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European Proteomics Infrastructure Consortium providing Access

Risultati finali

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

Pubblicazioni

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

Autori: Sidhaye, Jaydeep; Trepte, Philipp; Sepke, Natalie; Novatchkova, Maria; Schutzbier, Michael; Duernberger, Gerhard; Mechtler, Karl; Knoblich, Juergen A.
Pubblicato in: eLife, Numero 12, 2023, Pagina/e e85135, ISSN 2050-084X
Editore: eLife Sciences Publications
DOI: 10.7554/elife.85135

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

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

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

Autori: 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. 
Pubblicato in: Scientific data, 2022, ISSN 2052-4463
Editore: Nature Pub
DOI: 10.1038/s41597-022-01380-9

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

Autori: Klykov, Oleg; Kopylov, Mykhailo; Carragher, Bridget; Heck, Albert J. R.; Noble, Alex J.; Scheltema, Richard A.
Pubblicato in: Mol. Cell, Numero 82/2, 2022, Pagina/e 285-303, ISSN 1097-2765
Editore: 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

Autori: Walzer, Mathias; Jeong, Kyowon; Tabb, David L.; Vizcaino, Juan Antonio
Pubblicato in: Proteomics, 2023, ISSN 1615-9861
Editore: WILEY
DOI: 10.1002/pmic.202200403

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

Autori: 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
Pubblicato in: Science Advances, Numero 6/33, 2020, Pagina/e eabb9110, ISSN 2375-2548
Editore: Amercian Assoc for the Advancement of Science
DOI: 10.1126/sciadv.abb9110

Investigating pathological epigenetic aberrations by epi-proteomics

Autori: Robusti G, Vai A, Bonaldi T, Noberini R.
Pubblicato in: Clinical Epigenetics, 2022, ISSN 1868-7083
Editore: BMC
DOI: 10.1186/s13148-022-01371-y

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

Autori: Charlotte A.G.H. van Gelder, Maarten Altelaar
Pubblicato in: Molecular & Cellular Proteomics, Numero 20, 2021, Pagina/e 100087, ISSN 1535-9476
Editore: 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

Autori: Bras, Ana Rita; Fernandes, Pedro; Moreira, Tiago; Morales-Sanfrutos, Julia; Sabido, Eduard; Antunes, Alexandra M. M.; Valente, Andreia; Preto, Ana
Pubblicato in: Pharmaceutics, Numero 15/6, 2023, Pagina/e 1731, ISSN 1999-4923
Editore: 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. 

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

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

Autori: Dhenin, Jonathan; Dupre, Mathieu; Druart, Karen; Krick, Alain; Mauriac, Christine; Chamot-Rooke, Julia
Pubblicato in: J. Mass Spectrom., Numero 58/3, 2023, Pagina/e e4909, ISSN 1076-5174
Editore: IM Publications
DOI: 10.1002/jms.4909

Protein Processing in Plant Mitochondria Compared to Yeast and Mammals

Autori: Heidorn-Czarna M, Maziak A, Janska H
Pubblicato in: Front. Plant Sci., 2022, ISSN 1664-462X
Editore: 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

Autori: Jones AR, Deutsch EW, Vizcaíno JA. 
Pubblicato in: Proteomics, 2022, ISSN 1615-9861
Editore: Wiley
DOI: 10.1002/pmic.202200014

Mimicked synthetic ribosomal protein complex for benchmarking crosslinking mass spectrometry workflows

Autori: Matzinger M, Vasiu A, Madalinski M, Müller F, Stanek F, Mechtler K
Pubblicato in: Nature Communications, 2022, ISSN 2041-1723
Editore: Nature Publishing Group
DOI: 10.1038/s41467-022-31701-w

High-Resolution mRNA and Secretome Atlas of Human Enteroendocrine Cells

Autori: 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
Pubblicato in: Cell, Numero 181/6, 2020, Pagina/e 1291-1306.e19, ISSN 0092-8674
Editore: Cell Press
DOI: 10.1016/j.cell.2020.04.036

