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European Proteomics Infrastructure Consortium providing Access

Resultado final

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

Publicaciones

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

Autores: Sidhaye, Jaydeep; Trepte, Philipp; Sepke, Natalie; Novatchkova, Maria; Schutzbier, Michael; Duernberger, Gerhard; Mechtler, Karl; Knoblich, Juergen A.
Publicado en: eLife, Edición 12, 2023, Página(s) e85135, ISSN 2050-084X
Editor: eLife Sciences Publications
DOI: 10.7554/elife.85135

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

Autores: Borges Lima D, Dupré M, Mariano Santos MD, Carvalho PC, Chamot-Rooke J.
Publicado en: J Am Soc Mass Spectrom, 2021, ISSN 1044-0305
Editor: Elsevier BV
DOI: 10.1021/jasms.1c00014

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

Autores: 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. 
Publicado en: Scientific data, 2022, ISSN 2052-4463
Editor: Nature Pub
DOI: 10.1038/s41597-022-01380-9

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

Autores: Klykov, Oleg; Kopylov, Mykhailo; Carragher, Bridget; Heck, Albert J. R.; Noble, Alex J.; Scheltema, Richard A.
Publicado en: Mol. Cell, Edición 82/2, 2022, Página(s) 285-303, ISSN 1097-2765
Editor: 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

Autores: Walzer, Mathias; Jeong, Kyowon; Tabb, David L.; Vizcaino, Juan Antonio
Publicado en: Proteomics, 2023, ISSN 1615-9861
Editor: WILEY
DOI: 10.1002/pmic.202200403

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

Autores: 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
Publicado en: Science Advances, Edición 6/33, 2020, Página(s) eabb9110, ISSN 2375-2548
Editor: Amercian Assoc for the Advancement of Science
DOI: 10.1126/sciadv.abb9110

Investigating pathological epigenetic aberrations by epi-proteomics

Autores: Robusti G, Vai A, Bonaldi T, Noberini R.
Publicado en: Clinical Epigenetics, 2022, ISSN 1868-7083
Editor: BMC
DOI: 10.1186/s13148-022-01371-y

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

Autores: Charlotte A.G.H. van Gelder, Maarten Altelaar
Publicado en: Molecular & Cellular Proteomics, Edición 20, 2021, Página(s) 100087, ISSN 1535-9476
Editor: 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

Autores: Bras, Ana Rita; Fernandes, Pedro; Moreira, Tiago; Morales-Sanfrutos, Julia; Sabido, Eduard; Antunes, Alexandra M. M.; Valente, Andreia; Preto, Ana
Publicado en: Pharmaceutics, Edición 15/6, 2023, Página(s) 1731, ISSN 1999-4923
Editor: 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. 

Autores: Fuertes-Perez S, Abele M, Ludwig C, Vogel RF, Hilgarth M.
Publicado en: Frontiers in Microbiology, 2022, ISSN 1664-302X
Editor: Frontiers Media
DOI: 10.3389/fmicb.2022.866629

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

Autores: Dhenin, Jonathan; Dupre, Mathieu; Druart, Karen; Krick, Alain; Mauriac, Christine; Chamot-Rooke, Julia
Publicado en: J. Mass Spectrom., Edición 58/3, 2023, Página(s) e4909, ISSN 1076-5174
Editor: IM Publications
DOI: 10.1002/jms.4909

Protein Processing in Plant Mitochondria Compared to Yeast and Mammals

Autores: Heidorn-Czarna M, Maziak A, Janska H
Publicado en: Front. Plant Sci., 2022, ISSN 1664-462X
Editor: 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

Autores: Jones AR, Deutsch EW, Vizcaíno JA. 
Publicado en: Proteomics, 2022, ISSN 1615-9861
Editor: Wiley
DOI: 10.1002/pmic.202200014

Mimicked synthetic ribosomal protein complex for benchmarking crosslinking mass spectrometry workflows

Autores: Matzinger M, Vasiu A, Madalinski M, Müller F, Stanek F, Mechtler K
Publicado en: Nature Communications, 2022, ISSN 2041-1723
Editor: Nature Publishing Group
DOI: 10.1038/s41467-022-31701-w

High-Resolution mRNA and Secretome Atlas of Human Enteroendocrine Cells

Autores: 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
Publicado en: Cell, Edición 181/6, 2020, Página(s) 1291-1306.e19, ISSN 0092-8674
Editor: Cell Press
DOI: 10.1016/j.cell.2020.04.036

Complementary omics strategies to dissect p53 signaling networks under nutrient stress

Autores: 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.;
Publicado en: Cell. Mol. Life Sci., Edición 79/6, 2022, Página(s) 326, ISSN 1420-682X
Editor: Birkhauser Verlag
DOI: 10.1007/s00018-022-04345-8

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

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

Proteomics contributions to epigenetic drug discovery

Autores: Noberini, Roberta; Bonaldi, Tiziana
Publicado en: Proteomics, 2023, ISSN 1615-9853
Editor: 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

Autores: Eismann, Lena; Fijalkowski, Igor; Galmozzi, Carla Veronica; Koubek, Jiri; Tippmann, Frank; Van Damme, Petra; Kramer, Guenter
Publicado en: Cell Reports, Edición 41/10, 2022, Página(s) 111776, ISSN 2211-1247
Editor: Cell Press
DOI: 10.1016/j.celrep.2022.111776

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

Autores: 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.
Publicado en: Open Biol, Edición 9/11, 2019, Página(s) 190192, ISSN 2046-2441
Editor: Royal Society Publishing
DOI: 10.1098/rsob.190192

The emerging landscape of spatial profiling technologie

Autores: Moffitt JR, Lundberg E, Heyn H. 
Publicado en: Nature Reviews Genetics, 2022, ISSN 1471-0056
Editor: Nature Publishing Group
DOI: 10.1038/s41576-022-00515-3

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

Autores: 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.
Publicado en: Antioxidants, Edición 11/6, 2022, ISSN 2076-3921
Editor: MDPI
DOI: 10.3390/antiox11061110

The Human Proteoform Project: Defining the human proteome

Autores: Smith LM, Agar J, Chamot-Rooke J, Danis P, Ge Y, Loo J, Pasa-Tolic L, Tsybin YO, Kelleher N.
Publicado en: Science Advances, 2021, ISSN 2375-2548
Editor: 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

Autores: Pascal Albanese, Sem Tamara, Guido Saracco, Richard A. Scheltema, Cristina Pagliano
Publicado en: Nature Communications, Edición 11/1, 2020, ISSN 2041-1723
Editor: Nature Publishing Group
DOI: 10.1038/s41467-020-15184-1

Panoramic Perspective on Human Phosphosites

Autores: Ramasamy P, Vandermarliere E, Vranken WF, Martens L.
Publicado en: J. Proteome Research, 2022, ISSN 1535-3893
Editor: American Chemical Society
DOI: 10.1021/acs.jproteome.2c00164

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

Autores: Brucher, Dominik; Franc, Vojtech; Smith, Sheena N.; Heck, Albert J. R.; Pluckthun, Andreas
Publicado en: mAbs, Edición 12/1, 2020, Página(s) 1792084, ISSN 1942-0862
Editor: TAYLOR & FRANCIS INC
DOI: 10.1080/19420862.2020.1792084

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

Autores: Heames, Brennen; Buchel, Filip; Aubel, Margaux; Tretyachenko, Vyacheslav; Loginov, Dmitry; Novak, Petr; Lange, Andreas; Bornberg-Bauer, Erich; Hlouchova, Klara
Publicado en: Nat. Ecol. Evol., Edición 7/4, 2023, Página(s) 570, ISSN 2397-334X
Editor: 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

Autores: Gabriels, Ralf; Martens, Lennart; Degroeve, Sven
Publicado en: Nucleic Acids Res., Edición 47/W1, 2019, Página(s) W295-W299, ISSN 0305-1048
Editor: Oxford University Press
DOI: 10.1093/nar/gkz299

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

Autores: Sem Tamara, Vojtech Franc, Albert J. R. Heck
Publicado en: Proceedings of the National Academy of Sciences, Edición 117/27, 2020, Página(s) 15554-15564, ISSN 0027-8424
Editor: National Academy of Sciences
DOI: 10.1073/pnas.2002483117

Quality standards in proteomics research facilities

Autores: 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
Publicado en: EMBO reports, Edición 22/6, 2021, ISSN 1469-221X
Editor: 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

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

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

Autores: 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
Publicado en: Cell Reports, Edición 42/4, 2023, Página(s) 112380, ISSN 2211-1247
Editor: Cell Press
DOI: 10.1016/j.celrep.2023.112380

Spatial-proteomics reveals phospho-signaling dynamics at subcellular resolution

Autores: 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.
Publicado en: Nature Communications, 2021, ISSN 2041-1723
Editor: Nature Publishing Group
DOI: 10.1038/s41467-021-27398-y

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

Autores: 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. 
Publicado en: EMBO Molecular Medicine, 2022, ISSN 1757-4676
Editor: John Wiley & Sons Ltd.
DOI: 10.15252/emmm.202215705

Peroxiredoxin 2 is required for the redox mediated adaptation to exercise

Autores: Xia, Qin; Casas-Martinez, Jose C.; Zarzuela, Eduardo; Munoz, Javier; Miranda-Vizuete, Antonio; Goljanek-Whysall, Katarzyna; McDonagh, Brian
Publicado en: Redox Biol., Edición 60, 2023, Página(s) 102631, ISSN 2213-2317
Editor: Elsevier BV
DOI: 10.1016/j.redox.2023.102631

