021, Page(s) 84-94, ISSN 2628-5452
Publisher: WILEY
DOI: 10.1002/ansa.202000152

Meta-heterogeneity: Evaluating and Describing the Diversity in Glycosylation Between Sites on the Same Glycoprotein

Author(s): Tomislav Čaval, Albert J.R. Heck, Karli R. Reiding
Published in: Molecular & Cellular Proteomics, Issue 20, 2021, Page(s) 100010, ISSN 1535-9476
Publisher: American Society for Biochemistry and Molecular Biology Inc.
DOI: 10.1074/mcp.r120.002093

Phosphorylation-Dependent Interactome of Ryanodine Receptor Type 2 in the Heart

Author(s): 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
Published in: Proteomes, Issue 9/2, 2021, Page(s) 27, ISSN 2227-7382
Publisher: MDPI
DOI: 10.3390/proteomes9020027

Beneficial Effects of Mifepristone Treatment in Patients with Breast Cancer Selected by the Progesterone Receptor Isoform Ratio: Results from the MIPRA Trial

Author(s): 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;
Published in: Clin. Cancer Res., Issue 29/5, 2023, Page(s) 866-877, ISSN 1078-0432
Publisher: American Association for Cancer Research
DOI: 10.1158/1078-0432.ccr-22-2060

Volatilome and proteome responses to Colletotrichum lindemuthianum infection in a moderately resistant and a susceptible bean genotype

Author(s): Monti, Maurilia M.; Mancini, Ilaria; Gualtieri, Liberata; Domingo, Guido; Beccaccioli, Marzia; Bossa, Rosanna; Bracale, Marcella; Loreto, Francesco; Ruocco, Michelina
Published in: Physiol. Plant., Issue 175/5, 2023, Page(s) e14044, ISSN 0031-9317
Publisher: Blackwell Publishing Inc.
DOI: 10.1111/ppl.14044

The Key Role of Metal Adducts in the Differentiation of Phosphopeptide from Sulfopeptide Sequences by High-Resolution Mass Spectrometry. 

Author(s): Piovesana S, Capriotti AL, Cavaliere C, Cerrato A, Montone CM, Zenezini Chiozzi R, Laganà A.
Published in: Anal Chem, 2022, ISSN 0003-2700
Publisher: American Chemical Society
DOI: 10.1021/acs.analchem.1c05621

Molecular characterization of a complex of apoptosis-inducing factor 1 with cytochrome c oxidase of the mitochondrial respiratory chain

Author(s): Johannes F. Hevler, Riccardo Zenezeni Chiozzi, Alfredo Cabrera-Orefice, Ulrich Brandt, Susanne Arnold, Albert J. R. Heck
Published in: Proceedings of the National Academy of Sciences, Issue 118/39, 2021, Page(s) e2106950118, ISSN 0027-8424
Publisher: National Academy of Sciences
DOI: 10.1073/pnas.2106950118

Quality Control for the Target Decoy Approach for Peptide Identification

Author(s): Debrie, Elke; Malfait, Milan; Gabriels, Ralf; Declerq, Arthur; Sticker, Adriaan; Martens, Lennart; Clement, Lieven
Published in: J. Proteome Res., Issue 22/2, 2023, Page(s) 350-358, ISSN 1535-3893
Publisher: American Chemical Society
DOI: 10.1021/acs.jproteome.2c00423

MegaGO: A Fast Yet Powerful Approach to Assess Functional Gene Ontology Similarity across Meta-Omics Data Sets

Author(s): Pieter Verschaffelt, Tim Van Den Bossche, Wassim Gabriel, Michał Burdukiewicz, Alessio Soggiu, Lennart Martens, Bernhard Y. Renard, Henning Schiebenhoefer, Bart Mesuere
Published in: Journal of Proteome Research, Issue 20/4, 2021, Page(s) 2083-2088, ISSN 1535-3893
Publisher: American Chemical Society
DOI: 10.1021/acs.jproteome.0c00926

DAXX adds a de novo H3.3K9me3 deposition pathway to the histone chaperone network

Author(s): 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
Published in: Mol. Cell, Issue 83/7, 2023, Page(s) 1075, ISSN 1097-2765
Publisher: Cell Press
DOI: 10.1016/j.molcel.2023.02.009

Quantitative Accuracy and Precision in Multiplexed Single-Cell Proteomics. 

Author(s): Ctortecka C, Stejskal K, Krššáková G, Mendjan S, Mechtler K
Published in: Anal Chem, 2022, ISSN 0002-7863
Publisher: American Chemical Society
DOI: 10.1021/acs.analchem.1c04174

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

Author(s): Polak, Marek; Yassaghi, Ghazaleh; Kavan, Daniel; Filandr, Frantisek; Fiala, Jan; Kukacka, Zdenek; Halada, Petr; Loginov, Dmitry S.; Novak, Petr
Published in: Anal. Chem., Issue 94/7, 2022, Page(s) 3203-3210, ISSN 0003-2700
Publisher: American Chemical Society
DOI: 10.1021/acs.analchem.1c04746

Prosit Transformer: A transformer for Prediction of MS2 Spectrum Intensities

Author(s): Ekvall M, Truong P, Gabriel W, Wilhelm M, Käll L.
Published in: J. Proteome Research, 2022, ISSN 1535-3893
Publisher: American Chemical Society
DOI: 10.1021/acs.jproteome.1c00870

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

Author(s): Guzman, Ulises H. H.; Aksnes, Henriette; Ree, Rasmus; Krogh, Nicolai; Jakobsson, Magnus E. E.; Jensen, Lars J. J.; Arnesen, Thomas; Olsen, Jesper V. V.
Published in: Nat. Commun., Issue 14/1, 2023, Page(s) 4517, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-023-40224-x

Huntingtin structure is orchestrated by HAP40 and shows a polyglutamine expansion-specific interaction with exon 1

Author(s): Harding, R.J., Deme, J.C., Hevler, J.F. et al.
Published in: Nat Cell Biol., 2021, ISSN 1465-7392
Publisher: Nature Publishing Group
DOI: 10.1038/s42003-021-02895-4

lesSDRF is more: maximizing the value of proteomics data through streamlined metadata annotation

Author(s): Claeys, Tine; van den Bossche, Tim; Perez-Riverol, Yasset; Gevaert, Kris; Vizcaino, Juan Antonio; Martens, Lennart
Published in: Nat. Commun., Issue 14/1, 2023, Page(s) 6743, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-023-42543-5

The Q-junction and the inflammatory response are critical pathological and therapeutic factors in CoQ deficiency

Author(s): 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
Published in: Redox Biology, 2022, ISSN 2213-2317
Publisher: Elsevier BV
DOI: 10.1016/j.redox.2022.102403

A Sample Preparation Protocol for High Throughput Immunofluorescence of Suspension Cells on an Adherent Surface

Author(s): Anna Bäckström, Laura Kugel, Christian Gnann, Hao Xu, Joseph E. Aslan, Emma Lundberg, Charlotte Stadler
Published in: Journal of Histochemistry & Cytochemistry, Issue 68/7, 2020, Page(s) 473-489, ISSN 0022-1554
Publisher: Histochemical Society
DOI: 10.1369/0022155420935403

Coronary Artery Disease and Aortic Valve Stenosis: A Urine Proteomics Study

Author(s): Perpétuo L, Barros AS, Dalsuco J, Nogueira-Ferreira R, Resende-Gonçalves P, Falcão-Pires I, Ferreira R, Leite-Moreira A, Trindade F, Vitorino R. 
Published in: International Journal of Molecular Sciences, 2022, ISSN 1422-0067
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms232113579

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

Author(s): 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
Published in: Nucleic Acids Res., Issue 51/8, 2023, Page(s) 3770-3792, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkad171

Merits of Diazirine Photo-Immobilization for Target Profiling of Natural Products and Cofactors

Author(s): Prokofeva, Polina; Hoefer, Stefanie; Hornisch, Maximilian; Abele, Miriam; Kuster, Bernhard; Medard, Guillaume
Published in: ACS Chem. Biol., Issue 17/11, 2022, Page(s) 3100-3109, ISSN 1554-8929
Publisher: American Chemical Society
DOI: 10.1021/acschembio.2c00500

MRPS36 provides a structural link in the eukaryotic 2-oxoglutarate dehydrogenase complex

Author(s): 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.
Published in: Open Biol, Issue 13/3, 2023, Page(s) 220363, ISSN 2046-2441
Publisher: Royal Society Publishing
DOI: 10.1098/rsob.220363

Label-Free Quantitative Proteomic Analysis of Nitrogen Starvation in Arabidopsis Root Reveals New Aspects of H2S Signaling by Protein Persulfidation

Author(s): Ana Jurado-Flores, Luis C. Romero, Cecilia Gotor
Published in: Antioxidants, Issue 10/4, 2021, Page(s) 508, ISSN 2076-3921
Publisher: MDPI
DOI: 10.3390/antiox10040508

Robust and Easy-to-Use One-Pot Workflow for Label-Free Single-Cell Proteomics

Author(s): Matzinger, Manuel; Mueller, Elisabeth; Duernberger, Gerhard; Pichler, Peter; Mechtler, Karl
Published in: Anal. Chem., 2023, ISSN 0003-2700
Publisher: American Chemical Society
DOI: 10.1021/acs.analchem.2c05022

Subcellular Transcriptomics and Proteomics: A Comparative Methods Review

Author(s): Christopher JA, Geladaki A, Dawson CS, Vennard OL, Lilley KS.
Published in: Mol Cell Proteomics, 2022, ISSN 1535-9484
Publisher: Elsiver
DOI: 10.1016/j.mcpro.2021.100186

A universal GlycoDesign for lysosomal replacement enzymes to improve circulation time and biodistribution

Author(s): Chen, Yen-Hsi; Tian, Weihua; Yasuda, Makiko; Ye, Zilu; Song, Ming; Mandel, Ulla; Kristensen, Claus; Povolo, Lorenzo; Marques, Andre R. A.; Caval, Tomislav; Heck, Albert J. R.; Sampaio, Julio Lopes; Johannes, Ludger; Tsukimura, Takahiro; Desnick, Robert; Vakhrushev, Sergey Y. Y.; Yang, Zhang; Clausen, Henrik
Published in: Front. Bioeng. Biotechnol., Issue 11, 2023, Page(s) 1128371, ISSN 2296-4185
Publisher: FRONTIERS MEDIA SA
DOI: 10.3389/fbioe.2023.1128371

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

Author(s): Lilian M Fennell, Carlos Gomez Diaz, Luiza Deszcz, Anoop Kavirayani, David Hoffmann, Kota Yanagitani, Alexander Schleiffer, Karl Mechtler, Astrid Hagelkruys, Josef Penninger, Fumiyo Ikeda
Published in: The EMBO Journal, Issue 39/24, 2020, ISSN 0261-4189
Publisher: Nature Publishing Group
DOI: 10.15252/embj.2019103303

DNAJC9 integrates heat shock molecular chaperones into the histone chaperone network

Author(s): Colin M. Hammond, Hongyu Bao, Ivo A. Hendriks, Massimo Carraro, Alberto García-Nieto, Yanhong Liu, Nazaret Reverón-Gómez, Christos Spanos, Liu Chen, Juri Rappsilber, Michael L. Nielsen, Dinshaw J. Patel, Hongda Huang, Anja Groth
Published in: Molecular Cell, Issue 81/12, 2021, Page(s) 2533-2548.e9, ISSN 1097-2765
Publisher: Cell Press
DOI: 10.1016/j.molcel.2021.03.041

