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Next generation precision antibody profiling - from science fiction to reality

Deliverables

Draft Exploitation plan and Business strategy document

Draft plan of Exploitation plan and Business strategy document delivered

Scientific reports and publications

Scientific reports and publications delivered

Public demonstrations of TopSpec technology
Logo and Website launch and public accessibility

Project logo and website launch and public accessibility. Site will be constantly maintained and updated.

Prototype pI-Trap-ESI installed and tested- protocol

One prototype of the pI-Trap-ESI installed and tested at KI – protocol of test

IP protection strategy finalized

Publications

Exploring frontiers of orbitrap performance for long transients

Author(s): Eduard Denisov, Eugen Damoc, Alexander Makarov
Published in: International Journal of Mass Spectrometry, Issue 466, 2021, Page(s) 116607, ISSN 1387-3806
Publisher: Elsevier BV
DOI: 10.1016/j.ijms.2021.116607

Transient-Mediated Simulations of FTMS Isotopic Distributions and Mass Spectra to Guide Experiment Design and Data Analysis.

Author(s): Konstantin O. Nagornov; Anton N. Kozhinov; Natalia Gasilova; Laure Menin; Yury O. Tsybin
Published in: J. Am. Soc. Mass Spectrom., Issue 1, 2020, Page(s) 1927-1942, ISSN 1044-0305
Publisher: Elsevier BV
DOI: 10.1021/jasms.0c00190

Structural Analysis of Monoclonal Antibodies with Top-down and Middle-down Electron Transfer Dissociation Mass Spectrometry: The First Decade

Author(s): Fornelli, L., Ayoub, D., Srzentic, K. Nagornov, K. O. Kozhinov, A. N. Gasilova, N. Menin, L. Beck, A. Tsybin, Y. O.
Published in: Chimia, Issue 2, 2022, Page(s) 114-126, ISSN 0009-4293
Publisher: Schweizerische Chemische Gedellschaft
DOI: 10.2533/chimia.2022.114

The Omnitrap Platform: A Versatile Segmented Linear Ion Trap for Multidimensional Multiple-Stage Tandem Mass Spectrometry

Author(s): Dimitris Papanastasiou, Diamantis Kounadis, Alexandros Lekkas, Ioannis Orfanopoulos, Andreas Mpozatzidis, Athanasios Smyrnakis, Elias Panagiotopoulos, Mariangela Kosmopoulou, Maria Reinhardt-Szyba, Kyle Fort, Alexander Makarov, and Roman A. Zubarev
Published in: J. Am. Soc. Mass Spectrom., Issue 3, 2021, Page(s) 1990–2007, ISSN 1044-0305
Publisher: Elsevier BV
DOI: 10.1021/jasms.2c00214

Drug-to-Antibody Ratio Estimation via Proteoform Peak Integration in the Analysis of Antibody-Oligonucleotide Conjugates with Orbitrap Fourier Transform Mass Spectrometry.

Author(s): Konstantin O. Nagornov; Natalia Gasilova; Anton N. Kozhinov; Pasi Virta; Patrik Holm; Laure Menin; Victor J Nesatyy; Yury O. Tsybin
Published in: Anal Chem, Issue 14/9, 2021, Page(s) 12930–12937, ISSN 1520-6882
Publisher: ACS Publications
DOI: 10.1021/acs.analchem.1c02247

The Human Proteoform Project: Defining the human proteome

Author(s): Smith, L. M., Agar, J. N., Chamot-Rooke, J., Danis, P. O., Ge, Y., Loo, J. A., Pasa-Tolic, L., Tsybin, Y.O.. Kelleher, N. L. Consortium for Top-Down, Proteomics
Published in: Sci Adv, Issue 12/11, 2021, Page(s) eabk0734, ISSN 2375-2548
Publisher: Sciense.org
DOI: 10.1126/sciadv.abk0734

Interlaboratory Study for Characterizing Monoclonal Antibodies by Top-Down and Middle-Down Mass Spectrometry.