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

Autores: 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
Publicado en: Cell, Edición 184/2, 2021, Página(s) 545-559.e22, ISSN 0092-8674
Editor: Cell Press
DOI: 10.1016/j.cell.2020.12.021

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

Autores: 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
Publicado en: Nature Publishing Group, 2021, ISSN 2041-1723
Editor: Nature Publishing Group
DOI: 10.1038/s41467-021-27542-8

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

Autores: 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
Publicado en: Structure, Edición 29/4, 2021, Página(s) 345-356.e8, ISSN 0969-2126
Editor: Cell Press
DOI: 10.1016/j.str.2020.11.018

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

Autores: 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
Publicado en: Nat Commun, 2022, ISSN 2041-1723
Editor: 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

Autores: Dmitry S. Loginov, Jan Fiala, Josef Chmelik, Peter Brechlin, Gary Kruppa, Petr Novak
Publicado en: ACS Omega, Edición 6/15, 2021, Página(s) 10352-10361, ISSN 2470-1343
Editor: AMER CHEMICAL SOC
DOI: 10.1021/acsomega.1c00732

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

Autores: Holstein, Tanja; Kistner, Franziska; Martens, Lennart; Muth, Thilo
Publicado en: Bioinformatics, Edición 39/5, 2023, Página(s) btad289, ISSN 1367-4803
Editor: Oxford University Press
DOI: 10.1093/bioinformatics/btad289

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

Autores: Claeys, Tine; Menu, Maxime; Bouwmeester, Robbin; Gevaert, Kris; Martens, Lennart
Publicado en: J. Proteome Res., Edición 22/4, 2023, Página(s) 1181-1192, ISSN 1535-3893
Editor: American Chemical Society
DOI: 10.1021/acs.jproteome.2c00644

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

Autores: 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.
Publicado en: Science Data, 2022, ISSN 2052-4463
Editor: 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

Autores: 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
Publicado en: Cancer Gene Ther., Edición 30/5, 2023, Página(s) 671-682, ISSN 0929-1903
Editor: Nature Publishing Group
DOI: 10.1038/s41417-022-00576-w

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

Autores: 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
Publicado en: Small, 2021, ISSN 1613-6810
Editor: 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

Autores: Mullari, Meeli; Fossat, Nicolas; Skotte, Niels H.; Asenjo-Martinez, Andrea; Humphreys, David T.; Bukh, Jens; Kirkeby, Agnete; Scheel, Troels K. H.; Nielsen, Michael L.
Publicado en: Nat. Commun., Edición 14/1, 2023, ISSN 2041-1723
Editor: 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

Autores: Vargas-Diaz D, Altelaar M
Publicado en: J Proteome Res, 2022, ISSN 1535-3893
Editor: American Chemical Society
DOI: 10.1021/acs.jproteome.1c00743

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

Autores: 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
Publicado en: Molecular Systems Biology, Edición 17/5, 2021, ISSN 1744-4292
Editor: Nature Publishing Group
DOI: 10.15252/msb.20209536

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

Autores: 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
Publicado en: Sci. Adv., Edición 8/30, 2022, Página(s) eabo0517, ISSN 2375-2548
Editor: AMER ASSOC ADVANCEMENT SCIENCE
DOI: 10.1126/sciadv.abo0517

The rise of single-cell proteomics

Autores: Ctortecka, Claudia; Mechtler, Karl
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Editor: WILEY
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Meta-heterogeneity: Evaluating and Describing the Diversity in Glycosylation Between Sites on the Same Glycoprotein

Autores: Tomislav Čaval, Albert J.R. Heck, Karli R. Reiding
Publicado en: Molecular & Cellular Proteomics, Edición 20, 2021, Página(s) 100010, ISSN 1535-9476
Editor: American Society for Biochemistry and Molecular Biology Inc.
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Phosphorylation-Dependent Interactome of Ryanodine Receptor Type 2 in the Heart

Autores: David Y. Chiang, Satadru Lahiri, Guoliang Wang, Jason Karch, Meng C. Wang, Sung Y. Jung, Albert J. R. Heck, Arjen Scholten, Xander H. T. Wehrens
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Beneficial Effects of Mifepristone Treatment in Patients with Breast Cancer Selected by the Progesterone Receptor Isoform Ratio: Results from the MIPRA Trial

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

Autores: Monti, Maurilia M.; Mancini, Ilaria; Gualtieri, Liberata; Domingo, Guido; Beccaccioli, Marzia; Bossa, Rosanna; Bracale, Marcella; Loreto, Francesco; Ruocco, Michelina
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The Key Role of Metal Adducts in the Differentiation of Phosphopeptide from Sulfopeptide Sequences by High-Resolution Mass Spectrometry. 

Autores: Piovesana S, Capriotti AL, Cavaliere C, Cerrato A, Montone CM, Zenezini Chiozzi R, Laganà A.
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Editor: American Chemical Society
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Molecular characterization of a complex of apoptosis-inducing factor 1 with cytochrome c oxidase of the mitochondrial respiratory chain

Autores: Johannes F. Hevler, Riccardo Zenezeni Chiozzi, Alfredo Cabrera-Orefice, Ulrich Brandt, Susanne Arnold, Albert J. R. Heck
Publicado en: Proceedings of the National Academy of Sciences, Edición 118/39, 2021, Página(s) e2106950118, ISSN 0027-8424
Editor: National Academy of Sciences
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Quality Control for the Target Decoy Approach for Peptide Identification

Autores: Debrie, Elke; Malfait, Milan; Gabriels, Ralf; Declerq, Arthur; Sticker, Adriaan; Martens, Lennart; Clement, Lieven
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Editor: American Chemical Society
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MegaGO: A Fast Yet Powerful Approach to Assess Functional Gene Ontology Similarity across Meta-Omics Data Sets

Autores: Pieter Verschaffelt, Tim Van Den Bossche, Wassim Gabriel, Michał Burdukiewicz, Alessio Soggiu, Lennart Martens, Bernhard Y. Renard, Henning Schiebenhoefer, Bart Mesuere
Publicado en: Journal of Proteome Research, Edición 20/4, 2021, Página(s) 2083-2088, ISSN 1535-3893
Editor: American Chemical Society
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DAXX adds a de novo H3.3K9me3 deposition pathway to the histone chaperone network

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

Autores: Ctortecka C, Stejskal K, Krššáková G, Mendjan S, Mechtler K
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Editor: American Chemical Society
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Utilization of Fast Photochemical Oxidation of Proteins and Both Bottom-up and Top-down Mass Spectrometry for Structural Characterization of a Transcription Factor-dsDNA Complex

Autores: Polak, Marek; Yassaghi, Ghazaleh; Kavan, Daniel; Filandr, Frantisek; Fiala, Jan; Kukacka, Zdenek; Halada, Petr; Loginov, Dmitry S.; Novak, Petr
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Editor: American Chemical Society
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Prosit Transformer: A transformer for Prediction of MS2 Spectrum Intensities

Autores: Ekvall M, Truong P, Gabriel W, Wilhelm M, Käll L.
Publicado en: J. Proteome Research, 2022, ISSN 1535-3893
Editor: American Chemical Society
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Loss of N-terminal acetyltransferase A activity induces thermally unstable ribosomal proteins and increases their turnover in Saccharomyces cerevisiae

Autores: Guzman, Ulises H. H.; Aksnes, Henriette; Ree, Rasmus; Krogh, Nicolai; Jakobsson, Magnus E. E.; Jensen, Lars J. J.; Arnesen, Thomas; Olsen, Jesper V. V.
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Huntingtin structure is orchestrated by HAP40 and shows a polyglutamine expansion-specific interaction with exon 1

Autores: Harding, R.J., Deme, J.C., Hevler, J.F. et al.
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Editor: Nature Publishing Group
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lesSDRF is more: maximizing the value of proteomics data through streamlined metadata annotation

Autores: Claeys, Tine; van den Bossche, Tim; Perez-Riverol, Yasset; Gevaert, Kris; Vizcaino, Juan Antonio; Martens, Lennart
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The Q-junction and the inflammatory response are critical pathological and therapeutic factors in CoQ deficiency

Autores: 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
Publicado en: Redox Biology, 2022, ISSN 2213-2317
Editor: Elsevier BV
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A Sample Preparation Protocol for High Throughput Immunofluorescence of Suspension Cells on an Adherent Surface

Autores: Anna Bäckström, Laura Kugel, Christian Gnann, Hao Xu, Joseph E. Aslan, Emma Lundberg, Charlotte Stadler
Publicado en: Journal of Histochemistry & Cytochemistry, Edición 68/7, 2020, Página(s) 473-489, ISSN 0022-1554
Editor: Histochemical Society
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Coronary Artery Disease and Aortic Valve Stenosis: A Urine Proteomics Study

Autores: Perpétuo L, Barros AS, Dalsuco J, Nogueira-Ferreira R, Resende-Gonçalves P, Falcão-Pires I, Ferreira R, Leite-Moreira A, Trindade F, Vitorino R. 
Publicado en: International Journal of Molecular Sciences, 2022, ISSN 1422-0067
Editor: Multidisciplinary Digital Publishing Institute (MDPI)
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CAF-1 deposits newly synthesized histones during DNA replication using distinct mechanisms on the leading and lagging strands

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

Autores: Prokofeva, Polina; Hoefer, Stefanie; Hornisch, Maximilian; Abele, Miriam; Kuster, Bernhard; Medard, Guillaume
Publicado en: ACS Chem. Biol., Edición 17/11, 2022, Página(s) 3100-3109, ISSN 1554-8929
Editor: American Chemical Society
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MRPS36 provides a structural link in the eukaryotic 2-oxoglutarate dehydrogenase complex