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

Author(s): A. Manuel Liaci, Barbara Steigenberger, Paulo Cesar Telles de Souza, Sem Tamara, Mariska Gröllers-Mulderij, Patrick Ogrissek, Siewert J. Marrink, Richard A. Scheltema, Friedrich Förster
Published in: Molecular Cell, Issue 81/19, 2021, Page(s) 3934-3948.e11, ISSN 1097-2765
Publisher: Cell Press
DOI: 10.1016/j.molcel.2021.07.031

Subcellular proteomics

Author(s): 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
Published in: Nature Reviews Methods Primers, Issue 1/1, 2021, ISSN 2662-8449
Publisher: Springer Nature
DOI: 10.1038/s43586-021-00029-y

Top-Down Detection of Oxidative Protein Footprinting by Collision-Induced Dissociation, Electron-Transfer Dissociation, and Electron-Capture Dissociation

Author(s): Yassaghi G, Kukačka Z, Fiala J, Kavan D, Halada P, Volný M, Novák P
Published in: Analytical Chemistry, 2022, ISSN 0003-2700
Publisher: American Chemical Society
DOI: 10.1021/acs.analchem.1c05476

Deciphering the signaling network of breast cancer improves drug sensitivity prediction

Author(s): 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
Published in: Cell Systems, Issue 12/5, 2021, Page(s) 401-418.e12, ISSN 2405-4712
Publisher: CELL PRESS
DOI: 10.1016/j.cels.2021.04.002

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

Author(s): Li, Bohui; Altelaar, Maarten; van Breukelen, Bas
Published in: Int. J. Mol. Sci., Issue 24/9, 2023, Page(s) 7884, ISSN 1661-6596
Publisher: MDPI
DOI: 10.3390/ijms24097884

Monitoring mAb proteoforms in mouse plasma using an automated immunocapture combined with top-down and middle-down mass spectrometry

Author(s): Dhenin, Jonathan; Lafont, Valerie; Dupre, Mathieu; Krick, Alain; Mauriac, Christine; Chamot-Rooke, Julia
Published in: Proteomics, 2023, ISSN 1615-9853
Publisher: John Wiley & Sons Ltd.
DOI: 10.1002/pmic.202300069

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

Author(s): Zecha, Jana; Lee, Chien-Yun; Bayer, Florian P.; Meng, Chen; Grass, Vincent; Zerweck, Johannes; Schnatbaum, Karsten; Michler, Thomas; Pichlmair, Andreas; Ludwig, Christina; Kuster, Bernhard
Published in: Mol. Cell. Proteomics, Issue 19/9, 2020, ISSN 1535-9476
Publisher: American Society for Biochemistry and Molecular Biology Inc.
DOI: 10.1074/mcp.ra120.002164

Fasting improves therapeutic response in hepatocellular carcinoma through p53-dependent metabolic synergism

Author(s): Krstic J, Reinisch I, Schindlmaier K, Galhuber M, Riahi Z, Berger N, Kupper N, Moyschewitz E, Auer M, Michenthaler H, Nössing C, Depaoli MR, Ramadani-Muja J, Usluer S, Stryeck S, Pichler M, Rinner B, Deutsch AJA, Reinisch A, Madl T, Chiozzi RZ, Heck AJR, Huch M, Malli R, Prokesch A.
Published in: Science Advances, 2022, ISSN 2375-2548
Publisher: Am soc for the advancement of Science
DOI: 10.1126/sciadv.abh2635

Deep learning boosts sensitivity of mass spectrometry-based immunopeptidomics

Author(s): Mathias Wilhelm, Daniel P. Zolg, Michael Graber, Siegfried Gessulat, Tobias Schmidt, Karsten Schnatbaum, Celina Schwencke-Westphal, Philipp Seifert, Niklas de Andrade Krätzig, Johannes Zerweck, Tobias Knaute, Eva Bräunlein, Patroklos Samaras, Ludwig Lautenbacher, Susan Klaeger, Holger Wenschuh, Roland Rad, Bernard Delanghe, Andreas Huhmer, Steven A. Carr, Karl R. Clauser, Angela M. Krackhardt, U
Published in: Nature Communications, Issue 12/1, 2021, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-021-23713-9

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

Author(s): Cereghetti G, Wilson-Zbinden C, Kissling VM, Diether M, Arm A, Yoo H, Piazza I, Saad S, Picotti P, Drummond DA, Sauer U, Dechant R, Peter M
Published in: Nature Cell Biology, 2021, ISSN 1465-7392
Publisher: Nature Publishing Group
DOI: 10.1038/s41556-021-00760-4

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

Author(s): Meena Choi, Jeremy Carver, Cristina Chiva, Manuel Tzouros, Ting Huang, Tsung-Heng Tsai, Benjamin Pullman, Oliver M. Bernhardt, Ruth Hüttenhain, Guo Ci Teo, Yasset Perez-Riverol, Jan Muntel, Maik Müller, Sandra Goetze, Maria Pavlou, Erik Verschueren, Bernd Wollscheid, Alexey I. Nesvizhskii, Lukas Reiter, Tom Dunkley, Eduard Sabidó, Nuno Bandeira, Olga Vitek
Published in: Nature Methods, Issue 17/10, 2020, Page(s) 981-984, ISSN 1548-7091
Publisher: Nature Publishing Group
DOI: 10.1038/s41592-020-0955-0

Bap-Independent Biofilm Formation in Staphylococcus xylosus

Author(s): Schiffer, Carolin J.; Abele, Miriam; Ehrmann, Matthias A.; Vogel, Rudi F.
Published in: Microorganisms, Issue 9/12, 2021, Page(s) 2610, ISSN 2076-2607
Publisher: MDPI
DOI: 10.3390/microorganisms9122610

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

Author(s): André M. Almeida, Syed Azmal Ali, Fabrizio Ceciliani, P. David Eckersall, Lorenzo E. Hernández-Castellano, Rongwei Han, Jaka J. Hodnik, Shalini Jaswal, John D. Lippolis, Mark McLaughlin, Ingrid Miller, Ashok Kumar Mohanty, Vladimir Mrljak, Jarlath E. Nally, Paolo Nanni, Jeffrey E. Plowman, Mirele D. Poleti, David M. Ribeiro, Pedro Rodrigues, Bernd Roschitzki, Ralph Schlapbach, Jože Starič, Yon
Published in: Journal of Proteomics, Issue 241, 2021, Page(s) 104220, ISSN 1874-3919
Publisher: Elsevier BV
DOI: 10.1016/j.jprot.2021.104220

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

Author(s): Kaige Yan, Jing Yang, Ziguo Zhang, Stephen H. McLaughlin, Leifu Chang, Domenico Fasci, Ann E. Ehrenhofer-Murray, Albert J. R. Heck, David Barford
Published in: Nature, Issue 574/7777, 2019, Page(s) 278-282, ISSN 0028-0836
Publisher: Nature Publishing Group
DOI: 10.1038/s41586-019-1609-1

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

Author(s): Jurado-Flores, Ana; Gotor, Cecilia; Romero, Luis C. C.
Published in: Antioxidants, Issue 12/4, 2023, Page(s) 789, ISSN 2076-3921
Publisher: MDPI
DOI: 10.3390/antiox12040789

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

Author(s): den Boer MA, Lai SH, Xue X, van Kampen MD, Bleijlevens B, Heck AJR
Published in: Anal Chem, 2022, ISSN 0002-7863
Publisher: American Chemical Society
DOI: 10.1021/acs.analchem.1c03656

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

Author(s): Richards, Frederick; Llorca-Cardenosa, Marta J.; Langton, Jamie; Buch-Larsen, Sara C.; Shamkhi, Noor F.; Sharma, Abhishek Bharadwaj; Nielsen, Michael L.; Lakin, Nicholas D.
Published in: Nat. Commun., Issue 14/1, 2023, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-023-40071-w

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

Author(s): Perez-Riverol Y, Bai J, Bandla C, Hewapathirana S, García-Seisdedos D, Kamatchinathan S, Kundu D, Prakash A, Frericks-Zipper A, Eisenacher M, Walzer M, Wang S, Brazma A, Vizcaíno JA
Published in: Nucleic Acids Research, 2021, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkab1038

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

Author(s): Fojtík L, Fiala J, Pompach P, Chmelík J, Matoušek V, Beier P, Kukačka Z, Novák P.
Published in: J.Am.Chem. Soc., 2021, ISSN 0002-7863
Publisher: American Chemical Society
DOI: 10.1021/jacs.1c07771

Decoding protein methylation function with thermal stability analysis

Author(s): Sayago, Cristina; Sanchez-Wandelmer, Jana; Garcia, Fernando; Hurtado, Begona; Lafarga, Vanesa; Prieto, Patricia; Zarzuela, Eduardo; Ximenez-Embun, Pilar; Ortega, Sagrario; Megias, Diego; Fernandez-Capetillo, Oscar; Malumbres, Marcos; Munoz, Javier
Published in: Nat. Commun., Issue 14/1, 2023, Page(s) 3016, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-023-38863-1

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

Author(s): Roberta Noberini, Evelyn Oliva Savoia, Stefania Brandini, Francesco Greco, Francesca Marra, Giovanni Bertalot, Giancarlo Pruneri, Liam A. McDonnell, Tiziana Bonaldi
Published in: Clinical Epigenetics, Issue 13/1, 2021, ISSN 1868-7075
Publisher: Springer Verlag
DOI: 10.1186/s13148-021-01120-7

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

Author(s): Parmar, Bhavesh S.; Kieswetter, Amanda; Geens, Ellen; Vandewyer, Elke; Ludwig, Christina; Temmerman, Liesbet
Published in: PLoS. Biol., Issue 21/9, 2023, Page(s) e3002300, ISSN 1544-9173
Publisher: Public Library of Science
DOI: 10.1371/journal.pbio.3002300

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

Author(s): Nicosia, L., Boffo, F.L., Ceccacci, E. et al.
Published in: Oncogene, 2021, ISSN 0950-9232
Publisher: Nature Publishing Group
DOI: 10.1038/s41388-021-02123-7

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

Author(s): Laura del Amo-Maestro, Amin Sagar, Petr Pompach, Theodoros Goulas, Carsten Scavenius, Diego S. Ferrero, Mariana Castrillo-Briceño, Marta Taulés, Jan J. Enghild, Pau Bernadó, F. Xavier Gomis-Rüth
Published in: Journal of Molecular Biology, Issue 433/13, 2021, Page(s) 166954, ISSN 0022-2836
Publisher: Academic Press
DOI: 10.1016/j.jmb.2021.166954

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

Author(s): Wael Kamel, Marko Noerenberg, Berati Cerikan, Honglin Chen, Aino I. Järvelin, Mohamed Kammoun, Jeffrey Y. Lee, Ni Shuai, Manuel Garcia-Moreno, Anna Andrejeva, Michael J. Deery, Natasha Johnson, Christopher J. Neufeldt, Mirko Cortese, Michael L. Knight, Kathryn S. Lilley, Javier Martinez, Ilan Davis, Ralf Bartenschlager, Shabaz Mohammed, Alfredo Castello
Published in: Molecular Cell, Issue 81/13, 2021, Page(s) 2851-2867.e7, ISSN 1097-2765
Publisher: Cell Press
DOI: 10.1016/j.molcel.2021.05.023