Complementary omics strategies to dissect p53 signaling networks under nutrient stress

Autori: 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.;
Pubblicato in: Cell. Mol. Life Sci., Numero 79/6, 2022, Pagina/e 326, ISSN 1420-682X
Editore: Birkhauser Verlag
DOI: 10.1007/s00018-022-04345-8

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

Autori: Martial Rey, Jonathan Dhenin, Youxin Kong, Lucienne Nouchikian, Isaac Filella, Magalie Duchateau, Mathieu Dupré, Riccardo Pellarin, Guillaume Duménil, Julia Chamot-Rooke
Pubblicato in: Analytical Chemistry, Numero 93/9, 2021, Pagina/e 4166-4174, ISSN 0003-2700
Editore: American Chemical Society
DOI: 10.1021/acs.analchem.0c04430

Proteomics contributions to epigenetic drug discovery

Autori: Noberini, Roberta; Bonaldi, Tiziana
Pubblicato in: Proteomics, 2023, ISSN 1615-9853
Editore: 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

Autori: Eismann, Lena; Fijalkowski, Igor; Galmozzi, Carla Veronica; Koubek, Jiri; Tippmann, Frank; Van Damme, Petra; Kramer, Guenter
Pubblicato in: Cell Reports, Numero 41/10, 2022, Pagina/e 111776, ISSN 2211-1247
Editore: Cell Press
DOI: 10.1016/j.celrep.2022.111776

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

Autori: 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.
Pubblicato in: Open Biol, Numero 9/11, 2019, Pagina/e 190192, ISSN 2046-2441
Editore: Royal Society Publishing
DOI: 10.1098/rsob.190192

The emerging landscape of spatial profiling technologie

Autori: Moffitt JR, Lundberg E, Heyn H. 
Pubblicato in: Nature Reviews Genetics, 2022, ISSN 1471-0056
Editore: Nature Publishing Group
DOI: 10.1038/s41576-022-00515-3

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

Autori: 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.
Pubblicato in: Antioxidants, Numero 11/6, 2022, ISSN 2076-3921
Editore: MDPI
DOI: 10.3390/antiox11061110

The Human Proteoform Project: Defining the human proteome

Autori: Smith LM, Agar J, Chamot-Rooke J, Danis P, Ge Y, Loo J, Pasa-Tolic L, Tsybin YO, Kelleher N.
Pubblicato in: Science Advances, 2021, ISSN 2375-2548
Editore: 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

Autori: Pascal Albanese, Sem Tamara, Guido Saracco, Richard A. Scheltema, Cristina Pagliano
Pubblicato in: Nature Communications, Numero 11/1, 2020, ISSN 2041-1723
Editore: Nature Publishing Group
DOI: 10.1038/s41467-020-15184-1

Panoramic Perspective on Human Phosphosites

Autori: Ramasamy P, Vandermarliere E, Vranken WF, Martens L.
Pubblicato in: J. Proteome Research, 2022, ISSN 1535-3893
Editore: American Chemical Society
DOI: 10.1021/acs.jproteome.2c00164

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

Autori: Brucher, Dominik; Franc, Vojtech; Smith, Sheena N.; Heck, Albert J. R.; Pluckthun, Andreas
Pubblicato in: mAbs, Numero 12/1, 2020, Pagina/e 1792084, ISSN 1942-0862
Editore: TAYLOR & FRANCIS INC
DOI: 10.1080/19420862.2020.1792084

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

Autori: Heames, Brennen; Buchel, Filip; Aubel, Margaux; Tretyachenko, Vyacheslav; Loginov, Dmitry; Novak, Petr; Lange, Andreas; Bornberg-Bauer, Erich; Hlouchova, Klara
Pubblicato in: Nat. Ecol. Evol., Numero 7/4, 2023, Pagina/e 570, ISSN 2397-334X
Editore: 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