Autores: 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.
Publicado en: Open Biol, Edición 13/3, 2023, Página(s) 220363, ISSN 2046-2441
Editor: Royal Society Publishing
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Label-Free Quantitative Proteomic Analysis of Nitrogen Starvation in Arabidopsis Root Reveals New Aspects of H2S Signaling by Protein Persulfidation

Autores: Ana Jurado-Flores, Luis C. Romero, Cecilia Gotor
Publicado en: Antioxidants, Edición 10/4, 2021, Página(s) 508, ISSN 2076-3921
Editor: MDPI
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Robust and Easy-to-Use One-Pot Workflow for Label-Free Single-Cell Proteomics

Autores: Matzinger, Manuel; Mueller, Elisabeth; Duernberger, Gerhard; Pichler, Peter; Mechtler, Karl
Publicado en: Anal. Chem., 2023, ISSN 0003-2700
Editor: American Chemical Society
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Subcellular Transcriptomics and Proteomics: A Comparative Methods Review

Autores: Christopher JA, Geladaki A, Dawson CS, Vennard OL, Lilley KS.
Publicado en: Mol Cell Proteomics, 2022, ISSN 1535-9484
Editor: Elsiver
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A universal GlycoDesign for lysosomal replacement enzymes to improve circulation time and biodistribution

Autores: 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
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Editor: FRONTIERS MEDIA SA
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Site‐specific ubiquitination of the E3 ligase HOIP regulates apoptosis and immune signaling

Autores: Lilian M Fennell, Carlos Gomez Diaz, Luiza Deszcz, Anoop Kavirayani, David Hoffmann, Kota Yanagitani, Alexander Schleiffer, Karl Mechtler, Astrid Hagelkruys, Josef Penninger, Fumiyo Ikeda
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DNAJC9 integrates heat shock molecular chaperones into the histone chaperone network

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

Autores: 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
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Editor: Cell Press
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Subcellular proteomics

Autores: 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
Publicado en: Nature Reviews Methods Primers, Edición 1/1, 2021, ISSN 2662-8449
Editor: Springer Nature
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Top-Down Detection of Oxidative Protein Footprinting by Collision-Induced Dissociation, Electron-Transfer Dissociation, and Electron-Capture Dissociation

Autores: Yassaghi G, Kukačka Z, Fiala J, Kavan D, Halada P, Volný M, Novák P
Publicado en: Analytical Chemistry, 2022, ISSN 0003-2700
Editor: American Chemical Society
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Deciphering the signaling network of breast cancer improves drug sensitivity prediction

Autores: 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
Publicado en: Cell Systems, Edición 12/5, 2021, Página(s) 401-418.e12, ISSN 2405-4712
Editor: CELL PRESS
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Identification of Protein Complexes by Integrating Protein Abundance and Interaction Features Using a Deep Learning Strategy

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

Autores: Dhenin, Jonathan; Lafont, Valerie; Dupre, Mathieu; Krick, Alain; Mauriac, Christine; Chamot-Rooke, Julia
Publicado en: Proteomics, 2023, ISSN 1615-9853
Editor: John Wiley & Sons Ltd.
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Data, Reagents, Assays and Merits of Proteomics for SARS-CoV-2 Research and Testing

Autores: Zecha, Jana; Lee, Chien-Yun; Bayer, Florian P.; Meng, Chen; Grass, Vincent; Zerweck, Johannes; Schnatbaum, Karsten; Michler, Thomas; Pichlmair, Andreas; Ludwig, Christina; Kuster, Bernhard
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Editor: American Society for Biochemistry and Molecular Biology Inc.
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Fasting improves therapeutic response in hepatocellular carcinoma through p53-dependent metabolic synergism

Autores: 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.
Publicado en: Science Advances, 2022, ISSN 2375-2548
Editor: Am soc for the advancement of Science
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Deep learning boosts sensitivity of mass spectrometry-based immunopeptidomics

Autores: 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
Publicado en: Nature Communications, Edición 12/1, 2021, ISSN 2041-1723
Editor: Nature Publishing Group
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Reversible amyloids of pyruvate kinase couple cell metabolism and stress granule assembly

Autores: 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
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Editor: Nature Publishing Group
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MassIVE.quant: a community resource of quantitative mass spectrometry–based proteomics datasets

Autores: 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
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Bap-Independent Biofilm Formation in Staphylococcus xylosus

Autores: Schiffer, Carolin J.; Abele, Miriam; Ehrmann, Matthias A.; Vogel, Rudi F.
Publicado en: Microorganisms, Edición 9/12, 2021, Página(s) 2610, ISSN 2076-2607
Editor: MDPI
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Domestic animal proteomics in the 21st century: A global retrospective and viewpoint analysis

Autores: 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
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Editor: Elsevier BV
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Structure of the inner kinetochore CCAN complex assembled onto a centromeric nucleosome

Autores: Kaige Yan, Jing Yang, Ziguo Zhang, Stephen H. McLaughlin, Leifu Chang, Domenico Fasci, Ann E. Ehrenhofer-Murray, Albert J. R. Heck, David Barford
Publicado en: Nature, Edición 574/7777, 2019, Página(s) 278-282, ISSN 0028-0836
Editor: Nature Publishing Group
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Proteome Dynamics of Persulfidation in Leaf Tissue under Light/Dark Conditions and Carbon Deprivation

Autores: Jurado-Flores, Ana; Gotor, Cecilia; Romero, Luis C. C.
Publicado en: Antioxidants, Edición 12/4, 2023, Página(s) 789, ISSN 2076-3921
Editor: 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

Autores: den Boer MA, Lai SH, Xue X, van Kampen MD, Bleijlevens B, Heck AJR
Publicado en: Anal Chem, 2022, ISSN 0002-7863
Editor: American Chemical Society
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Regulation of Rad52-dependent replication fork recovery through serine ADP-ribosylation of PolD3

Autores: Richards, Frederick; Llorca-Cardenosa, Marta J.; Langton, Jamie; Buch-Larsen, Sara C.; Shamkhi, Noor F.; Sharma, Abhishek Bharadwaj; Nielsen, Michael L.; Lakin, Nicholas D.
Publicado en: Nat. Commun., Edición 14/1, 2023, ISSN 2041-1723
Editor: Nature Publishing Group
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The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences

Autores: 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
Publicado en: Nucleic Acids Research, 2021, ISSN 0305-1048
Editor: Oxford University Press
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Fast Fluoroalkylation of Proteins Uncovers the Structure and Dynamics of Biological Macromolecules

Autores: Fojtík L, Fiala J, Pompach P, Chmelík J, Matoušek V, Beier P, Kukačka Z, Novák P.
Publicado en: J.Am.Chem. Soc., 2021, ISSN 0002-7863
Editor: American Chemical Society
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Decoding protein methylation function with thermal stability analysis

Autores: 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
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Editor: Nature Publishing Group
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Spatial epi-proteomics enabled by histone post-translational modification analysis from low-abundance clinical samples

Autores: Roberta Noberini, Evelyn Oliva Savoia, Stefania Brandini, Francesco Greco, Francesca Marra, Giovanni Bertalot, Giancarlo Pruneri, Liam A. McDonnell, Tiziana Bonaldi
Publicado en: Clinical Epigenetics, Edición 13/1, 2021, ISSN 1868-7075
Editor: Springer Verlag
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azyx-1 is a new gene that overlaps with zyxin and affects its translation in C. elegans, impacting muscular integrity and locomotion

Autores: Parmar, Bhavesh S.; Kieswetter, Amanda; Geens, Ellen; Vandewyer, Elke; Ludwig, Christina; Temmerman, Liesbet
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Pharmacological inhibition of LSD1 triggers myeloid differentiation by targeting GSE1 oncogenic functions in AML. 

Autores: Nicosia, L., Boffo, F.L., Ceccacci, E. et al.
Publicado en: Oncogene, 2021, ISSN 0950-9232
Editor: Nature Publishing Group
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An Integrative Structural Biology Analysis of Von Willebrand Factor Binding and Processing by ADAMTS-13 in Solution

Autores: 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
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Editor: Academic Press
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Global analysis of protein-RNA interactions in SARS-CoV-2-infected cells reveals key regulators of infection

Autores: 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
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Editor: Cell Press
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Pout2Prot:AnEfficient Tool to Create Protein (Sub)groups from Percolator Output Files

Autores: Schallert, Kay; Verschaffelt, Pieter; Mesuere, Bart; Benndorf, Dirk; Martens, Lennart; Van den Bossche, Tim
Publicado en: J. Proteome Res., Edición 21/4, 2022, Página(s) 1175-1180, ISSN 1535-3893
Editor: American Chemical Society
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Deep (phospho)proteomics profiling of pre- treatment needle biopsies identifies signatures of treatment resistance in HER2+breast cancer

Autores: Debets, Donna O.; Stecker, Kelly E.; Piskopou, Anastasia; Liefaard, Marte C.; Wesseling, Jelle; Sonke, Gabe S.; Lips, Esther H.; Altelaar, Maarten
Publicado en: Cell Rep. Med., Edición 4/10, 2023, Página(s) 101203, ISSN 2666-3791
Editor: CELL PRESS
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Deep Single-Shot NanoLC-MS Proteome Profiling with a 1500 Bar UHPLC System, Long Fully Porous Columns, and HRAM MS

Autores: Zheng R, Stejskal K, Pynn C, Mechtler K, Boychenko A
Publicado en: J. Proteome Research, 2022, ISSN 1535-3893
Editor: American Chemical Society
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Precursor deconvolution error estimation: The missing puzzle piece in false discovery rate in top-down proteomics