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

Author(s): Schallert, Kay; Verschaffelt, Pieter; Mesuere, Bart; Benndorf, Dirk; Martens, Lennart; Van den Bossche, Tim
Published in: J. Proteome Res., Issue 21/4, 2022, Page(s) 1175-1180, ISSN 1535-3893
Publisher: American Chemical Society
DOI: 10.1021/acs.jproteome.1c00685

Deep (phospho)proteomics profiling of pre- treatment needle biopsies identifies signatures of treatment resistance in HER2+breast cancer

Author(s): Debets, Donna O.; Stecker, Kelly E.; Piskopou, Anastasia; Liefaard, Marte C.; Wesseling, Jelle; Sonke, Gabe S.; Lips, Esther H.; Altelaar, Maarten
Published in: Cell Rep. Med., Issue 4/10, 2023, Page(s) 101203, ISSN 2666-3791
Publisher: CELL PRESS
DOI: 10.1016/j.xcrm.2023.101203

Deep Single-Shot NanoLC-MS Proteome Profiling with a 1500 Bar UHPLC System, Long Fully Porous Columns, and HRAM MS

Author(s): Zheng R, Stejskal K, Pynn C, Mechtler K, Boychenko A
Published in: J. Proteome Research, 2022, ISSN 1535-3893
Publisher: American Chemical Society
DOI: 10.1021/acs.jproteome.2c00270

Precursor deconvolution error estimation: The missing puzzle piece in false discovery rate in top-down proteomics

Author(s): Jeong, Kyowon; Kaulich, Philipp T.; Jung, Wonhyeuk; Kim, Jihyung; Tholey, Andreas; Kohlbacher, Oliver
Published in: Proteomics, 2023, ISSN 1615-9853
Publisher: John Wiley & Sons Ltd.
DOI: 10.1002/pmic.202300068

The histone code of the fungal genus Aspergillus uncovered by evolutionary and proteomic analyses

Author(s): Zhang X, Noberini R, Bonaldi T, Collemare J, Seidl MF. 
Published in: Microbial Genomics, 2022, ISSN 2057-5858
Publisher: MICROBIOLOGY SOC
DOI: 10.1099/mgen.0.000856

ANGEL2 is a member of the CCR4 family of deadenylases with 2′,3′-cyclic phosphatase activity

Author(s): Pinto, Paola H.; Kroupova, Alena; Schleiffer, Alexander; Mechtler, Karl; Jinek, Martin; Weitzer, Stefan; Martinez, Javier
Published in: Science, Issue 369/6503, 2020, Page(s) 524, ISSN 0036-8075
Publisher: American Association for the Advancement of Science
DOI: 10.1126/science.aba9763

Generalized Calibration Across Liquid Chromatography Setups for Generic Prediction of Small-Molecule Retention Times

Author(s): Bouwmeester, Robbin; Martens, Lennart; Degroeve, Sven
Published in: Anal. Chem., Issue 92/9, 2020, Page(s) 6571-6578, ISSN 0003-2700
Publisher: American Chemical Society
DOI: 10.1021/acs.analchem.0c00233

Similarities and differences in the structures and proteoform profiles of the complement proteins C6 and C7

Author(s): Marie V. Lukassen, Vojtech Franc, Johannes F. Hevler, Albert J.R. Heck
Published in: PROTEOMICS, 2021, Page(s) 2000310, ISSN 1615-9853
Publisher: John Wiley & Sons Ltd.
DOI: 10.1002/pmic.202000310

Lipid nanoparticles allow efficient and harmless ex vivo gene editing of human hematopoietic cells

Author(s): 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
Published in: Blood, Issue 142/9, 2023, Page(s) 812-826, ISSN 0006-4971
Publisher: American Society of Hematology
DOI: 10.1182/blood.2022019333

Zebrafish Ski7 tunes RNA levels during the oocyte-to-embryo transition

Author(s): Luis Enrique Cabrera-Quio, Alexander Schleiffer, Karl Mechtler, Andrea Pauli
Published in: PLOS Genetics, Issue 17/2, 2021, Page(s) e1009390, ISSN 1553-7404
Publisher: Public Library Science
DOI: 10.1371/journal.pgen.1009390

Mass Spectrometry-Driven Discovery of Neuropeptides Mediating Nictation Behavior of Nematodes

Author(s): 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
Published in: Mol. Cell. Proteomics, Issue 22/2, 2023, Page(s) 100479, ISSN 1535-9476
Publisher: American Society for Biochemistry and Molecular Biology Inc.
DOI: 10.1016/j.mcpro.2022.100479

AKIRIN2 controls the nuclear import of proteasomes in vertebrates

Author(s): 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
Published in: Nature, Issue 599/7885, 2021, Page(s) 491-496, ISSN 0028-0836
Publisher: Nature Publishing Group
DOI: 10.1038/s41586-021-04035-8

In Vitro Evolution Reveals Noncationic Protein-RNA Interaction Mediated by Metal Ions

Author(s): Giacobelli VG, Fujishima K, Lepšík M, Tretyachenko V, Kadavá T, Makarov M, Bednárová L, Novák P, Hlouchová K
Published in: Mol Biol Evol, 2022, ISSN 0737-4038
Publisher: Oxford University Press
DOI: 10.1093/molbev/msac032

Benefits of Collisional Cross Section Assisted Precursor Selection (caps-PASEF) for Cross-linking Mass Spectrometry

Author(s): 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
Published in: Molecular & Cellular Proteomics, Issue 19/10, 2020, Page(s) 1677-1687, ISSN 1535-9476
Publisher: American Society for Biochemistry and Molecular Biology Inc.
DOI: 10.1074/mcp.ra120.002094

Decrypting drug actions and protein modifications by dose- and time-resolved proteomics

Author(s): 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
Published in: Science, Issue 380/6640, 2023, ISSN 0036-8075
Publisher: American Association for the Advancement of Science
DOI: 10.1126/science.ade3925

A combination of molecular and clinical parameters provides a new strategy for high-grade serous ovarian cancer patient management

Author(s): Bradbury, Melissa; Borras, Eva; Vilar, Marta; Castellvi, Josep; Luis Sanchez-Iglesias, Jose; Perez-Benavente, Assumpcio; Gil-Moreno, Antonio; Santamaria, Anna; Sabido, Eduard
Published in: J. Transl. Med., Issue 20/1, 2022, Page(s) 611, ISSN 1479-5876
Publisher: BioMed Central
DOI: 10.1186/s12967-022-03816-7

Scop3P: A Comprehensive Resource of Human Phosphosites within Their Full Context

Author(s): Ramasamy, Pathmanaban; Turan, Demet; Tichshenko, Natalia; Hulstaert, Niels; Vandermarliere, Elien; Vranken, Wim; Martens, Lennart
Published in: J. Proteome Res., Issue 19/8, 2020, Page(s) 3478-3486, ISSN 1535-3893
Publisher: American Chemical Society
DOI: 10.1021/acs.jproteome.0c00306

Label-Free Mass Spectrometry-Based Quantification of Linker Histone H1 Variants in Clinical Samples

Author(s): 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
Published in: International Journal of Molecular Sciences, Issue 21/19, 2020, Page(s) 7330, ISSN 1422-0067
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms21197330

Chromatin-Bound Proteome Profiling by Genome Capture

Author(s): Sergi Aranda, Eva Borràs, Eduard Sabidó, Luciano Di Croce
Published in: STAR Protocols, Issue 1/1, 2020, Page(s) 100014, ISSN 2666-1667
Publisher: Elsevier
DOI: 10.1016/j.xpro.2020.100014

Comparing Top-Down Proteoform Identification: Deconvolution, PrSM Overlap, and PTM Detection

Author(s): 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
Published in: J. Proteome Res., Issue 22/7, 2023, Page(s) 2199-2217, ISSN 1535-3893
Publisher: American Chemical Society
DOI: 10.1021/acs.jproteome.2c00673

Hybrid-DIA: intelligent data acquisition integrates targeted and discovery proteomics to analyze phospho-signaling in single spheroids

Author(s): 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.
Published in: Nat. Commun., Issue 14/1, 2023, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-023-39347-y

Feature-based molecular networking in the GNPS analysis environment

Author(s): 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
Published in: Nature Methods, Issue 17/9, 2020, Page(s) 905-908, ISSN 1548-7091
Publisher: Nature Publishing Group
DOI: 10.1038/s41592-020-0933-6

Combining CRISPRi and metabolomics for functional annotation of compound libraries

Author(s): Anglada-Girotto M, Handschin G, Ortmayr K, Campos AI, Gillet L, Manfredi P, Mulholland CV, Berney M, Jenal U, Picotti P, Zampieri M.
Published in: Nat Chem Biol, 2022, ISSN 1552-4450
Publisher: Nature Publishing Group
DOI: 10.1038/s41589-022-00970-3

Integrated Proteomics Unveils Nuclear PDE3A2 as a Regulator of Cardiac Myocyte Hypertrophy

Author(s): 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
Published in: Circ.Res., Issue 132/7, 2023, Page(s) 828-848, ISSN 0009-7330
Publisher: Lippincott Williams & Wilkins Ltd.
DOI: 10.1161/circresaha.122.321448

N-terminal acetylation shields proteins from degradation and promotes age-dependent motility and longevity

Author(s): 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
Published in: Nat. Commun., Issue 14/1, 2023, Page(s) 6774, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-023-42342-y

The Role of Pseudo-Orthocaspase (SyOC) of Synechocystis sp. PCC 6803 in Attenuating the Effect of Oxidative Stress

Author(s): Saul Lema A, Marina Klemenčič, Franziska Völlmy, Maarten Altelaar, Christiane Funk
Published in: Frontiers in Microbiology, Issue 12, 2021, ISSN 1664-302X
Publisher: Frontiers Media
DOI: 10.3389/fmicb.2021.634366

Optineurin links Hace1-dependent Rac ubiquitylation to integrin-mediated mechanotransduction to control bacterial invasion and cell division

Author(s): 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.
Published in: Nature Communications, 2022, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-022-33803-x

Spatiotemporal proteomic profiling of the pro-inflammatory response to lipopolysaccharide in the THP-1 human leukaemia cell line

Author(s): 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
Published in: Nature Communications, Issue 12/1, 2021, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-021-26000-9

Serine ADP-ribosylation in Drosophila provides insights into the evolution of reversible ADP-ribosylation signalling

Author(s): 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
Published in: Nat. Commun., Issue 14/1, 2023, Page(s) 3200, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-023-38793-y

Connecting MetaProteomeAnalyzer and PeptideShaker to Unipept for Seamless End-to-End Metaproteomics Data Analysis

Author(s): Van den Bossche, Tim; Verschaffelt, Pieter; Schallert, Kay; Barsnes, Harald; Dawyndt, Peter; Benndorf, Dirk; Renard, Bernhard Y.; Mesuere, Bart; Martens, Lennart; Muth, Thilo
Published in: J. Proteome Res., Issue 19/8, 2020, Page(s) 3562-3566, ISSN 1535-3893
Publisher: American Chemical Society
DOI: 10.1021/acs.jproteome.0c00136

Data Management of Sensitive Human Proteomics Data: Current Practices, Recommendations, and Perspectives for the Future

Author(s): Nuno Bandeira, Eric W. Deutsch, Oliver Kohlbacher, Lennart Martens, Juan Antonio Vizcaíno
Published in: Molecular & Cellular Proteomics, Issue 20, 2021, Page(s) 100071, ISSN 1535-9476
Publisher: American Society for Biochemistry and Molecular Biology Inc.
DOI: 10.1016/j.mcpro.2021.100071