Autori: Gabriels, Ralf; Martens, Lennart; Degroeve, Sven
Pubblicato in: Nucleic Acids Res., Numero 47/W1, 2019, Pagina/e W295-W299, ISSN 0305-1048
Editore: Oxford University Press
DOI: 10.1093/nar/gkz299

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

Autori: Sem Tamara, Vojtech Franc, Albert J. R. Heck
Pubblicato in: Proceedings of the National Academy of Sciences, Numero 117/27, 2020, Pagina/e 15554-15564, ISSN 0027-8424
Editore: National Academy of Sciences
DOI: 10.1073/pnas.2002483117

Quality standards in proteomics research facilities

Autori: 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
Pubblicato in: EMBO reports, Numero 22/6, 2021, ISSN 1469-221X
Editore: 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

Autori: Pagano, Andrea; Kunz, Laura; Dittmann, Antje; Araujo, Susana De Sousa; Macovei, Anca; Shridhar Gaonkar, Shraddha; Sincinelli, Federico; Wazeer, Hisham; Balestrazzi, Alma
Pubblicato in: Front. Plant Sci., Numero 14, 2023, Pagina/e 1188546, ISSN 1664-462X
Editore: Frontiers Media S. A.
DOI: 10.3389/fpls.2023.1188546

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

Autori: 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
Pubblicato in: Cell Reports, Numero 42/4, 2023, Pagina/e 112380, ISSN 2211-1247
Editore: Cell Press
DOI: 10.1016/j.celrep.2023.112380

Spatial-proteomics reveals phospho-signaling dynamics at subcellular resolution

Autori: 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.
Pubblicato in: Nature Communications, 2021, ISSN 2041-1723
Editore: Nature Publishing Group
DOI: 10.1038/s41467-021-27398-y

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

Autori: 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. 
Pubblicato in: EMBO Molecular Medicine, 2022, ISSN 1757-4676
Editore: John Wiley & Sons Ltd.
DOI: 10.15252/emmm.202215705

Peroxiredoxin 2 is required for the redox mediated adaptation to exercise

Autori: Xia, Qin; Casas-Martinez, Jose C.; Zarzuela, Eduardo; Munoz, Javier; Miranda-Vizuete, Antonio; Goljanek-Whysall, Katarzyna; McDonagh, Brian
Pubblicato in: Redox Biol., Numero 60, 2023, Pagina/e 102631, ISSN 2213-2317
Editore: Elsevier BV
DOI: 10.1016/j.redox.2023.102631

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

Autori: 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
Pubblicato in: Cell, Numero 184/2, 2021, Pagina/e 545-559.e22, ISSN 0092-8674
Editore: Cell Press
DOI: 10.1016/j.cell.2020.12.021

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

Autori: 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
Pubblicato in: Nature Publishing Group, 2021, ISSN 2041-1723
Editore: Nature Publishing Group
DOI: 10.1038/s41467-021-27542-8

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

Autori: 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
Pubblicato in: Structure, Numero 29/4, 2021, Pagina/e 345-356.e8, ISSN 0969-2126
Editore: Cell Press
DOI: 10.1016/j.str.2020.11.018

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

Autori: 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
Pubblicato in: Nat Commun, 2022, ISSN 2041-1723
Editore: 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

Autori: Dmitry S. Loginov, Jan Fiala, Josef Chmelik, Peter Brechlin, Gary Kruppa, Petr Novak
Pubblicato in: ACS Omega, Numero 6/15, 2021, Pagina/e 10352-10361, ISSN 2470-1343
Editore: AMER CHEMICAL SOC
DOI: 10.1021/acsomega.1c00732

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

Autori: Holstein, Tanja; Kistner, Franziska; Martens, Lennart; Muth, Thilo
Pubblicato in: Bioinformatics, Numero 39/5, 2023, Pagina/e btad289, ISSN 1367-4803
Editore: Oxford University Press
DOI: 10.1093/bioinformatics/btad289