Autores: Jeong, Kyowon; Kaulich, Philipp T.; Jung, Wonhyeuk; Kim, Jihyung; Tholey, Andreas; Kohlbacher, Oliver
Publicado en: Proteomics, 2023, ISSN 1615-9853
Editor: John Wiley & Sons Ltd.
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The histone code of the fungal genus Aspergillus uncovered by evolutionary and proteomic analyses

Autores: Zhang X, Noberini R, Bonaldi T, Collemare J, Seidl MF. 
Publicado en: Microbial Genomics, 2022, ISSN 2057-5858
Editor: MICROBIOLOGY SOC
DOI: 10.1099/mgen.0.000856

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

Autores: Pinto, Paola H.; Kroupova, Alena; Schleiffer, Alexander; Mechtler, Karl; Jinek, Martin; Weitzer, Stefan; Martinez, Javier
Publicado en: Science, Edición 369/6503, 2020, Página(s) 524, ISSN 0036-8075
Editor: American Association for the Advancement of Science
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Generalized Calibration Across Liquid Chromatography Setups for Generic Prediction of Small-Molecule Retention Times

Autores: Bouwmeester, Robbin; Martens, Lennart; Degroeve, Sven
Publicado en: Anal. Chem., Edición 92/9, 2020, Página(s) 6571-6578, ISSN 0003-2700
Editor: American Chemical Society
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Similarities and differences in the structures and proteoform profiles of the complement proteins C6 and C7

Autores: Marie V. Lukassen, Vojtech Franc, Johannes F. Hevler, Albert J.R. Heck
Publicado en: PROTEOMICS, 2021, Página(s) 2000310, ISSN 1615-9853
Editor: John Wiley & Sons Ltd.
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Lipid nanoparticles allow efficient and harmless ex vivo gene editing of human hematopoietic cells

Autores: 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
Publicado en: Blood, Edición 142/9, 2023, Página(s) 812-826, ISSN 0006-4971
Editor: American Society of Hematology
DOI: 10.1182/blood.2022019333

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

Autores: Luis Enrique Cabrera-Quio, Alexander Schleiffer, Karl Mechtler, Andrea Pauli
Publicado en: PLOS Genetics, Edición 17/2, 2021, Página(s) e1009390, ISSN 1553-7404
Editor: Public Library Science
DOI: 10.1371/journal.pgen.1009390

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

Autores: 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
Publicado en: Mol. Cell. Proteomics, Edición 22/2, 2023, Página(s) 100479, ISSN 1535-9476
Editor: American Society for Biochemistry and Molecular Biology Inc.
DOI: 10.1016/j.mcpro.2022.100479

AKIRIN2 controls the nuclear import of proteasomes in vertebrates

Autores: 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
Publicado en: Nature, Edición 599/7885, 2021, Página(s) 491-496, ISSN 0028-0836
Editor: Nature Publishing Group
DOI: 10.1038/s41586-021-04035-8

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

Autores: Giacobelli VG, Fujishima K, Lepšík M, Tretyachenko V, Kadavá T, Makarov M, Bednárová L, Novák P, Hlouchová K
Publicado en: Mol Biol Evol, 2022, ISSN 0737-4038
Editor: Oxford University Press
DOI: 10.1093/molbev/msac032

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

Autores: 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
Publicado en: Molecular & Cellular Proteomics, Edición 19/10, 2020, Página(s) 1677-1687, ISSN 1535-9476
Editor: 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

Autores: 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
Publicado en: Science, Edición 380/6640, 2023, ISSN 0036-8075
Editor: 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

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

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

Autores: Ramasamy, Pathmanaban; Turan, Demet; Tichshenko, Natalia; Hulstaert, Niels; Vandermarliere, Elien; Vranken, Wim; Martens, Lennart
Publicado en: J. Proteome Res., Edición 19/8, 2020, Página(s) 3478-3486, ISSN 1535-3893
Editor: American Chemical Society
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Label-Free Mass Spectrometry-Based Quantification of Linker Histone H1 Variants in Clinical Samples

Autores: 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
Publicado en: International Journal of Molecular Sciences, Edición 21/19, 2020, Página(s) 7330, ISSN 1422-0067
Editor: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms21197330

Chromatin-Bound Proteome Profiling by Genome Capture

Autores: Sergi Aranda, Eva Borràs, Eduard Sabidó, Luciano Di Croce
Publicado en: STAR Protocols, Edición 1/1, 2020, Página(s) 100014, ISSN 2666-1667
Editor: Elsevier
DOI: 10.1016/j.xpro.2020.100014

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

Autores: 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
Publicado en: J. Proteome Res., Edición 22/7, 2023, Página(s) 2199-2217, ISSN 1535-3893
Editor: 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

Autores: 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.
Publicado en: Nat. Commun., Edición 14/1, 2023, ISSN 2041-1723
Editor: Nature Publishing Group
DOI: 10.1038/s41467-023-39347-y

Feature-based molecular networking in the GNPS analysis environment

Autores: 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
Publicado en: Nature Methods, Edición 17/9, 2020, Página(s) 905-908, ISSN 1548-7091
Editor: Nature Publishing Group
DOI: 10.1038/s41592-020-0933-6

Combining CRISPRi and metabolomics for functional annotation of compound libraries

Autores: Anglada-Girotto M, Handschin G, Ortmayr K, Campos AI, Gillet L, Manfredi P, Mulholland CV, Berney M, Jenal U, Picotti P, Zampieri M.
Publicado en: Nat Chem Biol, 2022, ISSN 1552-4450
Editor: Nature Publishing Group
DOI: 10.1038/s41589-022-00970-3

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

Autores: 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
Publicado en: Circ.Res., Edición 132/7, 2023, Página(s) 828-848, ISSN 0009-7330
Editor: Lippincott Williams & Wilkins Ltd.
DOI: 10.1161/circresaha.122.321448

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

Autores: 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
Publicado en: Nat. Commun., Edición 14/1, 2023, Página(s) 6774, ISSN 2041-1723
Editor: 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

Autores: Saul Lema A, Marina Klemenčič, Franziska Völlmy, Maarten Altelaar, Christiane Funk
Publicado en: Frontiers in Microbiology, Edición 12, 2021, ISSN 1664-302X
Editor: 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

Autores: 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.
Publicado en: Nature Communications, 2022, ISSN 2041-1723
Editor: 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

Autores: 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
Publicado en: Nature Communications, Edición 12/1, 2021, ISSN 2041-1723
Editor: 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

Autores: 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
Publicado en: Nat. Commun., Edición 14/1, 2023, Página(s) 3200, ISSN 2041-1723
Editor: Nature Publishing Group
DOI: 10.1038/s41467-023-38793-y

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

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

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

Autores: Nuno Bandeira, Eric W. Deutsch, Oliver Kohlbacher, Lennart Martens, Juan Antonio Vizcaíno
Publicado en: Molecular & Cellular Proteomics, Edición 20, 2021, Página(s) 100071, ISSN 1535-9476
Editor: 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

Autores: 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
Publicado en: Nature Communications, Edición 11/1, 2020, ISSN 2041-1723
Editor: Nature Publishing Group
DOI: 10.1038/s41467-020-18071-x

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

Autores: Pajenda S, Wagner L, Gerges D, Herkner H, Tevdoradze T, Mechtler K, Schmidt A, Winnicki W. 
Publicado en: Life, 2022, ISSN 2075-1729
Editor: MDPI
DOI: 10.3390/life12091391

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

Autores: C Silva AS, Bouwmeester R, Martens L, Degroeve S
Publicado en: Bioinformatics, 2019, ISSN 1367-4803
Editor: Oxford University Press
DOI: 10.1093/bioinformatics/btz383

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

Autores: Karli R. Reiding, Yu-Hsien Lin, Floris P. J. van Alphen, Alexander B. Meijer, Albert J. R. Heck
Publicado en: Communications Biology, Edición 4/1, 2021, ISSN 2399-3642
Editor: 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

Autores: Zhang M, Chiozzi RZ, Skerrett-Byrne DA, Veenendaal T, Klumperman J, Heck AJR, Nixon B, Helms JB, Gadella BM, Bromfield EG
Publicado en: Front Cell Dev Biol, 2022, ISSN 2296-634X
Editor: 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

Autores: Anna-Kathrine Pedersen, Anamarija Pfeiffer, Gopal Karemore, Vyacheslav Akimov, Dorte B. Bekker-Jensen, Blagoy Blagoev, Chiara Francavilla, Jesper V. Olsen
Publicado en: iScience, Edición 24/4, 2021, Página(s) 102321, ISSN 2589-0042
Editor: EMBO PRESS
DOI: 10.1016/j.isci.2021.102321

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

Autores: 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
Publicado en: Life Science Alliance, Edición 4/9, 2021, Página(s) e202101099, ISSN 2575-1077
Editor: 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

Autores: Bradbury M, Borràs E, Castellví J, Méndez O, Sánchez-Iglesias JL, Pérez-Benavente A, Gil-Moreno A, Sabidó E, Santamaria A.
Publicado en: Scientific Reports, 2022, ISSN 2045-2322
Editor: 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

Autores: 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
Publicado en: Mol. Ther. Nucl. Acids, Edición 33, 2023, ISSN 2162-2531
Editor: Nature Publishing Group
DOI: 10.1016/j.omtn.2023.08.019

Waves of sumoylation support transcription dynamics during adipocyte differentiation

Autores: 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
Publicado en: Nucleic Acids Res, 2022, ISSN 1362-4962
Editor: OXFORD UNIV PRESS
DOI: 10.1093/nar/gkac027