A machine learning-based chemoproteomic approach to identify drug targets and binding sites in complex proteomes

Author(s): 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
Published in: Nature Communications, Issue 11/1, 2020, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-020-18071-x

Urinary Collectrin (TMEM27) as Novel Marker for Acute Kidney Injury

Author(s): Pajenda S, Wagner L, Gerges D, Herkner H, Tevdoradze T, Mechtler K, Schmidt A, Winnicki W. 
Published in: Life, 2022, ISSN 2075-1729
Publisher: MDPI
DOI: 10.3390/life12091391

Accurate peptide fragmentation predictions allow data driven approaches to replace and improve upon proteomics search engine scoring functions

Author(s): C Silva AS, Bouwmeester R, Martens L, Degroeve S
Published in: Bioinformatics, 2019, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btz383

Neutrophil azurophilic granule glycoproteins are distinctively decorated by atypical pauci- and phosphomannose glycans

Author(s): Karli R. Reiding, Yu-Hsien Lin, Floris P. J. van Alphen, Alexander B. Meijer, Albert J. R. Heck
Published in: Communications Biology, Issue 4/1, 2021, ISSN 2399-3642
Publisher: Nature Portfolio
DOI: 10.1038/s42003-021-02555-7

High Resolution Proteomic Analysis of Subcellular Fractionated Boar Spermatozoa Provides Comprehensive Insights Into Perinuclear Theca-Residing Proteins

Author(s): Zhang M, Chiozzi RZ, Skerrett-Byrne DA, Veenendaal T, Klumperman J, Heck AJR, Nixon B, Helms JB, Gadella BM, Bromfield EG
Published in: Front Cell Dev Biol, 2022, ISSN 2296-634X
Publisher: FRONTIERS MEDIA SA
DOI: 10.3389/fcell.2022.836208

Proteomic investigation of Cbl and Cbl-b in neuroblastoma cell differentiation highlights roles for SHP-2 and CDK16

Author(s): Anna-Kathrine Pedersen, Anamarija Pfeiffer, Gopal Karemore, Vyacheslav Akimov, Dorte B. Bekker-Jensen, Blagoy Blagoev, Chiara Francavilla, Jesper V. Olsen
Published in: iScience, Issue 24/4, 2021, Page(s) 102321, ISSN 2589-0042
Publisher: EMBO PRESS
DOI: 10.1016/j.isci.2021.102321

A serum proteome signature to predict mortality in severe COVID-19 patients

Author(s): 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
Published in: Life Science Alliance, Issue 4/9, 2021, Page(s) e202101099, ISSN 2575-1077
Publisher: EMBO Press
DOI: 10.26508/lsa.202101099

BRCA1 mutations in high-grade serous ovarian cancer are associated with proteomic changes in DNA repair, splicing, transcription regulation and signaling

Author(s): Bradbury M, Borràs E, Castellví J, Méndez O, Sánchez-Iglesias JL, Pérez-Benavente A, Gil-Moreno A, Sabidó E, Santamaria A.
Published in: Scientific Reports, 2022, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-022-08461-0

Expression of NORAD correlates with breast cancer aggressiveness and protects breast cancer cells from chemotherapy

Author(s): 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
Published in: Mol. Ther. Nucl. Acids, Issue 33, 2023, ISSN 2162-2531
Publisher: Nature Publishing Group
DOI: 10.1016/j.omtn.2023.08.019

Waves of sumoylation support transcription dynamics during adipocyte differentiation

Author(s): 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
Published in: Nucleic Acids Res, 2022, ISSN 1362-4962
Publisher: OXFORD UNIV PRESS
DOI: 10.1093/nar/gkac027

Comparative Proteome Signatures of Trace Samples by Multiplexed Data-Independent Acquisition

Author(s): Ctortecka C, Krššáková G, Stejskal K, Penninger JM, Mendjan S, Mechtler K, Stadlmann J.
Published in: Mol Cell Proteomics, 2022, ISSN 1535-9484
Publisher: Elsiver
DOI: 10.1016/j.mcpro.2021.100177

MS Annika 2.0 Identifies Cross-Linked Peptides in MS2-MS3-Based Workflows at High Sensitivity and Specificity

Author(s): Birklbauer, Micha J. J.; Matzinger, Manuel; Mueller, Fraenze; Mechtler, Karl; Dorfer, Viktoria
Published in: J. Proteome Res., Issue 22/9, 2023, Page(s) 3009-3021, ISSN 1535-3893
Publisher: American Chemical Society
DOI: 10.1021/acs.jproteome.3c00325

Cross-ID: Analysis and Visualization of Complex XL–MS-Driven Protein Interaction Networks

Author(s): Sebastiaan C. de Graaf, Oleg Klykov, Henk van den Toorn, Richard A. Scheltema
Published in: Journal of Proteome Research, Issue 18/2, 2018, Page(s) 642-651, ISSN 1535-3893
Publisher: American Chemical Society
DOI: 10.1021/acs.jproteome.8b00725

PhoX: An IMAC-Enrichable Cross-Linking Reagent

Author(s): Barbara Steigenberger, Roland J. Pieters, Albert J. R. Heck, Richard A. Scheltema
Published in: ACS Central Science, Issue 5/9, 2019, Page(s) 1514-1522, ISSN 2374-7943
Publisher: ACS CENTRAL SCIENCE
DOI: 10.1021/acscentsci.9b00416

Binding of eIF3 in complex with eIF5 and eIF1 to the 40S ribosomal subunit is accompanied by dramatic structural changes

Author(s): Jakub Zeman, Yuzuru Itoh, Zdeněk Kukačka, Michal Rosůlek, Daniel Kavan, Tomáš Kouba, Myrte E Jansen, Mahabub P Mohammad, Petr Novák, Leoš S Valášek
Published in: Nucleic Acids Research, Issue 47/15, 2019, Page(s) 8282-8300, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkz570

Quantifying the impact of public omics data

Author(s): 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
Published in: Nature Communications, Issue 10/1, 2019, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-019-11461-w

N-terminal β-strand underpins biochemical specialization of an ATG8 isoform

Author(s): 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
Published in: PLOS Biology, Issue 17/7, 2019, Page(s) e3000373, ISSN 1545-7885
Publisher: PLOS BIOL
DOI: 10.1371/journal.pbio.3000373

A Colorful Pallet of B-Phycoerythrin Proteoforms Exposed by a Multimodal Mass Spectrometry Approach

Author(s): Sem Tamara, Max Hoek, Richard A. Scheltema, Aneika C. Leney, Albert J.R. Heck
Published in: Chem, Issue 5/5, 2019, Page(s) 1302-1317, ISSN 2451-9294
Publisher: CHEM
DOI: 10.1016/j.chempr.2019.03.006

Isotopologue Multipoint Calibration for Proteomics Biomarker Quantification in Clinical Practice

Author(s): Cristina Chiva, Olga Pastor, Lucía Trilla-Fuertes, Angelo Gámez-Pozo, Juan Ángel Fresno Vara, Eduard Sabidó
Published in: Analytical Chemistry, Issue 91/8, 2019, Page(s) 4934-4938, ISSN 0003-2700
Publisher: American Chemical Society
DOI: 10.1021/acs.analchem.8b05802

Phosphopeptide Fragmentation and Site Localization by Mass Spectrometry: An Update

Author(s): Clement M. Potel, Simone Lemeer, Albert J. R. Heck
Published in: Analytical Chemistry, Issue 91/1, 2018, Page(s) 126-141, ISSN 0003-2700
Publisher: American Chemical Society
DOI: 10.1021/acs.analchem.8b04746

MS-Based Approaches Enable the Structural Characterization of Transcription Factor/DNA Response Element Complex

Author(s): Slavata, Chmelík, Kavan, Filandrová, Fiala, Rosůlek, Mrázek, Kukačka, Vališ, Man, Miller, McIntyre, Fabris, Novák
Published in: Biomolecules, Issue 9/10, 2019, Page(s) 535, ISSN 2218-273X
Publisher: MDPI
DOI: 10.3390/biom9100535

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

Author(s): Johannes Stadlmann, Otto Hudecz, Gabriela Krššáková, Claudia Ctortecka, Geert Van Raemdonck, Jeff Op De Beeck, Gert Desmet, Josef M. Penninger, Paul Jacobs, Karl Mechtler
Published in: Analytical Chemistry, Issue 91/22, 2019, Page(s) 14203-14207, ISSN 0003-2700
Publisher: American Chemical Society
DOI: 10.1021/acs.analchem.9b02899

Absolute quantification of cohesin, CTCF and their regulators in human cells

Author(s): 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
Published in: eLife, Issue 8, 2019, ISSN 2050-084X
Publisher: eLife Sciences Publications
DOI: 10.7554/elife.46269

Proteases Immobilization for In Situ Time-Limited Proteolysis on MALDI Chips

Author(s): Rosulek, Darebna, Pompach, Slavata, Novak
Published in: Catalysts, Issue 9/10, 2019, Page(s) 833, ISSN 2073-4344
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/catal9100833

Oncogenic Mutations Rewire Signaling Pathways by Switching Protein Recruitment to Phosphotyrosine Sites

Author(s): 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
Published in: Cell, Issue 179/2, 2019, Page(s) 543-560.e26, ISSN 0092-8674
Publisher: Cell Press
DOI: 10.1016/j.cell.2019.09.008

Missing regions within the molecular architecture of human fibrin clots structurally resolved by XL-MS and integrative structural modeling

Author(s): Oleg Klykov, Carmen van der Zwaan, Albert J. R. Heck, Alexander B. Meijer, Richard A. Scheltema
Published in: Proceedings of the National Academy of Sciences, Issue 117/4, 2020, Page(s) 1976-1987, ISSN 0027-8424
Publisher: National Academy of Sciences
DOI: 10.1073/pnas.1911785117

Targeting proline in (phospho)proteomics

Author(s): Saar A. M. Laarse, Charlotte A. G. H. Gelder, Marshall Bern, Michiel Akeroyd, Maurien M. A. Olsthoorn, Albert J. R. Heck
Published in: The FEBS Journal, 2020, ISSN 1742-464X
Publisher: Blackwell Publishing Inc.
DOI: 10.1111/febs.15190

Accurate peptide fragmentation predictions allow data driven approaches to replace and improve upon proteomics search engine scoring functions

Author(s): Ana S C. Silva, Robbin Bouwmeester, Lennart Martens, Sven Degroeve
Published in: Bioinformatics, Issue 35/24, 2019, Page(s) 5243-5248, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btz383

Rapid and site-specific deep phosphoproteome profiling by data-independent acquisition without the need for spectral libraries

Author(s): Dorte B. Bekker-Jensen, Oliver M. Bernhardt, Alexander Hogrebe, Ana Martinez-Val, Lynn Verbeke, Tejas Gandhi, Christian D. Kelstrup, Lukas Reiter, Jesper V. Olsen
Published in: Nature Communications, Issue 11/1, 2020, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-020-14609-1

EPIFANY: A Method for Efficient High-Confidence Protein Inference

Author(s): Julianus Pfeuffer, Timo Sachsenberg, Tjeerd M. H. Dijkstra, Oliver Serang, Knut Reinert, Oliver Kohlbacher
Published in: Journal of Proteome Research, 2020, ISSN 1535-3893
Publisher: American Chemical Society
DOI: 10.1021/acs.jproteome.9b00566