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

Autori: Claeys, Tine; Menu, Maxime; Bouwmeester, Robbin; Gevaert, Kris; Martens, Lennart
Pubblicato in: J. Proteome Res., Numero 22/4, 2023, Pagina/e 1181-1192, ISSN 1535-3893
Editore: American Chemical Society
DOI: 10.1021/acs.jproteome.2c00644

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

Autori: 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.
Pubblicato in: Science Data, 2022, ISSN 2052-4463
Editore: 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

Autori: 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
Pubblicato in: Cancer Gene Ther., Numero 30/5, 2023, Pagina/e 671-682, ISSN 0929-1903
Editore: Nature Publishing Group
DOI: 10.1038/s41417-022-00576-w

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

Autori: 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
Pubblicato in: Small, 2021, ISSN 1613-6810
Editore: 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

Autori: Mullari, Meeli; Fossat, Nicolas; Skotte, Niels H.; Asenjo-Martinez, Andrea; Humphreys, David T.; Bukh, Jens; Kirkeby, Agnete; Scheel, Troels K. H.; Nielsen, Michael L.
Pubblicato in: Nat. Commun., Numero 14/1, 2023, ISSN 2041-1723
Editore: 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

Autori: Vargas-Diaz D, Altelaar M
Pubblicato in: J Proteome Res, 2022, ISSN 1535-3893
Editore: American Chemical Society
DOI: 10.1021/acs.jproteome.1c00743

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

Autori: 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
Pubblicato in: Molecular Systems Biology, Numero 17/5, 2021, ISSN 1744-4292
Editore: Nature Publishing Group
DOI: 10.15252/msb.20209536

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

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

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

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

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

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

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

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

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

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AKIRIN2 controls the nuclear import of proteasomes in vertebrates

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

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

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

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

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

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Chromatin-Bound Proteome Profiling by Genome Capture

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

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

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Feature-based molecular networking in the GNPS analysis environment

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Combining CRISPRi and metabolomics for functional annotation of compound libraries

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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Waves of sumoylation support transcription dynamics during adipocyte differentiation

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

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

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

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PhoX: An IMAC-Enrichable Cross-Linking Reagent

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

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Quantifying the impact of public omics data

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

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

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Isotopologue Multipoint Calibration for Proteomics Biomarker Quantification in Clinical Practice

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Phosphopeptide Fragmentation and Site Localization by Mass Spectrometry: An Update

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

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

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

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

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

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EPIFANY: A Method for Efficient High-Confidence Protein Inference

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

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

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

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The omics discovery REST interface

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

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Removing the Hidden Data Dependency of DIA with Predicted Spectral Libraries

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To Cleave or Not To Cleave in XL-MS?

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

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Simple Peptide Quantification Approach for MS-Based Proteomics Quality Control

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N-Terminal Proteoforms in Human Disease

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

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

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

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

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Fishing for newly synthesized proteins with phosphonate-handles

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

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

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

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

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

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

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

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

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Notch–Jagged signaling complex defined by an interaction mosaic

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

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

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

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

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

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

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

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Deciphering of benzothiadiazole (BTH)-induced response of tomato (Solanum lycopersicum L.) and its effect on early response to virus infection through the multi-omics approach

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

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

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

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

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

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Human plasma IgG1 repertoires are simple, unique, and dynamic

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Autori: Matzinger, Manuel; Mayer, Rupert L.; Mechtler, Karl
Pubblicato in: Proteomics, Numero 23/13-14, 2023, ISSN 1615-9853
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Crosstalk between H2A variant-specific modifications impacts vital cell functions

Autori: Anna Schmücker, Bingkun Lei, Zdravko J. Lorković, Matías Capella, Sigurd Braun, Pierre Bourguet, Olivier Mathieu, Karl Mechtler, Frédéric Berger
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Spatial proteomics defines the content of trafficking vesicles captured by golgin tethers