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

Autores: Ctortecka C, Krššáková G, Stejskal K, Penninger JM, Mendjan S, Mechtler K, Stadlmann J.
Publicado en: Mol Cell Proteomics, 2022, ISSN 1535-9484
Editor: 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

Autores: Birklbauer, Micha J. J.; Matzinger, Manuel; Mueller, Fraenze; Mechtler, Karl; Dorfer, Viktoria
Publicado en: J. Proteome Res., Edición 22/9, 2023, Página(s) 3009-3021, ISSN 1535-3893
Editor: American Chemical Society
DOI: 10.1021/acs.jproteome.3c00325

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

Autores: Sebastiaan C. de Graaf, Oleg Klykov, Henk van den Toorn, Richard A. Scheltema
Publicado en: Journal of Proteome Research, Edición 18/2, 2018, Página(s) 642-651, ISSN 1535-3893
Editor: American Chemical Society
DOI: 10.1021/acs.jproteome.8b00725

PhoX: An IMAC-Enrichable Cross-Linking Reagent

Autores: Barbara Steigenberger, Roland J. Pieters, Albert J. R. Heck, Richard A. Scheltema
Publicado en: ACS Central Science, Edición 5/9, 2019, Página(s) 1514-1522, ISSN 2374-7943
Editor: 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

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

Quantifying the impact of public omics data

Autores: 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
Publicado en: Nature Communications, Edición 10/1, 2019, ISSN 2041-1723
Editor: Nature Publishing Group
DOI: 10.1038/s41467-019-11461-w

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

Autores: 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
Publicado en: PLOS Biology, Edición 17/7, 2019, Página(s) e3000373, ISSN 1545-7885
Editor: PLOS BIOL
DOI: 10.1371/journal.pbio.3000373

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

Autores: Sem Tamara, Max Hoek, Richard A. Scheltema, Aneika C. Leney, Albert J.R. Heck
Publicado en: Chem, Edición 5/5, 2019, Página(s) 1302-1317, ISSN 2451-9294
Editor: CHEM
DOI: 10.1016/j.chempr.2019.03.006

Isotopologue Multipoint Calibration for Proteomics Biomarker Quantification in Clinical Practice

Autores: Cristina Chiva, Olga Pastor, Lucía Trilla-Fuertes, Angelo Gámez-Pozo, Juan Ángel Fresno Vara, Eduard Sabidó
Publicado en: Analytical Chemistry, Edición 91/8, 2019, Página(s) 4934-4938, ISSN 0003-2700
Editor: American Chemical Society
DOI: 10.1021/acs.analchem.8b05802

Phosphopeptide Fragmentation and Site Localization by Mass Spectrometry: An Update

Autores: Clement M. Potel, Simone Lemeer, Albert J. R. Heck
Publicado en: Analytical Chemistry, Edición 91/1, 2018, Página(s) 126-141, ISSN 0003-2700
Editor: American Chemical Society
DOI: 10.1021/acs.analchem.8b04746

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

Autores: Slavata, Chmelík, Kavan, Filandrová, Fiala, Rosůlek, Mrázek, Kukačka, Vališ, Man, Miller, McIntyre, Fabris, Novák
Publicado en: Biomolecules, Edición 9/10, 2019, Página(s) 535, ISSN 2218-273X
Editor: MDPI
DOI: 10.3390/biom9100535

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

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

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

Autores: 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
Publicado en: eLife, Edición 8, 2019, ISSN 2050-084X
Editor: eLife Sciences Publications
DOI: 10.7554/elife.46269

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

Autores: Rosulek, Darebna, Pompach, Slavata, Novak
Publicado en: Catalysts, Edición 9/10, 2019, Página(s) 833, ISSN 2073-4344
Editor: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/catal9100833

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

Autores: 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
Publicado en: Cell, Edición 179/2, 2019, Página(s) 543-560.e26, ISSN 0092-8674
Editor: 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

Autores: Oleg Klykov, Carmen van der Zwaan, Albert J. R. Heck, Alexander B. Meijer, Richard A. Scheltema
Publicado en: Proceedings of the National Academy of Sciences, Edición 117/4, 2020, Página(s) 1976-1987, ISSN 0027-8424
Editor: National Academy of Sciences
DOI: 10.1073/pnas.1911785117

Targeting proline in (phospho)proteomics

Autores: Saar A. M. Laarse, Charlotte A. G. H. Gelder, Marshall Bern, Michiel Akeroyd, Maurien M. A. Olsthoorn, Albert J. R. Heck
Publicado en: The FEBS Journal, 2020, ISSN 1742-464X
Editor: 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

Autores: Ana S C. Silva, Robbin Bouwmeester, Lennart Martens, Sven Degroeve
Publicado en: Bioinformatics, Edición 35/24, 2019, Página(s) 5243-5248, ISSN 1367-4803
Editor: 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

Autores: Dorte B. Bekker-Jensen, Oliver M. Bernhardt, Alexander Hogrebe, Ana Martinez-Val, Lynn Verbeke, Tejas Gandhi, Christian D. Kelstrup, Lukas Reiter, Jesper V. Olsen
Publicado en: Nature Communications, Edición 11/1, 2020, ISSN 2041-1723
Editor: Nature Publishing Group
DOI: 10.1038/s41467-020-14609-1

EPIFANY: A Method for Efficient High-Confidence Protein Inference

Autores: Julianus Pfeuffer, Timo Sachsenberg, Tjeerd M. H. Dijkstra, Oliver Serang, Knut Reinert, Oliver Kohlbacher
Publicado en: Journal of Proteome Research, 2020, ISSN 1535-3893
Editor: American Chemical Society
DOI: 10.1021/acs.jproteome.9b00566

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

Autores: Roberta Noberini, Camilla Restellini, Evelyn Oliva Savoia, Tiziana Bonaldi
Publicado en: Methods, 2019, ISSN 1046-2023
Editor: Academic Press
DOI: 10.1016/j.ymeth.2019.10.001

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

Autores: Niels Hulstaert, Jim Shofstahl, Timo Sachsenberg, Mathias Walzer, Harald Barsnes, Lennart Martens, Yasset Perez-Riverol
Publicado en: Journal of Proteome Research, Edición 19/1, 2019, Página(s) 537-542, ISSN 1535-3893
Editor: American Chemical Society
DOI: 10.1021/acs.jproteome.9b00328

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

Autores: 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
Publicado en: Molecular & Cellular Proteomics, Edición 19/1, 2020, Página(s) 31-49, ISSN 1535-9476
Editor: 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

Autores: 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
Publicado en: eLife, Edición 9, 2020, ISSN 2050-084X
Editor: eLife Sciences Publications
DOI: 10.7554/elife.52091

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

Autores: Brian C. Searle, Kristian E. Swearingen, Christopher A. Barnes, Tobias Schmidt, Siegfried Gessulat, Bernhard Küster, Mathias Wilhelm
Publicado en: Nature Communications, Edición 11/1, 2020, ISSN 2041-1723
Editor: Nature Publishing Group
DOI: 10.1038/s41467-020-15346-1

The omics discovery REST interface

Autores: Gaurhari Dass, Manh-Tu Vu, Pan Xu, Enrique Audain, Marc-Phillip Hitz, Björn A Grüning, Henning Hermjakob, Yasset Perez-Riverol
Publicado en: Nucleic Acids Research, 2020, ISSN 0305-1048
Editor: Oxford University Press
DOI: 10.1093/nar/gkaa326

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

Autores: Kyowon Jeong, Jihyung Kim, Manasi Gaikwad, Siti Nurul Hidayah, Laura Heikaus, Hartmut Schlüter, Oliver Kohlbacher
Publicado en: Cell Systems, Edición 10/2, 2020, Página(s) 213-218.e6, ISSN 2405-4712
Editor: Cell Press, Elsevier Inc.
DOI: 10.1016/j.cels.2020.01.003

Removing the Hidden Data Dependency of DIA with Predicted Spectral Libraries

Autores: 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
Publicado en: PROTEOMICS, Edición 20/3-4, 2020, Página(s) 1900306, ISSN 1615-9853
Editor: John Wiley & Sons Ltd.
DOI: 10.1002/pmic.201900306

To Cleave or Not To Cleave in XL-MS?