Enrichment of histones from patient samples for mass spectrometry-based analysis of post-translational modifications

Author(s): Roberta Noberini, Camilla Restellini, Evelyn Oliva Savoia, Tiziana Bonaldi
Published in: Methods, 2019, ISSN 1046-2023
Publisher: Academic Press
DOI: 10.1016/j.ymeth.2019.10.001

ThermoRawFileParser: Modular, Scalable, and Cross-Platform RAW File Conversion

Author(s): Niels Hulstaert, Jim Shofstahl, Timo Sachsenberg, Mathias Walzer, Harald Barsnes, Lennart Martens, Yasset Perez-Riverol
Published in: Journal of Proteome Research, Issue 19/1, 2019, Page(s) 537-542, ISSN 1535-3893
Publisher: American Chemical Society
DOI: 10.1021/acs.jproteome.9b00328

The Human Immunopeptidome Project: A Roadmap to Predict and Treat Immune Diseases

Author(s): 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
Published in: Molecular & Cellular Proteomics, Issue 19/1, 2020, Page(s) 31-49, ISSN 1535-9476
Publisher: American Society for Biochemistry and Molecular Biology Inc.
DOI: 10.1074/mcp.r119.001743

ESCO1 and CTCF enable formation of long chromatin loops by protecting cohesinSTAG1 from WAPL

Author(s): 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
Published in: eLife, Issue 9, 2020, ISSN 2050-084X
Publisher: eLife Sciences Publications
DOI: 10.7554/elife.52091

Generating high quality libraries for DIA MS with empirically corrected peptide predictions

Author(s): Brian C. Searle, Kristian E. Swearingen, Christopher A. Barnes, Tobias Schmidt, Siegfried Gessulat, Bernhard Küster, Mathias Wilhelm
Published in: Nature Communications, Issue 11/1, 2020, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-020-15346-1

The omics discovery REST interface

Author(s): Gaurhari Dass, Manh-Tu Vu, Pan Xu, Enrique Audain, Marc-Phillip Hitz, Björn A Grüning, Henning Hermjakob, Yasset Perez-Riverol
Published in: Nucleic Acids Research, 2020, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkaa326

FLASHDeconv: Ultrafast, High-Quality Feature Deconvolution for Top-Down Proteomics

Author(s): Kyowon Jeong, Jihyung Kim, Manasi Gaikwad, Siti Nurul Hidayah, Laura Heikaus, Hartmut Schlüter, Oliver Kohlbacher
Published in: Cell Systems, Issue 10/2, 2020, Page(s) 213-218.e6, ISSN 2405-4712
Publisher: Cell Press, Elsevier Inc.
DOI: 10.1016/j.cels.2020.01.003

Removing the Hidden Data Dependency of DIA with Predicted Spectral Libraries

Author(s): 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
Published in: PROTEOMICS, Issue 20/3-4, 2020, Page(s) 1900306, ISSN 1615-9853
Publisher: John Wiley & Sons Ltd.
DOI: 10.1002/pmic.201900306

To Cleave or Not To Cleave in XL-MS?

Author(s): B. Steigenberger, P. Albanese, A. J. R. Heck, R. A. Scheltema
Published in: Journal of the American Society for Mass Spectrometry, Issue 31/2, 2020, Page(s) 196-206, ISSN 1044-0305
Publisher: Elsevier BV
DOI: 10.1021/jasms.9b00085

Resolving heterogeneous macromolecular assemblies by Orbitrap-based single-particle charge detection mass spectrometry

Author(s): Tobias P. Wörner, Joost Snijder, Antonette Bennett, Mavis Agbandje-McKenna, Alexander A. Makarov, Albert J. R. Heck
Published in: Nature Methods, Issue 17/4, 2020, Page(s) 395-398, ISSN 1548-7091
Publisher: Nature Publishing Group
DOI: 10.1038/s41592-020-0770-7

Simple Peptide Quantification Approach for MS-Based Proteomics Quality Control

Author(s): Teresa Mendes Maia, An Staes, Kim Plasman, Jarne Pauwels, Katie Boucher, Andrea Argentini, Lennart Martens, Tony Montoye, Kris Gevaert, Francis Impens
Published in: ACS Omega, Issue 5/12, 2020, Page(s) 6754-6762, ISSN 2470-1343
Publisher: American Chemical Society
DOI: 10.1021/acsomega.0c00080

N-Terminal Proteoforms in Human Disease

Author(s): Annelies Bogaert, Esperanza Fernandez, Kris Gevaert
Published in: Trends in Biochemical Sciences, Issue 45/4, 2020, Page(s) 308-320, ISSN 0968-0004
Publisher: Elsevier BV
DOI: 10.1016/j.tibs.2019.12.009

The ProteomeXchange consortium in 2020: enabling ‘big data’ approaches in proteomics

Author(s): 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
Published in: Nucleic Acids Research, 2019, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkz984

Influence of cross-linker polarity on selectivity towards lysine side chains

Author(s): Jan Fiala, Zdeněk Kukačka, Petr Novák
Published in: Journal of Proteomics, Issue 218, 2020, Page(s) 103716, ISSN 1874-3919
Publisher: Elsevier BV
DOI: 10.1016/j.jprot.2020.103716

COSS: A fast and user-friendly tool for spectral library searching

Author(s): Genet Abay Shiferaw, Elien Vandermarliere, Niels Hulstaert, Ralf Gabriels, Lennart Martens, Pieter-Jan Volders
Published in: Journal of Proteome Research, 2020, ISSN 1535-3893
Publisher: American Chemical Society
DOI: 10.1021/acs.jproteome.9b00743

Fast and Highly Efficient Affinity Enrichment of Azide-A-DSBSO Cross-Linked Peptides

Author(s): Manuel Matzinger, Wolfgang Kandioller, Philipp Doppler, Elke H. Heiss, Karl Mechtler
Published in: Journal of Proteome Research, Issue 19/5, 2020, Page(s) 2071-2079, ISSN 1535-3893
Publisher: American Chemical Society
DOI: 10.1021/acs.jproteome.0c00003

Fishing for newly synthesized proteins with phosphonate-handles

Author(s): Fleur Kleinpenning, Barbara Steigenberger, Wei Wu, Albert J. R. Heck
Published in: Nature Communications, Issue 11/1, 2020, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-020-17010-0

A synthetic peptide library for benchmarking crosslinking-mass spectrometry search engines for proteins and protein complexes

Author(s): Rebecca Beveridge, Johannes Stadlmann, Josef M. Penninger, Karl Mechtler
Published in: Nature Communications, Issue 11/1, 2020, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-020-14608-2

The Age of Data‐Driven Proteomics: How Machine Learning Enables Novel Workflows

Author(s): Robbin Bouwmeester, Ralf Gabriels, Tim Van Den Bossche, Lennart Martens, Sven Degroeve
Published in: PROTEOMICS, 2020, Page(s) 1900351, ISSN 1615-9853
Publisher: John Wiley & Sons Ltd.
DOI: 10.1002/pmic.201900351

Connecting MetaProteomeAnalyzer and PeptideShaker to Unipept for Seamless End-to-End Metaproteomics Data Analysis

Author(s): Tim Van Den Bossche, Pieter Verschaffelt, Kay Schallert, Harald Barsnes, Peter Dawyndt, Dirk Benndorf, Bernhard Y. Renard, Bart Mesuere, Lennart Martens, Thilo Muth
Published in: Journal of Proteome Research, 2020, ISSN 1535-3893
Publisher: American Chemical Society
DOI: 10.1021/acs.jproteome.0c00136

Robust Summarization and Inference in Proteome-wide Label-free Quantification

Author(s): Adriaan Sticker, Ludger Goeminne, Lennart Martens, Lieven Clement
Published in: Molecular & Cellular Proteomics, Issue 19/7, 2020, Page(s) 1209-1219, ISSN 1535-9476
Publisher: American Society for Biochemistry and Molecular Biology Inc.
DOI: 10.1074/mcp.ra119.001624

Generalized Calibration Across Liquid Chromatography Setups for Generic Prediction of Small-Molecule Retention Times

Author(s): Robbin Bouwmeester, Lennart Martens, Sven Degroeve
Published in: Analytical Chemistry, Issue 92/9, 2020, Page(s) 6571-6578, ISSN 0003-2700
Publisher: American Chemical Society
DOI: 10.1021/acs.analchem.0c00233

Scop3P: A Comprehensive Resource of Human Phosphosites within Their Full Context

Author(s): Pathmanaban Ramasamy, Demet Turan, Natalia Tichshenko, Niels Hulstaert, Elien Vandermarliere, Wim Vranken, Lennart Martens
Published in: Journal of Proteome Research, 2020, ISSN 1535-3893
Publisher: American Chemical Society
DOI: 10.1021/acs.jproteome.0c00306

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

Author(s): Ralf Gabriels, Lennart Martens, Sven Degroeve
Published in: Nucleic Acids Research, Issue 47/W1, 2019, Page(s) W295-W299, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkz299

New findings on the action of hypericin in hypoxic cancer cells with a focus on the modulation of side population cells

Author(s): Bukova, Viktoria; Vargova, Jana; Babincak, Marian; Jendzelovsky, Rastislav; Zdrahal, Zbynek; Roudnicky, Pavel; Kosuth, Jan; Fedorocko, Peter
Published in: Biomed. Pharmacother., Issue 163, 2023, Page(s) 114829, ISSN 0753-3322
Publisher: Elsevier Masson
DOI: 10.1016/j.biopha.2023.114829

Notch–Jagged signaling complex defined by an interaction mosaic

Author(s): Matthieu R. Zeronian, Oleg Klykov, Júlia Portell i de Montserrat, Maria J. Konijnenberg, Anamika Gaur, Richard A. Scheltema, Bert J. C. Janssen
Published in: Proceedings of the National Academy of Sciences, Issue 118/30, 2021, Page(s) e2102502118, ISSN 0027-8424
Publisher: National Academy of Sciences
DOI: 10.1073/pnas.2102502118

MSstats Version 4.0: Statistical Analyses of Quantitative Mass Spectrometry-Based Proteomic Experiments with Chromatography-Based Quantification at Scale

Author(s): 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
Published in: J. Proteome Res., Issue 22/5, 2023, Page(s) 1466-1482, ISSN 1535-3893
Publisher: American Chemical Society
DOI: 10.1021/acs.jproteome.2c00834

psm_utils: A High-Level Python API for Parsing and Handling Peptide-Spectrum Matches and Proteomics Search Results

Author(s): Gabriels, Ralf; Declercq, Arthur; Bouwmeester, Robbin; Degroeve, Sven; Martens, Lennart
Published in: J. Proteome Res., 2022, ISSN 1535-3893
Publisher: American Chemical Society
DOI: 10.1021/acs.jproteome.2c00609

Mass spectrometry‐based characterization of histones in clinical samples: applications, progresses, and challenges

Author(s): Roberta Noberini, Giulia Robusti, Tiziana Bonaldi
Published in: The FEBS Journal, 2021, ISSN 1742-464X
Publisher: Blackwell Publishing Inc.
DOI: 10.1111/febs.15707

The LncRNA LENOX Interacts with RAP2C to Regulate Metabolism and Promote Resistance to MAPK Inhibition in Melanoma