Author(s): Kristina Srzentić; Luca Fornelli; Yury O. Tsybin; Joseph A. Loo; Henrique S. Seckler; Jeffrey N. Agar; Lissa C. Anderson; Dina L. Bai; Alain Beck; Jennifer S. Brodbelt; Yuri E. M. van der Burgt; Julia Chamot-Rooke; Sneha Chatterjee; Yunqiu Chen; David Clarke; Paul O. Danis; Jolene K. Diedrich; Robert Anthony D’Ippolito; Mathieu Dupré; Natalia Gasilova; Ying Ge; Young Ah Goo; David R. Goodlett;
Published in: J Am Soc Mass Spectrom, Issue 1, 2020, Page(s) 1783-1802, ISSN 1044-0305
Publisher: Elsevier BV
DOI: 10.1021/jasms.0c00036

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

Author(s): Dhenin, J., Lima, D. B., Dupre, M., Chamot-Rooke, J.
Published in: Bioinformatics, Issue 18/11, 2021, Page(s) 1136-8, ISSN 1367-4811
Publisher: Oxford Academic
DOI: 10.1093/bioinformatics/btab784

Adding colour to mass spectra: Charge Determination Analysis (CHARDA) assigns charge state to every ion peak

Author(s): Y. Lyutvinskiy, K.O. Nagornov, A.N. Kozhinov, N. Gasilova, L. Menin, Z. Meng, X. Zhang, A. Ata Saei, Y.O. Tsybin, A. Makarov, R.A. Zubarev
Published in: ChemRxiv, Issue 17/9, 2021
Publisher: Cambridge University Press
DOI: 10.26434/chemrxiv-2021-f6n9j

A Novel Family of Quadrupole-Orbitrap Mass Spectrometers for a Broad Range of Analytical Applications

Author(s): Jan-Peter Hauschild, Amelia Peterson, Erik Couzijn, Eduard Denisov, Denis Chernyshev, Christian Hock, Hamish Stewart, Ralf Hartmer, Dmitry Grinfeld, Christian Thoeing, Bastian Reitemeier, Arne Kreutzmann, Oliver Lange, Wilko Balschun, Aivaras Venckus, Sebastian Kanngiesser, Alexander Kholomeev, Gregor Quiring, Frank Czemper, Eloy Wouters, Michael Belford, Mathias Mueller, Jens Grote, Tabiwang N
Published in: Preprints, Issue 7, 2020
Publisher: Preprints.org
DOI: 10.20944/preprints202006.0111.v1

Next-generation precision antibody profiling; from science fiction to reality

Author(s): Roman Zubarev, Dimitris Papanastasiou, Alexander Makarov, Yury Tsybin, Thorleif Lavold,David Kilgour, Julia Chamot-Rooke, Jan Commandeur
Published in: The Project Repository Journal, Issue Volume 15, 2022, Page(s) 38-41
Publisher: EDMA
DOI: 10.54050/prj1519532

The TopSpec system: new levels in antibody characterisation by top-down mass spectrometry

Author(s): Roman A. Zubarev, Dimitris Papanastasiou, Julia Chamot-Rooke, Yury O. Tsybin, Alexander Makarov, David P A Kilgour, Thorleif Lavold, Jan Commandeur
Published in: The Project Repository Journal, Issue Volume 16, 2023, Page(s) 42-46
Publisher: EDMA
DOI: 10.54050/prj1619878

Intellectual Property Rights

ANALYSIS OF FRAGMENT IONS BY ION MOBILITY SEPARATION FOLLOWED BY MASS ANALYSIS

Application/Publication number: 19 174615
Date: 2019-05-15
Applicant(s): FASMATECH EPISTIMONIKI KAI TECHNOLOGIKI ANONYMI ETAIREIA

SEGMENTED LINEAR ION TRAP FOR ENHANCED ION ACTIVATION AND STORAGE

Application/Publication number: 17 704530
Date: 2017-02-02
Applicant(s): FASMATECH EPISTIMONIKI KAI TECHNOLOGIKI ANONYMI ETAIREIA

METHOD FOR CAPILLARY ISOELECTRIC FOCUSING SEPARATION OF POLYPEPTIDES

Application/Publication number: 20 21064686
Date: 2021-06-01
Applicant(s): BIOMOTIF AB

APPARATUS AND METHOD FOR ION ANYALYSIS USING MASS SPECTROMETRY

Application/Publication number: 21 170210
Date: 2021-04-23
Applicant(s): FASMATECH EPISTIMONIKI KAI TECHNOLOGIKI ANONYMI ETAIREIA

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