Autores: B. Steigenberger, P. Albanese, A. J. R. Heck, R. A. Scheltema
Publicado en: Journal of the American Society for Mass Spectrometry, Edición 31/2, 2020, Página(s) 196-206, ISSN 1044-0305
Editor: Elsevier BV
DOI: 10.1021/jasms.9b00085

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

Autores: Tobias P. Wörner, Joost Snijder, Antonette Bennett, Mavis Agbandje-McKenna, Alexander A. Makarov, Albert J. R. Heck
Publicado en: Nature Methods, Edición 17/4, 2020, Página(s) 395-398, ISSN 1548-7091
Editor: Nature Publishing Group
DOI: 10.1038/s41592-020-0770-7

Simple Peptide Quantification Approach for MS-Based Proteomics Quality Control

Autores: Teresa Mendes Maia, An Staes, Kim Plasman, Jarne Pauwels, Katie Boucher, Andrea Argentini, Lennart Martens, Tony Montoye, Kris Gevaert, Francis Impens
Publicado en: ACS Omega, Edición 5/12, 2020, Página(s) 6754-6762, ISSN 2470-1343
Editor: American Chemical Society
DOI: 10.1021/acsomega.0c00080

N-Terminal Proteoforms in Human Disease

Autores: Annelies Bogaert, Esperanza Fernandez, Kris Gevaert
Publicado en: Trends in Biochemical Sciences, Edición 45/4, 2020, Página(s) 308-320, ISSN 0968-0004
Editor: Elsevier BV
DOI: 10.1016/j.tibs.2019.12.009

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

Autores: 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
Publicado en: Nucleic Acids Research, 2019, ISSN 0305-1048
Editor: Oxford University Press
DOI: 10.1093/nar/gkz984

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

Autores: Jan Fiala, Zdeněk Kukačka, Petr Novák
Publicado en: Journal of Proteomics, Edición 218, 2020, Página(s) 103716, ISSN 1874-3919
Editor: Elsevier BV
DOI: 10.1016/j.jprot.2020.103716

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

Autores: Genet Abay Shiferaw, Elien Vandermarliere, Niels Hulstaert, Ralf Gabriels, Lennart Martens, Pieter-Jan Volders
Publicado en: Journal of Proteome Research, 2020, ISSN 1535-3893
Editor: American Chemical Society
DOI: 10.1021/acs.jproteome.9b00743

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

Autores: Manuel Matzinger, Wolfgang Kandioller, Philipp Doppler, Elke H. Heiss, Karl Mechtler
Publicado en: Journal of Proteome Research, Edición 19/5, 2020, Página(s) 2071-2079, ISSN 1535-3893
Editor: American Chemical Society
DOI: 10.1021/acs.jproteome.0c00003

Fishing for newly synthesized proteins with phosphonate-handles

Autores: Fleur Kleinpenning, Barbara Steigenberger, Wei Wu, Albert J. R. Heck
Publicado en: Nature Communications, Edición 11/1, 2020, ISSN 2041-1723
Editor: 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

Autores: Rebecca Beveridge, Johannes Stadlmann, Josef M. Penninger, Karl Mechtler
Publicado en: Nature Communications, Edición 11/1, 2020, ISSN 2041-1723
Editor: Nature Publishing Group
DOI: 10.1038/s41467-020-14608-2

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

Autores: Robbin Bouwmeester, Ralf Gabriels, Tim Van Den Bossche, Lennart Martens, Sven Degroeve
Publicado en: PROTEOMICS, 2020, Página(s) 1900351, ISSN 1615-9853
Editor: John Wiley & Sons Ltd.
DOI: 10.1002/pmic.201900351

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

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

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

Autores: Adriaan Sticker, Ludger Goeminne, Lennart Martens, Lieven Clement
Publicado en: Molecular & Cellular Proteomics, Edición 19/7, 2020, Página(s) 1209-1219, ISSN 1535-9476
Editor: 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

Autores: Robbin Bouwmeester, Lennart Martens, Sven Degroeve
Publicado en: Analytical Chemistry, Edición 92/9, 2020, Página(s) 6571-6578, ISSN 0003-2700
Editor: American Chemical Society
DOI: 10.1021/acs.analchem.0c00233

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

Autores: Pathmanaban Ramasamy, Demet Turan, Natalia Tichshenko, Niels Hulstaert, Elien Vandermarliere, Wim Vranken, Lennart Martens
Publicado en: Journal of Proteome Research, 2020, ISSN 1535-3893
Editor: 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

Autores: Ralf Gabriels, Lennart Martens, Sven Degroeve
Publicado en: Nucleic Acids Research, Edición 47/W1, 2019, Página(s) W295-W299, ISSN 0305-1048
Editor: 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

Autores: Bukova, Viktoria; Vargova, Jana; Babincak, Marian; Jendzelovsky, Rastislav; Zdrahal, Zbynek; Roudnicky, Pavel; Kosuth, Jan; Fedorocko, Peter
Publicado en: Biomed. Pharmacother., Edición 163, 2023, Página(s) 114829, ISSN 0753-3322
Editor: Elsevier Masson
DOI: 10.1016/j.biopha.2023.114829

Notch–Jagged signaling complex defined by an interaction mosaic

Autores: Matthieu R. Zeronian, Oleg Klykov, Júlia Portell i de Montserrat, Maria J. Konijnenberg, Anamika Gaur, Richard A. Scheltema, Bert J. C. Janssen
Publicado en: Proceedings of the National Academy of Sciences, Edición 118/30, 2021, Página(s) e2102502118, ISSN 0027-8424
Editor: 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

Autores: 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
Publicado en: J. Proteome Res., Edición 22/5, 2023, Página(s) 1466-1482, ISSN 1535-3893
Editor: 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

Autores: Gabriels, Ralf; Declercq, Arthur; Bouwmeester, Robbin; Degroeve, Sven; Martens, Lennart
Publicado en: J. Proteome Res., 2022, ISSN 1535-3893
Editor: American Chemical Society
DOI: 10.1021/acs.jproteome.2c00609

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

Autores: Roberta Noberini, Giulia Robusti, Tiziana Bonaldi
Publicado en: The FEBS Journal, 2021, ISSN 1742-464X
Editor: 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

Autores: Gambi, Giovanni; Mengus, Gabrielle; Davidson, Guillaume; Demesmaeker, Ewout; Cuomo, Alessandro; Bonaldi, Tiziana; Katopodi, Vicky; Malouf, Gabriel G.; Leucci, Eleonora; Davidson, Irwin
Publicado en: Cancer Res., Edición 82/24, 2022, Página(s) 4555-4570, ISSN 0008-5472
Editor: 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

Autores: Agustín Hidalgo-Gutiérrez, Eliana Barriocanal-Casado, María Elena Díaz-Casado, Pilar González-García, Riccardo Zenezini Chiozzi, Darío Acuña-Castroviejo, Luis Carlos López
Publicado en: Biomedicines, Edición 9/10, 2021, Página(s) 1457, ISSN 2227-9059
Editor: MDPI
DOI: 10.3390/biomedicines9101457

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

Autores: Mathieu Dupré, Magalie Duchateau, Christian Malosse, Diogo Borges-Lima, Valeria Calvaresi, Isabelle Podglajen, Dominique Clermont, Martial Rey, Julia Chamot-Rooke
Publicado en: Journal of Proteome Research, 2020, ISSN 1535-3893
Editor: American Chemical Society
DOI: 10.1021/acs.jproteome.0c00351

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

Autores: Campolungo, Daniele; Salome, Mara; Biferali, Beatrice; Tascini, Anna Sofia; Gabellini, Davide
Publicado en: Sci. Adv., Edición 9/37, 2023, Página(s) eadi3771, ISSN 2375-2548
Editor: 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

Autores: Frackowiak, Patryk; Wrzesinska, Barbara; Wieczorek, Przemyslaw; Sanchez-Bel, Paloma; Kunz, Laura; Dittmann, Antje; Obrepalska-Steplowska, Aleksandra
Publicado en: Plant Soil, Edición 481/1-2, 2022, Página(s) 511-534, ISSN 0032-079X
Editor: Kluwer Academic Publishers
DOI: 10.1007/s11104-022-05651-7

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

Autores: Zhang, Xin; Noberini, Roberta; Vai, Alessandro; Bonaldi, Tiziana; Seidl, Michael F.; Collemare, Jerome
Publicado en: Fungal Genet. Biol., Edición 167, 2023, Página(s) 103800, ISSN 1087-1845
Editor: Academic Press
DOI: 10.1016/j.fgb.2023.103800

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

Autores: Gabriel W, Giurcoiu V, Lautenbacher L, Wilhelm M.
Publicado en: Proteomics, 2022, ISSN 1615-9853
Editor: 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

Autores: Greisch, Jean-Francois; den Boer, Maurits A.; Lai, Szu-Hsueh; Gallagher, Kelly; Bondt, Albert; Commandeur, Jan; Heck, Albert J. R.
Publicado en: Anal. Chem., Edición 93/48, 2021, Página(s) 16068-16075, ISSN 0003-2700
Editor: 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

Autores: Wu, Chenhao; Mori, Matteo; Abele, Miriam; Banaei-Esfahani, Amir; Zhang, Zhongge; Okano, Hiroyuki; Aebersold, Ruedi; Ludwig, Christina; Hwa, Terence
Publicado en: NAT. MICROBIOL, Edición 8/2, 2023, Página(s) 347, ISSN 2058-5276
Editor: 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

Autores: Manuel Matzinger, Karl Mechtler
Publicado en: Journal of Proteome Research, Edición 20/1, 2021, Página(s) 78-93, ISSN 1535-3893
Editor: American Chemical Society
DOI: 10.1021/acs.jproteome.0c00583

Human plasma IgG1 repertoires are simple, unique, and dynamic

Autores: 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.
Publicado en: Cell Syst., Edición 12/12, 2021, Página(s) 1131, ISSN 2405-4712
Editor: 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

Autores: Karel Stejskal, Jeff Op de Beeck, Gerhard Dürnberger, Paul Jacobs, Karl Mechtler
Publicado en: Analytical Chemistry, Edición 93/25, 2021, Página(s) 8704-8710, ISSN 0003-2700
Editor: American Chemical Society
DOI: 10.1021/acs.analchem.1c00990

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

Autores: 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
Publicado en: Genes & Development, Edición 35/5-6, 2021, Página(s) 392-409, ISSN 0890-9369
Editor: Cold Spring Harbor Laboratory Press
DOI: 10.1101/gad.347989.120

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

Autores: 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
Publicado en: JCI Insight, Edición 8/9, 2023, Página(s) e165024, ISSN 2379-3708
Editor: 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

Autores: 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
Publicado en: Cancers, 2022, ISSN 2072-6694
Editor: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/cancers14102414