Author(s): Gambi, Giovanni; Mengus, Gabrielle; Davidson, Guillaume; Demesmaeker, Ewout; Cuomo, Alessandro; Bonaldi, Tiziana; Katopodi, Vicky; Malouf, Gabriel G.; Leucci, Eleonora; Davidson, Irwin
Published in: Cancer Res., Issue 82/24, 2022, Page(s) 4555-4570, ISSN 0008-5472
Publisher: American Association for Cancer Research
DOI: 10.1158/0008-5472.can-22-0959

β-RA Targets Mitochondrial Metabolism and Adipogenesis, Leading to Therapeutic Benefits against CoQ Deficiency and Age-Related Overweight

Author(s): Agustín Hidalgo-Gutiérrez, Eliana Barriocanal-Casado, María Elena Díaz-Casado, Pilar González-García, Riccardo Zenezini Chiozzi, Darío Acuña-Castroviejo, Luis Carlos López
Published in: Biomedicines, Issue 9/10, 2021, Page(s) 1457, ISSN 2227-9059
Publisher: MDPI
DOI: 10.3390/biomedicines9101457

Optimization of a Top-Down Proteomics Platform for Closely Related Pathogenic Bacterial Discrimination

Author(s): Mathieu Dupré, Magalie Duchateau, Christian Malosse, Diogo Borges-Lima, Valeria Calvaresi, Isabelle Podglajen, Dominique Clermont, Martial Rey, Julia Chamot-Rooke
Published in: Journal of Proteome Research, 2020, ISSN 1535-3893
Publisher: American Chemical Society
DOI: 10.1021/acs.jproteome.0c00351

DUX4-r exerts a neomorphic activity that depends on GTF2I in acute lymphoblastic leukemia

Author(s): Campolungo, Daniele; Salome, Mara; Biferali, Beatrice; Tascini, Anna Sofia; Gabellini, Davide
Published in: Sci. Adv., Issue 9/37, 2023, Page(s) eadi3771, ISSN 2375-2548
Publisher: AMER ASSOC ADVANCEMENT SCIENCE
DOI: 10.1126/sciadv.adi3771

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

Author(s): Frackowiak, Patryk; Wrzesinska, Barbara; Wieczorek, Przemyslaw; Sanchez-Bel, Paloma; Kunz, Laura; Dittmann, Antje; Obrepalska-Steplowska, Aleksandra
Published in: Plant Soil, Issue 481/1-2, 2022, Page(s) 511-534, ISSN 0032-079X
Publisher: Kluwer Academic Publishers
DOI: 10.1007/s11104-022-05651-7

Detection and quantification of the histone code in the fungal genus Aspergillus

Author(s): Zhang, Xin; Noberini, Roberta; Vai, Alessandro; Bonaldi, Tiziana; Seidl, Michael F.; Collemare, Jerome
Published in: Fungal Genet. Biol., Issue 167, 2023, Page(s) 103800, ISSN 1087-1845
Publisher: Academic Press
DOI: 10.1016/j.fgb.2023.103800

 Predicting fragment intensities and retention time of iTRAQ- and TMTPro-labeled peptides with Prosit-TMT

Author(s): Gabriel W, Giurcoiu V, Lautenbacher L, Wilhelm M.
Published in: Proteomics, 2022, ISSN 1615-9853
Publisher: John Wiley & Sons Ltd.
DOI: 10.1002/pmic.202100257

Extending Native Top-Down Electron Capture Dissociation to MDa Immunoglobulin Complexes Provides Useful Sequence Tags Covering Their Critical Variable Complementarity-Determining Regions

Author(s): Greisch, Jean-Francois; den Boer, Maurits A.; Lai, Szu-Hsueh; Gallagher, Kelly; Bondt, Albert; Commandeur, Jan; Heck, Albert J. R.
Published in: Anal. Chem., Issue 93/48, 2021, Page(s) 16068-16075, ISSN 0003-2700
Publisher: American Chemical Society
DOI: 10.1021/acs.analchem.1c03740

Enzyme expression kinetics by Escherichia coli during transition from rich to minimal media depends on proteome reserves

Author(s): Wu, Chenhao; Mori, Matteo; Abele, Miriam; Banaei-Esfahani, Amir; Zhang, Zhongge; Okano, Hiroyuki; Aebersold, Ruedi; Ludwig, Christina; Hwa, Terence
Published in: NAT. MICROBIOL, Issue 8/2, 2023, Page(s) 347, ISSN 2058-5276
Publisher: NATURE PORTFOLIO
DOI: 10.1038/s41564-022-01310-w

Cleavable Cross-Linkers and Mass Spectrometry for the Ultimate Task of Profiling Protein–Protein Interaction Networks in Vivo

Author(s): Manuel Matzinger, Karl Mechtler
Published in: Journal of Proteome Research, Issue 20/1, 2021, Page(s) 78-93, ISSN 1535-3893
Publisher: American Chemical Society
DOI: 10.1021/acs.jproteome.0c00583

Human plasma IgG1 repertoires are simple, unique, and dynamic

Author(s): 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.
Published in: Cell Syst., Issue 12/12, 2021, Page(s) 1131, ISSN 2405-4712
Publisher: CELL PRESS
DOI: 10.1016/j.cels.2021.08.008

Ultrasensitive NanoLC-MS of Subnanogram Protein Samples Using Second Generation Micropillar Array LC Technology with Orbitrap Exploris 480 and FAIMS PRO

Author(s): Karel Stejskal, Jeff Op de Beeck, Gerhard Dürnberger, Paul Jacobs, Karl Mechtler
Published in: Analytical Chemistry, Issue 93/25, 2021, Page(s) 8704-8710, ISSN 0003-2700
Publisher: American Chemical Society
DOI: 10.1021/acs.analchem.1c00990

Molecular principles of Piwi-mediated cotranscriptional silencing through the dimeric SFiNX complex

Author(s): 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
Published in: Genes & Development, Issue 35/5-6, 2021, Page(s) 392-409, ISSN 0890-9369
Publisher: Cold Spring Harbor Laboratory Press
DOI: 10.1101/gad.347989.120

Repurposing the antipsychotic drug amisulpride for targeting synovial fibroblast activation in arthritis

Author(s): 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
Published in: JCI Insight, Issue 8/9, 2023, Page(s) e165024, ISSN 2379-3708
Publisher: AMER SOC CLINICAL INVESTIGATION INC
DOI: 10.1172/jci.insight.165024

Identification of Carcinogenesis and Tumor Progression Processes in Pancreatic Ductal Adenocarcinoma Using High-Throughput Proteomics

Author(s): 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
Published in: Cancers, 2022, ISSN 2072-6694
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/cancers14102414

Quantifying Positional Isomers (QPI) by Top-Down Mass Spectrometry

Author(s): Andrea M. Brunner, Philip Lössl, Paul P. Geurink, Huib Ovaa, P. Albanese, A.F. Maarten Altelaar, Albert J.R. Heck, Richard A. Scheltema
Published in: Molecular & Cellular Proteomics, Issue 20, 2021, Page(s) 100070, ISSN 1535-9476
Publisher: American Society for Biochemistry and Molecular Biology Inc.
DOI: 10.1016/j.mcpro.2021.100070

FLASHIda enables intelligent data acquisition for top-down proteomics to boost proteoform identification counts

Author(s): Jeong, Kyowon; Babovic, Masa; Gorshkov, Vladimir; Kim, Jihyung; Jensen, Ole N.; Kohlbacher, Oliver
Published in: Nat. Commun., Issue 13/1, 2022, Page(s) 4407, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-022-31922-z

Systemic LRG1 Expression in Melanoma is Associated with Disease Progression and Recurrence

Author(s): 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.
Published in: Cancer Res. Commun., 2023, ISSN 2767-9764
Publisher: AMER ASSOC CANCER RESEARCH
DOI: 10.1158/2767-9764.crc-23-0015

Nse5/6 inhibits the Smc5/6 ATPase and modulates DNA substrate binding

Author(s): Michael Taschner, Jérôme Basquin, Barbara Steigenberger, Ingmar B Schäfer, Young‐Min Soh, Claire Basquin, Esben Lorentzen, Markus Räschle, Richard A Scheltema, Stephan Gruber
Published in: The EMBO Journal, Issue 40/15, 2021, ISSN 0261-4189
Publisher: Nature Publishing Group
DOI: 10.15252/embj.2021107807

Single-cell derived tumor organoids display diversity in HLA class I peptide presentation

Author(s): 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
Published in: Nature Communications, Issue 11/1, 2020, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-020-19142-9

Quantitative Longitudinal Inventory of the N -Glycoproteome of Human Milk from a Single Donor Reveals the Highly Variable Repertoire and Dynamic Site-Specific Changes

Author(s): Jing Zhu, Yu-Hsien Lin, Kelly A. Dingess, Marko Mank, Bernd Stahl, Albert J. R. Heck
Published in: Journal of Proteome Research, Issue 19/5, 2020, Page(s) 1941-1952, ISSN 1535-3893
Publisher: American Chemical Society
DOI: 10.1021/acs.jproteome.9b00753

Staphylococcal protein A inhibits complement activation by interfering with IgG hexamer formation

Author(s): 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
Published in: Proceedings of the National Academy of Sciences, Issue 118/7, 2021, Page(s) e2016772118, ISSN 0027-8424
Publisher: National Academy of Sciences
DOI: 10.1073/pnas.2016772118

Cov-MS: A Community-Based Template Assay for Mass-Spectrometry-Based Protein Detection in SARS-CoV-2 Patients

Author(s): 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
Published in: JACS Au, Issue 1/6, 2021, Page(s) 750-765, ISSN 2691-3704
Publisher: Amer Chem Soc
DOI: 10.1021/jacsau.1c00048

ProteomicsML: An Online Platform for Community-Curated Data sets and Tutorials for Machine Learning in Proteomics

Author(s): 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.
Published in: J. Proteome Res., 2023, ISSN 1535-3893
Publisher: American Chemical Society
DOI: 10.1021/acs.jproteome.2c00629

Label-free single cell proteomics utilizing ultrafast LC and MS instrumentation: A valuable complementary technique to multiplexing

Author(s): Matzinger, Manuel; Mayer, Rupert L.; Mechtler, Karl
Published in: Proteomics, Issue 23/13-14, 2023, ISSN 1615-9853
Publisher: John Wiley & Sons Ltd.
DOI: 10.1002/pmic.202200162

Crosstalk between H2A variant-specific modifications impacts vital cell functions

Author(s): Anna Schmücker, Bingkun Lei, Zdravko J. Lorković, Matías Capella, Sigurd Braun, Pierre Bourguet, Olivier Mathieu, Karl Mechtler, Frédéric Berger
Published in: PLOS Genetics, Issue 17/6, 2021, Page(s) e1009601, ISSN 1553-7404
Publisher: PUBLIC LIBRARY SCIENCE
DOI: 10.1371/journal.pgen.1009601

Spatial proteomics defines the content of trafficking vesicles captured by golgin tethers

Author(s): 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
Published in: Nature Communications, Issue 11/1, 2020, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-020-19840-4

Mapping Physiological ADP-Ribosylation Using Activated Ion Electron Transfer Dissociation

Author(s): 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
Published in: Cell Reports, Issue 32/12, 2020, Page(s) 108176, ISSN 2211-1247
Publisher: Cell Press
DOI: 10.1016/j.celrep.2020.108176

MS(2)Rescore: Data-Driven Rescoring Dramatically Boosts Immunopeptide Identification Rates