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

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

Autori: Declercq A, Bouwmeester R, Hirschler A, Carapito C, Degroeve S, Martens L, Gabriels R.
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Sensitive and Specific Spectral Library Searching with CompOmics Spectral Library Searching Tool and Percolator

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

Autori: Ivo A. Hendriks, Vyacheslav Akimov, Blagoy Blagoev, Michael L. Nielsen
Pubblicato in: Journal of Proteome Research, Numero 20/4, 2021, Pagina/e 2042-2055, ISSN 1535-3893
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MS Annika: A New Cross-Linking Search Engine

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

Autori: Bai, Mingze; Deng, Jingwen; Dai, Chengxin; Pfeuffer, Julianus; Sachsenberg, Timo; Perez-Riverol, Yasset
Pubblicato in: J. Proteome Res., Numero 22/6, 2023, Pagina/e 2114-2123, ISSN 1535-3893
Editore: American Chemical Society
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Optimal analytical strategies for sensitive and quantitative phosphoproteomics using TMT-based multiplexing

Autori: Koenig C, Martinez-Val A, Franciosa G, Olsen JV.
Pubblicato in: Proteomics, Numero 16159853, 2022, ISSN 1615-9853
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"Response to ""BAP1 Germline Mutation Associated with Bilateral Primary Uveal Melanoma"

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

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

Autori: PDBe-KB consortium
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Obtaining Complete Human Proteomes

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

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

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

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

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

Autori: Car, Iris; Dittmann, Antje; Klobucar, Marko; Grbcic, Petra; Pavelic, Sandra Kraljevic; Sedic, Mirela
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De Novo Sequencing of Antibody Light Chain Proteoforms from Patients with Multiple Myeloma

Autori: Mathieu Dupré, Magalie Duchateau, Rebecca Sternke-Hoffmann, Amelie Boquoi, Christian Malosse, Roland Fenk, Rainer Haas, Alexander K. Buell, Martial Rey, Julia Chamot-Rooke
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System-wide analysis of RNA and protein subcellular localization dynamics

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

Autori: Mukherjee, Soumya; Jankevics, Andris; Busch, Florian; Lubeck, Markus; Zou, Yang; Kruppa, Gary; Heck, Albert J. R.; Scheltema, Richard A.; Reiding, Karli R.
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Real-Time Spectral Library Matching for Sample Multiplexed Quantitative Proteomics

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

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

Autori: Loginov DS, Fiala J, Brechlin P, Kruppa G, Novak P.
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Bacterial-type ferroxidase tunes iron-dependent phosphate sensing during Arabidopsis root development. 

Autori: 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.
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Updated MS2PIP web server supports cutting-edge proteomics applications

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

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

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

Autori: Sara C. Buch-Larsen, Alexandra K.L.F.S.rebak, Ivo. A. Hendriks and Michael L. Nielsen
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Use of Linear Ion Traps in Data-Independent Acquisition Methods Benefits Low-Input Proteomics

Autori: Eva Borràs, Olga Pastor, Eduard Sabidó
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MS Amanda 2.0: Advancements in the standalone implementation

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

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

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

Autori: Ye Z, Batth TS, Rüther P, Olsen JV
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Glycoproteoform Profiles of Individual Patients’ Plasma Alpha-1-Antichymotrypsin are Unique and Extensively Remodeled Following a Septic Episode

Autori: Tomislav Čaval, Yu-Hsien Lin, Meri Varkila, Karli R. Reiding, Marc J. M. Bonten, Olaf L. Cremer, Vojtech Franc, Albert J. R. Heck
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Spectral Prediction Features as a Solution for the Search Space Size Problem in Proteogenomics

Autori: 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
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The ProteomeXchange consortium at 10 years: 2023 update