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

Autores: Andrea M. Brunner, Philip Lössl, Paul P. Geurink, Huib Ovaa, P. Albanese, A.F. Maarten Altelaar, Albert J.R. Heck, Richard A. Scheltema
Publicado en: Molecular & Cellular Proteomics, Edición 20, 2021, Página(s) 100070, ISSN 1535-9476
Editor: 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

Autores: Jeong, Kyowon; Babovic, Masa; Gorshkov, Vladimir; Kim, Jihyung; Jensen, Ole N.; Kohlbacher, Oliver
Publicado en: Nat. Commun., Edición 13/1, 2022, Página(s) 4407, ISSN 2041-1723
Editor: Nature Publishing Group
DOI: 10.1038/s41467-022-31922-z

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

Autores: 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.
Publicado en: Cancer Res. Commun., 2023, ISSN 2767-9764
Editor: AMER ASSOC CANCER RESEARCH
DOI: 10.1158/2767-9764.crc-23-0015

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

Autores: Michael Taschner, Jérôme Basquin, Barbara Steigenberger, Ingmar B Schäfer, Young‐Min Soh, Claire Basquin, Esben Lorentzen, Markus Räschle, Richard A Scheltema, Stephan Gruber
Publicado en: The EMBO Journal, Edición 40/15, 2021, ISSN 0261-4189
Editor: Nature Publishing Group
DOI: 10.15252/embj.2021107807

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

Autores: 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
Publicado en: Nature Communications, Edición 11/1, 2020, ISSN 2041-1723
Editor: 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

Autores: Jing Zhu, Yu-Hsien Lin, Kelly A. Dingess, Marko Mank, Bernd Stahl, Albert J. R. Heck
Publicado en: Journal of Proteome Research, Edición 19/5, 2020, Página(s) 1941-1952, ISSN 1535-3893
Editor: American Chemical Society
DOI: 10.1021/acs.jproteome.9b00753

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

Autores: 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
Publicado en: Proceedings of the National Academy of Sciences, Edición 118/7, 2021, Página(s) e2016772118, ISSN 0027-8424
Editor: 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

Autores: 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
Publicado en: JACS Au, Edición 1/6, 2021, Página(s) 750-765, ISSN 2691-3704
Editor: Amer Chem Soc
DOI: 10.1021/jacsau.1c00048

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

Autores: 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.
Publicado en: J. Proteome Res., 2023, ISSN 1535-3893
Editor: 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

Autores: Matzinger, Manuel; Mayer, Rupert L.; Mechtler, Karl
Publicado en: Proteomics, Edición 23/13-14, 2023, ISSN 1615-9853
Editor: John Wiley & Sons Ltd.
DOI: 10.1002/pmic.202200162

Crosstalk between H2A variant-specific modifications impacts vital cell functions

Autores: Anna Schmücker, Bingkun Lei, Zdravko J. Lorković, Matías Capella, Sigurd Braun, Pierre Bourguet, Olivier Mathieu, Karl Mechtler, Frédéric Berger
Publicado en: PLOS Genetics, Edición 17/6, 2021, Página(s) e1009601, ISSN 1553-7404
Editor: PUBLIC LIBRARY SCIENCE
DOI: 10.1371/journal.pgen.1009601

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

Autores: 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
Publicado en: Nature Communications, Edición 11/1, 2020, ISSN 2041-1723
Editor: Nature Publishing Group
DOI: 10.1038/s41467-020-19840-4

Mapping Physiological ADP-Ribosylation Using Activated Ion Electron Transfer Dissociation

Autores: 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
Publicado en: Cell Reports, Edición 32/12, 2020, Página(s) 108176, ISSN 2211-1247
Editor: Cell Press
DOI: 10.1016/j.celrep.2020.108176

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

Autores: Declercq A, Bouwmeester R, Hirschler A, Carapito C, Degroeve S, Martens L, Gabriels R.
Publicado en: Mol Cell Proteomics, 2022, ISSN 1535-9476
Editor: 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

Autores: Shiferaw, Genet Abay; Gabriels, Ralf; Bouwmeester, Robbin; Van den Bossche, Tim; Vandermarliere, Elien; Martens, Lennart; Volders, Pieter-Jan
Publicado en: J. Proteome Res., Edición 21/5, 2022, Página(s) 1365-1370, ISSN 1535-3893
Editor: American Chemical Society
DOI: 10.1021/acs.jproteome.2c00075

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

Autores: Ivo A. Hendriks, Vyacheslav Akimov, Blagoy Blagoev, Michael L. Nielsen
Publicado en: Journal of Proteome Research, Edición 20/4, 2021, Página(s) 2042-2055, ISSN 1535-3893
Editor: American Chemical Society
DOI: 10.1021/acs.jproteome.0c00892

MS Annika: A New Cross-Linking Search Engine

Autores: Georg J. Pirklbauer, Christian E. Stieger, Manuel Matzinger, Stephan Winkler, Karl Mechtler, Viktoria Dorfer
Publicado en: Journal of Proteome Research, Edición 20/5, 2021, Página(s) 2560-2569, ISSN 1535-3893
Editor: American Chemical Society
DOI: 10.1021/acs.jproteome.0c01000

LFQ-Based Peptide and Protein Intensity Differential Expression Analysis

Autores: Bai, Mingze; Deng, Jingwen; Dai, Chengxin; Pfeuffer, Julianus; Sachsenberg, Timo; Perez-Riverol, Yasset
Publicado en: J. Proteome Res., Edición 22/6, 2023, Página(s) 2114-2123, ISSN 1535-3893
Editor: American Chemical Society
DOI: 10.1021/acs.jproteome.2c00812

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

Autores: Koenig C, Martinez-Val A, Franciosa G, Olsen JV.
Publicado en: Proteomics, Edición 16159853, 2022, ISSN 1615-9853
Editor: John Wiley & Sons Ltd.
DOI: 10.1002/pmic.202100245

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

Autores: Herwig-Carl MC, Sharma A, Melzer C, Holz FG, Loeffler KU.
Publicado en: Ocular Oncology and Pathlogy, 2021, ISSN 2296-4681
Editor: Kager AG
DOI: 10.1159/000513554

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

Autores: Koenig, Claire; Martinez-Val, Ana; Naicker, Previn; Stoychev, Stoyan; Jordaan, Justin; Oslen, Jesper, V
Publicado en: STAR Protoc., Edición 4/3, 2023, Página(s) 102536, ISSN 2666-1667
Editor: ELSEVIER
DOI: 10.1016/j.xpro.2023.102536

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

Autores: PDBe-KB consortium
Publicado en: Nucleic Acids Research, 2021, ISSN 0305-1048
Editor: Oxford University Press
DOI: 10.1093/nar/gkab988

Obtaining Complete Human Proteomes

Autores: Martinez-Val, Ana; Guzman, Ulises H.; Olsen, Jesper, V
Publicado en: Annu. Rev. Genomics Hum. Genet., Edición 23, 2022, Página(s) 99-121, ISSN 1527-8204
Editor: Annual Reviews, Inc.
DOI: 10.1146/annurev-genom-112921-024948

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

Autores: Sticker, Adriaan; Goeminne, Ludger; Martens, Lennart; Clement, Lieven
Publicado en: Mol. Cell. Proteomics, Edición 19/7, 2020, Página(s) 1209-1219, ISSN 1535-9476
Editor: 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

Autores: 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.
Publicado en: BMC Biol., Edición 21/1, 2023, Página(s) 21, ISSN 1741-7007
Editor: BioMed Central
DOI: 10.1186/s12915-022-01506-w

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

Autores: 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
Publicado en: Proteomics, 2023, ISSN 1615-9853
Editor: John Wiley & Sons Ltd.
DOI: 10.1002/pmic.202300112

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

Autores: 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
Publicado en: Nature Communications, Edición 12/1, 2021, ISSN 2041-1723
Editor: Nature Publishing Group
DOI: 10.1038/s41467-021-26172-4

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

Autores: Car, Iris; Dittmann, Antje; Klobucar, Marko; Grbcic, Petra; Pavelic, Sandra Kraljevic; Sedic, Mirela
Publicado en: Biology, Edición 12/4, 2023, Página(s) 608, ISSN 2079-7737
Editor: MDPI
DOI: 10.3390/biology12040608

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

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

System-wide analysis of RNA and protein subcellular localization dynamics

Autores: 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.
Publicado en: Nat. Methods, 2023, ISSN 1548-7091
Editor: Nature Publishing Group
DOI: 10.1038/s41592-023-02101-9

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

Autores: Mukherjee, Soumya; Jankevics, Andris; Busch, Florian; Lubeck, Markus; Zou, Yang; Kruppa, Gary; Heck, Albert J. R.; Scheltema, Richard A.; Reiding, Karli R.
Publicado en: Mol. Cell. Proteomics, Edición 22/2, 2023, Página(s) 100486, ISSN 1535-9476
Editor: 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

Autores: 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.
Publicado en: J. Proteome Res., Edición 22/9, 2023, Página(s) 2836-2846, ISSN 1535-3893
Editor: American Chemical Society
DOI: 10.1021/acs.jproteome.3c00085

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

Autores: Fischer ES, Yu CWH, Hevler JF, McLaughlin SH, Maslen SL, Heck AJR, Freund SMV, Barford D. 
Publicado en: Nature Communication, 2022, ISSN 2041-1723
Editor: Nature Publishing Group
DOI: 10.1038/s41467-022-34058-2

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

Autores: Loginov DS, Fiala J, Brechlin P, Kruppa G, Novak P.
Publicado en: Biochemica et Biophysica Acta, 2021, ISSN 1570-9639
Editor: Elsevier BV
DOI: 10.1016/j.bbapap.2021.140735