Author(s): Declercq A, Bouwmeester R, Hirschler A, Carapito C, Degroeve S, Martens L, Gabriels R.
Published in: Mol Cell Proteomics, 2022, ISSN 1535-9476
Publisher: American Society for Biochemistry and Molecular Biology Inc.
DOI: 10.1016/j.mcpro.2022.100266

Sensitive and Specific Spectral Library Searching with CompOmics Spectral Library Searching Tool and Percolator

Author(s): Shiferaw, Genet Abay; Gabriels, Ralf; Bouwmeester, Robbin; Van den Bossche, Tim; Vandermarliere, Elien; Martens, Lennart; Volders, Pieter-Jan
Published in: J. Proteome Res., Issue 21/5, 2022, Page(s) 1365-1370, ISSN 1535-3893
Publisher: American Chemical Society
DOI: 10.1021/acs.jproteome.2c00075

MaxQuant.Live Enables Enhanced Selectivity and Identification of Peptides Modified by Endogenous SUMO and Ubiquitin

Author(s): Ivo A. Hendriks, Vyacheslav Akimov, Blagoy Blagoev, Michael L. Nielsen
Published in: Journal of Proteome Research, Issue 20/4, 2021, Page(s) 2042-2055, ISSN 1535-3893
Publisher: American Chemical Society
DOI: 10.1021/acs.jproteome.0c00892

MS Annika: A New Cross-Linking Search Engine

Author(s): Georg J. Pirklbauer, Christian E. Stieger, Manuel Matzinger, Stephan Winkler, Karl Mechtler, Viktoria Dorfer
Published in: Journal of Proteome Research, Issue 20/5, 2021, Page(s) 2560-2569, ISSN 1535-3893
Publisher: American Chemical Society
DOI: 10.1021/acs.jproteome.0c01000

LFQ-Based Peptide and Protein Intensity Differential Expression Analysis

Author(s): Bai, Mingze; Deng, Jingwen; Dai, Chengxin; Pfeuffer, Julianus; Sachsenberg, Timo; Perez-Riverol, Yasset
Published in: J. Proteome Res., Issue 22/6, 2023, Page(s) 2114-2123, ISSN 1535-3893
Publisher: American Chemical Society
DOI: 10.1021/acs.jproteome.2c00812

Optimal analytical strategies for sensitive and quantitative phosphoproteomics using TMT-based multiplexing

Author(s): Koenig C, Martinez-Val A, Franciosa G, Olsen JV.
Published in: Proteomics, Issue 16159853, 2022, ISSN 1615-9853
Publisher: John Wiley & Sons Ltd.
DOI: 10.1002/pmic.202100245

"Response to ""BAP1 Germline Mutation Associated with Bilateral Primary Uveal Melanoma"

Author(s): Herwig-Carl MC, Sharma A, Melzer C, Holz FG, Loeffler KU.
Published in: Ocular Oncology and Pathlogy, 2021, ISSN 2296-4681
Publisher: Kager AG
DOI: 10.1159/000513554

Protocol for high-throughput semi-automated label-free- or TMT-based phosphoproteome profiling

Author(s): Koenig, Claire; Martinez-Val, Ana; Naicker, Previn; Stoychev, Stoyan; Jordaan, Justin; Oslen, Jesper, V
Published in: STAR Protoc., Issue 4/3, 2023, Page(s) 102536, ISSN 2666-1667
Publisher: ELSEVIER
DOI: 10.1016/j.xpro.2023.102536

PDBe-KB: collaboratively defining the biological context of structural data,

Author(s): PDBe-KB consortium
Published in: Nucleic Acids Research, 2021, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkab988

Obtaining Complete Human Proteomes

Author(s): Martinez-Val, Ana; Guzman, Ulises H.; Olsen, Jesper, V
Published in: Annu. Rev. Genomics Hum. Genet., Issue 23, 2022, Page(s) 99-121, ISSN 1527-8204
Publisher: Annual Reviews, Inc.
DOI: 10.1146/annurev-genom-112921-024948

Robust Summarization and Inference in Proteome-wide Label-free Quantification

Author(s): Sticker, Adriaan; Goeminne, Ludger; Martens, Lennart; Clement, Lieven
Published in: Mol. Cell. Proteomics, Issue 19/7, 2020, Page(s) 1209-1219, ISSN 1535-9476
Publisher: American Society for Biochemistry and Molecular Biology Inc.
DOI: 10.1074/mcp.ra119.001624

Widespread amyloidogenicity potential of multiple myeloma patient-derived immunoglobulin light chains

Author(s): 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.
Published in: BMC Biol., Issue 21/1, 2023, Page(s) 21, ISSN 1741-7007
Publisher: BioMed Central
DOI: 10.1186/s12915-022-01506-w

Oktoberfest: Open-source spectral library generation and rescoring pipeline based on Prosit

Author(s): 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
Published in: Proteomics, 2023, ISSN 1615-9853
Publisher: John Wiley & Sons Ltd.
DOI: 10.1002/pmic.202300112

The regulatory landscape of the human HPF1- and ARH3-dependent ADP-ribosylome

Author(s): 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
Published in: Nature Communications, Issue 12/1, 2021, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-021-26172-4

Secretome Screening of BRAFV600E-Mutated Colon Cancer Cells Resistant to Vemurafenib

Author(s): Car, Iris; Dittmann, Antje; Klobucar, Marko; Grbcic, Petra; Pavelic, Sandra Kraljevic; Sedic, Mirela
Published in: Biology, Issue 12/4, 2023, Page(s) 608, ISSN 2079-7737
Publisher: MDPI
DOI: 10.3390/biology12040608

De Novo Sequencing of Antibody Light Chain Proteoforms from Patients with Multiple Myeloma

Author(s): Mathieu Dupré, Magalie Duchateau, Rebecca Sternke-Hoffmann, Amelie Boquoi, Christian Malosse, Roland Fenk, Rainer Haas, Alexander K. Buell, Martial Rey, Julia Chamot-Rooke
Published in: Analytical Chemistry, Issue 93/30, 2021, Page(s) 10627-10634, ISSN 0003-2700
Publisher: American Chemical Society
DOI: 10.1021/acs.analchem.1c01955

System-wide analysis of RNA and protein subcellular localization dynamics

Author(s): 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.
Published in: Nat. Methods, 2023, ISSN 1548-7091
Publisher: Nature Publishing Group
DOI: 10.1038/s41592-023-02101-9

Oxonium Ion-Guided Optimization of Ion Mobility-Assisted Glycoproteomics on the timsTOF Pro

Author(s): Mukherjee, Soumya; Jankevics, Andris; Busch, Florian; Lubeck, Markus; Zou, Yang; Kruppa, Gary; Heck, Albert J. R.; Scheltema, Richard A.; Reiding, Karli R.
Published in: Mol. Cell. Proteomics, Issue 22/2, 2023, Page(s) 100486, ISSN 1535-9476
Publisher: American Society for Biochemistry and Molecular Biology Inc.
DOI: 10.1016/j.mcpro.2022.100486

Real-Time Spectral Library Matching for Sample Multiplexed Quantitative Proteomics

Author(s): 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.
Published in: J. Proteome Res., Issue 22/9, 2023, Page(s) 2836-2846, ISSN 1535-3893
Publisher: American Chemical Society
DOI: 10.1021/acs.jproteome.3c00085

Juxtaposition of Bub1 and Cdc20 on phosphorylated Mad1 during catalytic mitotic checkpoint complex assembly

Author(s): Fischer ES, Yu CWH, Hevler JF, McLaughlin SH, Maslen SL, Heck AJR, Freund SMV, Barford D. 
Published in: Nature Communication, 2022, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-022-34058-2

Hydroxyl radical footprinting analysis of a human haptoglobin-hemoglobin complex.

Author(s): Loginov DS, Fiala J, Brechlin P, Kruppa G, Novak P.
Published in: Biochemica et Biophysica Acta, 2021, ISSN 1570-9639
Publisher: Elsevier BV
DOI: 10.1016/j.bbapap.2021.140735

Bacterial-type ferroxidase tunes iron-dependent phosphate sensing during Arabidopsis root development. 

Author(s): 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.
Published in: Current Biology, 2022, ISSN 0960-9822
Publisher: Cell Press
DOI: 10.1016/j.cub.2022.04.005

Updated MS2PIP web server supports cutting-edge proteomics applications

Author(s): Declercq, Arthur; Bouwmeester, Robbin; Chiva, Cristina; Sabido, Eduard; Hirschler, Aurelie; Carapito, Christine; Martens, Lennart; Degroeve, Sven; Gabriels, Ralf
Published in: Nucleic Acids Res., Issue 51/W1, 2023, Page(s) W338-W342, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkad335

Selectivity over coverage in de novo sequencing of IgGs

Author(s): den Boer, Maurits A.; Greisch, Jean-Francois; Tamara, Sem; Bondt, Albert; Heck, Albert J. R.
Published in: Chem. Sci., Issue 11/43, 2020, Page(s) 11886-11896, ISSN 2041-6520
Publisher: Royal Society of Chemistry
DOI: 10.1039/d0sc03438j

Optimized Suspension Trapping Method for Phosphoproteomics Sample Preparation

Author(s): Wang, Fujia; Veth, Tim; Kuipers, Marije; Altelaar, Maarten; Stecker, Kelly E.
Published in: Anal. Chem., Issue 95/25, 2023, Page(s) 9471-9479, ISSN 0003-2700
Publisher: American Chemical Society
DOI: 10.1021/acs.analchem.3c00324

Temporal and Site-Specific ADP-Ribosylation Dynamics upon Different Genotoxic Stresses

Author(s): Sara C. Buch-Larsen, Alexandra K.L.F.S.rebak, Ivo. A. Hendriks and Michael L. Nielsen
Published in: Cells, 2021, ISSN 2073-4409
Publisher: MDPI
DOI: 10.3390/cells10112927

Use of Linear Ion Traps in Data-Independent Acquisition Methods Benefits Low-Input Proteomics

Author(s): Eva Borràs, Olga Pastor, Eduard Sabidó
Published in: Analytical Chemistry, Issue 93/34, 2021, Page(s) 11649-11653, ISSN 0003-2700
Publisher: American Chemical Society
DOI: 10.1021/acs.analchem.1c01885

MS Amanda 2.0: Advancements in the standalone implementation

Author(s): Viktoria Dorfer, Marina Strobl, Stephan Winkler, Karl Mechtler
Published in: Rapid Communications in Mass Spectrometry, Issue 35/11, 2021, ISSN 0951-4198
Publisher: John Wiley & Sons Inc.
DOI: 10.1002/rcm.9088

Profiling of the Helicobacter pylori redox switch HP1021 regulon using a multi-omics approach

Author(s): Noszka, Mateusz; Strzalka, Agnieszka; Muraszko, Jakub; Kolenda, Rafal; Meng, Chen; Ludwig, Christina; Stingl, Kerstin; Zawilak-Pawlik, Anna
Published in: Nat. Commun., Issue 14/1, 2023, Page(s) 6715, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-023-42364-6

Platelet factor 4 is a biomarker for lymphatic-promoted disorders

Author(s): Wanshu Ma, Hyea Jin Gil, Noelia Escobedo, Alberto Benito-Martín, Pilar Ximénez-Embún, Javier Muñoz, Héctor Peinado, Stanley G. Rockson, Guillermo Oliver
Published in: JCI Insight, Issue 5/13, 2020, ISSN 2379-3708
Publisher: Amercian Soc Clinical Investigation
DOI: 10.1172/jci.insight.135109