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

Autori: Gasparri, Roberto; Noberini, Roberta; Cuomo, Alessandro; Yadav, Avinash; Tricarico, Davide; Salvetto, Carola; Maisonneuve, Patrick; Caminiti, Valentina; Sedda, Giulia; Sabalic, Angela; Bonaldi, Tiziana; Spaggiari, Lorenzo
Pubblicato in: Proteom. Clin. Appl., 2023, ISSN 1862-8346
Editore: Wiley - VCH Verlag GmbH & CO. KGaA
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Foresight in clinical proteomics: current status, ethical considerations, and future perspectives

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

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

Autori: Alves, Sara; Pereira, Joana M.; Mayer, Rupert L.; Goncalves, Alexandre D. A.; Impens, Francis; Cabanes, Didier; Sousa, Sandra
Pubblicato in: Toxins, Numero 15/1, 2023, Pagina/e 4, ISSN 2072-6651
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Selective cross‐linking of coinciding protein assemblies by in‐gel cross‐linking mass spectrometry

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

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

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

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

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

Autori: 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.
Pubblicato in: Cell Reports, 2022, ISSN 2211-1247
Editore: Cell Press
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Proteomics of resistance to Notch1 inhibition in acute lymphoblastic leukemia reveals targetable kinase signatures

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

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

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

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

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

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

Autori: Bouwmeester, R., Gabriels, R., Hulstaert, N. et al.
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Systems approach reveals distinct and shared signaling networks of the four PGE 2 receptors in T cells

Autori: Anna M. Lone, Piero Giansanti, Marthe Jøntvedt Jørgensen, Enio Gjerga, Aurelien Dugourd, Arjen Scholten, Julio Saez-Rodriguez, Albert J. R. Heck, Kjetil Taskén
Pubblicato in: Science Signaling, Numero 14/703, 2021, ISSN 1937-9145
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Proteomics Standards Initiative's ProForma 2.0: Unifying the Encoding of Proteoforms and Peptidoforms

Autori: LeDuc, Richard D.; Deutsch, Eric W.; Binz, Pierre-Alain; Fellers, Ryan T.; Cesnik, Anthony J.; Klein, Joshua A.; Van den Bossche, Tim; Gabriels, Ralf; Yalavarthi, Arshika; Perez-Riverol, Yasset; Carver, Jeremy; Bittremieux, Wout; Kawano, Shin; Pullman, Benjamin; Bandeira, Nuno; Kelleher, Neil L.; Thomas, Paul M.; Vizcaino, Juan Antonio
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Universal Spectrum Explorer: A Standalone (Web-)Application for Cross-Resource Spectrum Comparison

Autori: 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
Pubblicato in: Journal of Proteome Research, Numero 20/6, 2021, Pagina/e 3388-3394, ISSN 1535-3893
Editore: American Chemical Society
DOI: 10.1021/acs.jproteome.1c00096

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

Autori: Dhenin J, Borges Lima D, Dupré M, Chamot-Rooke J.
Pubblicato in: Bioinformatics, 2021, ISSN 1367-4803
Editore: Oxford University Press
DOI: 10.1093/bioinformatics/btab784

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

Autori: Susana García-Silva, Pilar Ximénez-Embún, Javier Muñoz, Héctor Peinado
Pubblicato in: Melanoma - Methods and Protocols, Numero 2265, 2021, Pagina/e 345-359, ISBN 978-1-0716-1204-0
Editore: 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

Autori: Dorte B. Bekker-Jensen, Ana Martínez-Val, Sophia Steigerwald, Patrick Rüther, Kyle L. Fort, Tabiwang N. Arrey, Alexander Harder, Alexander Makarov, Jesper V. Olsen
Pubblicato in: Molecular & Cellular Proteomics, Numero 19/4, 2020, Pagina/e 716-729, ISSN 1535-9476
Editore: American Society for Biochemistry and Molecular Biology Inc.
DOI: 10.1074/mcp.tir119.001906

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