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

Autores: 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.
Publicado en: Current Biology, 2022, ISSN 0960-9822
Editor: Cell Press
DOI: 10.1016/j.cub.2022.04.005

Updated MS2PIP web server supports cutting-edge proteomics applications

Autores: Declercq, Arthur; Bouwmeester, Robbin; Chiva, Cristina; Sabido, Eduard; Hirschler, Aurelie; Carapito, Christine; Martens, Lennart; Degroeve, Sven; Gabriels, Ralf
Publicado en: Nucleic Acids Res., Edición 51/W1, 2023, Página(s) W338-W342, ISSN 0305-1048
Editor: Oxford University Press
DOI: 10.1093/nar/gkad335

Selectivity over coverage in de novo sequencing of IgGs

Autores: den Boer, Maurits A.; Greisch, Jean-Francois; Tamara, Sem; Bondt, Albert; Heck, Albert J. R.
Publicado en: Chem. Sci., Edición 11/43, 2020, Página(s) 11886-11896, ISSN 2041-6520
Editor: Royal Society of Chemistry
DOI: 10.1039/d0sc03438j

Optimized Suspension Trapping Method for Phosphoproteomics Sample Preparation

Autores: Wang, Fujia; Veth, Tim; Kuipers, Marije; Altelaar, Maarten; Stecker, Kelly E.
Publicado en: Anal. Chem., Edición 95/25, 2023, Página(s) 9471-9479, ISSN 0003-2700
Editor: American Chemical Society
DOI: 10.1021/acs.analchem.3c00324

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

Autores: Sara C. Buch-Larsen, Alexandra K.L.F.S.rebak, Ivo. A. Hendriks and Michael L. Nielsen
Publicado en: Cells, 2021, ISSN 2073-4409
Editor: MDPI
DOI: 10.3390/cells10112927

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

Autores: Eva Borràs, Olga Pastor, Eduard Sabidó
Publicado en: Analytical Chemistry, Edición 93/34, 2021, Página(s) 11649-11653, ISSN 0003-2700
Editor: American Chemical Society
DOI: 10.1021/acs.analchem.1c01885

MS Amanda 2.0: Advancements in the standalone implementation

Autores: Viktoria Dorfer, Marina Strobl, Stephan Winkler, Karl Mechtler
Publicado en: Rapid Communications in Mass Spectrometry, Edición 35/11, 2021, ISSN 0951-4198
Editor: John Wiley & Sons Inc.
DOI: 10.1002/rcm.9088

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

Autores: Noszka, Mateusz; Strzalka, Agnieszka; Muraszko, Jakub; Kolenda, Rafal; Meng, Chen; Ludwig, Christina; Stingl, Kerstin; Zawilak-Pawlik, Anna
Publicado en: Nat. Commun., Edición 14/1, 2023, Página(s) 6715, ISSN 2041-1723
Editor: Nature Publishing Group
DOI: 10.1038/s41467-023-42364-6

Platelet factor 4 is a biomarker for lymphatic-promoted disorders

Autores: Wanshu Ma, Hyea Jin Gil, Noelia Escobedo, Alberto Benito-Martín, Pilar Ximénez-Embún, Javier Muñoz, Héctor Peinado, Stanley G. Rockson, Guillermo Oliver
Publicado en: JCI Insight, Edición 5/13, 2020, ISSN 2379-3708
Editor: Amercian Soc Clinical Investigation
DOI: 10.1172/jci.insight.135109

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

Autores: Ye Z, Batth TS, Rüther P, Olsen JV
Publicado en: Commun Biol, 2022, ISSN 2399-3642
Editor: 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

Autores: Tomislav Čaval, Yu-Hsien Lin, Meri Varkila, Karli R. Reiding, Marc J. M. Bonten, Olaf L. Cremer, Vojtech Franc, Albert J. R. Heck
Publicado en: Frontiers in Immunology, Edición 11, 2021, ISSN 1664-3224
Editor: FRONTIERS MEDIA SA
DOI: 10.3389/fimmu.2020.608466

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

Autores: 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
Publicado en: Molecular & Cellular Proteomics, Edición 20, 2021, Página(s) 100076, ISSN 1535-9476
Editor: American Society for Biochemistry and Molecular Biology Inc.
DOI: 10.1016/j.mcpro.2021.100076

The ProteomeXchange consortium at 10 years: 2023 update

Autores: 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
Publicado en: Nucleic Acids Res., Edición 51/D1, 2023, Página(s) D1539-D1548, ISSN 0305-1048
Editor: Oxford University Press
DOI: 10.1093/nar/gkac1040

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

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

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

Autores: Mundt F, Albrechtsen NJW, Mann SP, Treit P, Ghodgaonkar-Steger M, O'Flaherty M, Raijmakers R, Vizcaíno JA, Heck AJR, Mann M
Publicado en: Open Res Eur, Edición 3/59, 2023, ISSN 2732-5121
Editor: 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

Autores: 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;
Publicado en: Nat. Commun., Edición 14/1, 2020, Página(s) 6316, ISSN 2041-1723
Editor: 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

Autores: Alves, Sara; Pereira, Joana M.; Mayer, Rupert L.; Goncalves, Alexandre D. A.; Impens, Francis; Cabanes, Didier; Sousa, Sandra
Publicado en: Toxins, Edición 15/1, 2023, Página(s) 4, ISSN 2072-6651
Editor: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/toxins15010004

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

Autores: Johannes F Hevler, Marie V Lukassen, Alfredo Cabrera‐Orefice, Susanne Arnold, Matti F Pronker, Vojtech Franc, Albert J R Heck
Publicado en: The EMBO Journal, Edición 40/4, 2021, ISSN 0261-4189
Editor: Nature Publishing Group
DOI: 10.15252/embj.2020106174

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

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

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

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

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

Autores: 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
Publicado en: Journal of Proteome Research, Edición 20/4, 2021, Página(s) 2010-2013, ISSN 1535-3893
Editor: American Chemical Society
DOI: 10.1021/acs.jproteome.0c00853

Operation of a TCA cycle subnetwork in the mammalian nucleus

Autores: 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
Publicado en: Sci. Adv., Edición 8/35, 2022, Página(s) eabq5206, ISSN 2375-2548
Editor: 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

Autores: 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.
Publicado en: Cell Reports, 2022, ISSN 2211-1247
Editor: Cell Press
DOI: 10.1016/j.celrep.2022.111177

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

Autores: Giulia Franciosa, Jos G. A. Smits, Sonia Minuzzo, Ana Martinez-Val, Stefano Indraccolo, Jesper V. Olsen
Publicado en: Nature Communications, Edición 12/1, 2021, ISSN 2041-1723
Editor: 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

Autores: Clemens, A. C.; Loeffler, K. U.; Holz, F. G.; Herwig-Carl, M. C.
Publicado en: Graefes Arch. Clin. Exp. Ophthalmol., Edición 260/4, 2022, Página(s) 1415-1425, ISSN 0721-832X
Editor: Springer Verlag
DOI: 10.1007/s00417-021-05464-x

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

Autores: Adam J. Wargacki, Tobias P. Wörner, Michiel van de Waterbeemd, Daniel Ellis, Albert J. R. Heck, Neil P. King
Publicado en: Nature Communications, Edición 12/1, 2021, ISSN 2041-1723
Editor: Nature Publishing Group
DOI: 10.1038/s41467-021-21251-y

Structural basis of soluble membrane attack complex packaging for clearance

Autores: Anaïs Menny, Marie V. Lukassen, Emma C. Couves, Vojtech Franc, Albert J. R. Heck, Doryen Bubeck
Publicado en: Nature Communications, Edición 12/1, 2021, ISSN 2041-1723
Editor: 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

Autores: 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
Publicado en: PROTEOMICS, 2021, Página(s) 2100110, ISSN 1615-9853
Editor: John Wiley & Sons Ltd.
DOI: 10.1002/pmic.202100110

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

Autores: 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
Publicado en: Cancer, Edición 129/16, 2023, Página(s) 2581-2592, ISSN 0008-543X
Editor: John Wiley & Sons Inc.
DOI: 10.1002/cncr.34797

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

Autores: Bouwmeester, R., Gabriels, R., Hulstaert, N. et al.
Publicado en: Nature Methods, 2021, ISSN 1548-7091
Editor: 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

Autores: Anna M. Lone, Piero Giansanti, Marthe Jøntvedt Jørgensen, Enio Gjerga, Aurelien Dugourd, Arjen Scholten, Julio Saez-Rodriguez, Albert J. R. Heck, Kjetil Taskén
Publicado en: Science Signaling, Edición 14/703, 2021, ISSN 1937-9145
Editor: 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

Autores: 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
Publicado en: J. Proteome Res., Edición 21/4, 2022, Página(s) 1189-1195, ISSN 1535-3893
Editor: American Chemical Society
DOI: 10.1021/acs.jproteome.1c00771

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

Autores: 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
Publicado en: Journal of Proteome Research, Edición 20/6, 2021, Página(s) 3388-3394, ISSN 1535-3893
Editor: American Chemical Society
DOI: 10.1021/acs.jproteome.1c00096

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

Autores: Dhenin J, Borges Lima D, Dupré M, Chamot-Rooke J.
Publicado en: Bioinformatics, 2021, ISSN 1367-4803
Editor: Oxford University Press
DOI: 10.1093/bioinformatics/btab784

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

Autores: Susana García-Silva, Pilar Ximénez-Embún, Javier Muñoz, Héctor Peinado
Publicado en: Melanoma - Methods and Protocols, Edición 2265, 2021, Página(s) 345-359, ISBN 978-1-0716-1204-0
Editor: 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

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

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