A deeper look at carrier proteome effects for single-cell proteomics

Author(s): Ye Z, Batth TS, Rüther P, Olsen JV
Published in: Commun Biol, 2022, ISSN 2399-3642
Publisher: Nature portfolio
DOI: 10.1038/s42003-022-03095-4

Glycoproteoform Profiles of Individual Patients’ Plasma Alpha-1-Antichymotrypsin are Unique and Extensively Remodeled Following a Septic Episode

Author(s): Tomislav Čaval, Yu-Hsien Lin, Meri Varkila, Karli R. Reiding, Marc J. M. Bonten, Olaf L. Cremer, Vojtech Franc, Albert J. R. Heck
Published in: Frontiers in Immunology, Issue 11, 2021, ISSN 1664-3224
Publisher: FRONTIERS MEDIA SA
DOI: 10.3389/fimmu.2020.608466

Spectral Prediction Features as a Solution for the Search Space Size Problem in Proteogenomics

Author(s): 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
Published in: Molecular & Cellular Proteomics, Issue 20, 2021, Page(s) 100076, ISSN 1535-9476
Publisher: American Society for Biochemistry and Molecular Biology Inc.
DOI: 10.1016/j.mcpro.2021.100076

The ProteomeXchange consortium at 10 years: 2023 update

Author(s): 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
Published in: Nucleic Acids Res., Issue 51/D1, 2023, Page(s) D1539-D1548, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkac1040

Serum proteomics profiling identifies a preliminary signature for the diagnosis of early-stage lung cancer

Author(s): Gasparri, Roberto; Noberini, Roberta; Cuomo, Alessandro; Yadav, Avinash; Tricarico, Davide; Salvetto, Carola; Maisonneuve, Patrick; Caminiti, Valentina; Sedda, Giulia; Sabalic, Angela; Bonaldi, Tiziana; Spaggiari, Lorenzo
Published in: Proteom. Clin. Appl., 2023, ISSN 1862-8346
Publisher: Wiley - VCH Verlag GmbH & CO. KGaA
DOI: 10.1002/prca.202200093

Foresight in clinical proteomics: current status, ethical considerations, and future perspectives

Author(s): Mundt F, Albrechtsen NJW, Mann SP, Treit P, Ghodgaonkar-Steger M, O'Flaherty M, Raijmakers R, Vizcaíno JA, Heck AJR, Mann M
Published in: Open Res Eur, Issue 3/59, 2023, ISSN 2732-5121
Publisher: F1000 Research Limited on behalf of the European Commission
DOI: 10.12688/openreseurope.15810.2

A cyclin-dependent kinase-mediated phosphorylation switch of disordered protein condensation

Author(s): 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;
Published in: Nat. Commun., Issue 14/1, 2020, Page(s) 6316, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-023-42049-0

Cells Responding to Closely Related Cholesterol-Dependent Cytolysins Release Extracellular Vesicles with a Common Proteomic Content Including Membrane Repair Proteins

Author(s): Alves, Sara; Pereira, Joana M.; Mayer, Rupert L.; Goncalves, Alexandre D. A.; Impens, Francis; Cabanes, Didier; Sousa, Sandra
Published in: Toxins, Issue 15/1, 2023, Page(s) 4, ISSN 2072-6651
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/toxins15010004

Selective cross‐linking of coinciding protein assemblies by in‐gel cross‐linking mass spectrometry

Author(s): Johannes F Hevler, Marie V Lukassen, Alfredo Cabrera‐Orefice, Susanne Arnold, Matti F Pronker, Vojtech Franc, Albert J R Heck
Published in: The EMBO Journal, Issue 40/4, 2021, ISSN 0261-4189
Publisher: Nature Publishing Group
DOI: 10.15252/embj.2020106174

A novel dynamic proteomics approach for the measurement of broiler chicken protein fractional synthesis rate

Author(s): Peinado-Izaguerri, Jorge; Zarzuela, Eduardo; McLaughlin, Mark; Small, Alexandra C.; Riva, Francesca; McKeegan, Dorothy E. F.; Bain, Maureen; Munoz, Javier; Bhide, Mangesh; Preston, Tom
Published in: Rapid Commun. Mass Spectrom., Issue 37/10, 2023, Page(s) e9497, ISSN 0951-4198
Publisher: John Wiley & Sons Inc.
DOI: 10.1002/rcm.9497

BioContainers Registry: Searching Bioinformatics and Proteomics Tools, Packages, and Containers

Author(s): Jingwen Bai, Chakradhar Bandla, Jiaxin Guo, Roberto Vera Alvarez, Mingze Bai, Juan Antonio Vizcaíno, Pablo Moreno, Björn Grüning, Olivier Sallou, Yasset Perez-Riverol
Published in: Journal of Proteome Research, Issue 20/4, 2021, Page(s) 2056-2061, ISSN 1535-3893
Publisher: American Chemical Society
DOI: 10.1021/acs.jproteome.0c00904

QCloud2: An Improved Cloud-based Quality-Control System for Mass-Spectrometry-based Proteomics Laboratories

Author(s): 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
Published in: Journal of Proteome Research, Issue 20/4, 2021, Page(s) 2010-2013, ISSN 1535-3893
Publisher: American Chemical Society
DOI: 10.1021/acs.jproteome.0c00853

Operation of a TCA cycle subnetwork in the mammalian nucleus

Author(s): 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
Published in: Sci. Adv., Issue 8/35, 2022, Page(s) eabq5206, ISSN 2375-2548
Publisher: AMER ASSOC ADVANCEMENT SCIENCE
DOI: 10.1126/sciadv.abq5206

Phosphoproteomics of primary AML patient samples reveals rationale for AKT combination therapy and p53 context to overcome selinexor resistance

Author(s): 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.
Published in: Cell Reports, 2022, ISSN 2211-1247
Publisher: Cell Press
DOI: 10.1016/j.celrep.2022.111177

Proteomics of resistance to Notch1 inhibition in acute lymphoblastic leukemia reveals targetable kinase signatures

Author(s): Giulia Franciosa, Jos G. A. Smits, Sonia Minuzzo, Ana Martinez-Val, Stefano Indraccolo, Jesper V. Olsen
Published in: Nature Communications, Issue 12/1, 2021, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-021-22787-9

Clinico-pathological correlation of lacrimal caruncle tumors: a retrospective analysis over 22 years at the University Eye Hospital Bonn

Author(s): Clemens, A. C.; Loeffler, K. U.; Holz, F. G.; Herwig-Carl, M. C.
Published in: Graefes Arch. Clin. Exp. Ophthalmol., Issue 260/4, 2022, Page(s) 1415-1425, ISSN 0721-832X
Publisher: Springer Verlag
DOI: 10.1007/s00417-021-05464-x

Complete and cooperative in vitro assembly of computationally designed self-assembling protein nanomaterials

Author(s): Adam J. Wargacki, Tobias P. Wörner, Michiel van de Waterbeemd, Daniel Ellis, Albert J. R. Heck, Neil P. King
Published in: Nature Communications, Issue 12/1, 2021, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-021-21251-y

Structural basis of soluble membrane attack complex packaging for clearance

Author(s): Anaïs Menny, Marie V. Lukassen, Emma C. Couves, Vojtech Franc, Albert J. R. Heck, Doryen Bubeck
Published in: Nature Communications, Issue 12/1, 2021, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-021-26366-w

Molecular characterization of triple negative breast cancer formaldehyde‐fixed paraffin‐embedded samples by data‐independent acquisition proteomics

Author(s): 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
Published in: PROTEOMICS, 2021, Page(s) 2100110, ISSN 1615-9853
Publisher: John Wiley & Sons Ltd.
DOI: 10.1002/pmic.202100110

Utility of CYP2D6 copy number variants as prognostic biomarker in localized anal squamous cell carcinoma

Author(s): 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
Published in: Cancer, Issue 129/16, 2023, Page(s) 2581-2592, ISSN 0008-543X
Publisher: John Wiley & Sons Inc.
DOI: 10.1002/cncr.34797

DeepLC can predict retention times for peptides that carry as-yet unseen modifications

Author(s): Bouwmeester, R., Gabriels, R., Hulstaert, N. et al.
Published in: Nature Methods, 2021, ISSN 1548-7091
Publisher: Nature Publishing Group
DOI: 10.1038/s41592-021-01301-5

Systems approach reveals distinct and shared signaling networks of the four PGE 2 receptors in T cells

Author(s): Anna M. Lone, Piero Giansanti, Marthe Jøntvedt Jørgensen, Enio Gjerga, Aurelien Dugourd, Arjen Scholten, Julio Saez-Rodriguez, Albert J. R. Heck, Kjetil Taskén
Published in: Science Signaling, Issue 14/703, 2021, ISSN 1937-9145
Publisher: American Association for the Advancement of Science
DOI: 10.1126/scisignal.abc8579

Proteomics Standards Initiative's ProForma 2.0: Unifying the Encoding of Proteoforms and Peptidoforms

Author(s): 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
Published in: J. Proteome Res., Issue 21/4, 2022, Page(s) 1189-1195, ISSN 1535-3893
Publisher: American Chemical Society
DOI: 10.1021/acs.jproteome.1c00771

Universal Spectrum Explorer: A Standalone (Web-)Application for Cross-Resource Spectrum Comparison

Author(s): 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
Published in: Journal of Proteome Research, Issue 20/6, 2021, Page(s) 3388-3394, ISSN 1535-3893
Publisher: American Chemical Society
DOI: 10.1021/acs.jproteome.1c00096

TDFragMapper: a visualization tool for evaluating experimental parameters in top-down proteomics

Author(s): Dhenin J, Borges Lima D, Dupré M, Chamot-Rooke J.
Published in: Bioinformatics, 2021, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btab784

Postlymphadenectomy Analysis of Exosomes from Lymphatic Exudate/Exudative Seroma of Melanoma Patients

Author(s): Susana García-Silva, Pilar Ximénez-Embún, Javier Muñoz, Héctor Peinado
Published in: Melanoma - Methods and Protocols, Issue 2265, 2021, Page(s) 345-359, ISBN 978-1-0716-1204-0
Publisher: Springer US
DOI: 10.1007/978-1-0716-1205-7_25

A Compact Quadrupole-Orbitrap Mass Spectrometer with FAIMS Interface Improves Proteome Coverage in Short LC Gradients

Author(s): Dorte B. Bekker-Jensen, Ana Martínez-Val, Sophia Steigerwald, Patrick Rüther, Kyle L. Fort, Tabiwang N. Arrey, Alexander Harder, Alexander Makarov, Jesper V. Olsen
Published in: Molecular & Cellular Proteomics, Issue 19/4, 2020, Page(s) 716-729, ISSN 1535-9476
Publisher: American Society for Biochemistry and Molecular Biology Inc.
DOI: 10.1074/mcp.tir119.001906

Intellectual Property Rights

PHOSPHONATE-CONTAINING CROSSLINKERS

Application/Publication number: 19 828850
Date: 2019-09-20
Applicant(s): UNIVERSITEIT UTRECHT

METHOD AND TOOLS FOR THE DETERMINATION OF CONFORMATIONS AND CONFORMATIONAL CHANGES OF PROTEINS AND OF DERIVATIVES THEREOF

Application/Publication number: 20 22083223
Date: 2022-11-25
Applicant(s): EIDGENOESSISCHE TECHNISCHE HOCHSCHULE ZUERICH

Searching for OpenAIRE data...

There was an error trying to search data from OpenAIRE

No results available