Topspec – Next generation precision antibody profiling – from science fiction to reality

Patents:

Biomotif:

METHOD FOR CAPILLARY ISOELECTRIC FOCUSING SEPARATION OF POLYPEPTIDES

Fasmatech:

SEGMENTED LINEAR ION TRAP FOR ENHANCED ION ACTIVATION AND STORAGE

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

APPARATUS AND METHOD FOR ION ANYALYSIS USING MASS SPECTROMETRY

Peer-reviewed articles:

Interlaboratory Study for Characterizing Monoclonal Antibodies by Top-Down and Middle-Down Mass Spectrometry. Srzentic K, Fornelli L, Tsybin YO, Loo JA, Seckler H, Agar JN, et al. J Am Soc Mass Spectrom. 2020;31(9):1783-802. 

Transient-Mediated Simulations of FTMS Isotopic Distributions and Mass Spectra to Guide Experiment Design and Data Analysis, Nagornov KO, Kozhinov AN, Gasilova N, Menin L, Tsybin YO. J Am Soc Mass Spectrom. 2020;31(9):1927-42.

Exploring frontiers of orbitrap performance for long transients, Denisov E, Damoc E, Makarov A. Int J Mass Spectrom. 2021;466.

Drug-to-Antibody Ratio Estimation via Proteoform Peak Integration in the Analysis of Antibody–Oligonucleotide Conjugates with Orbitrap Fourier Transform Masspectrometry, Nagornov KO, Gasilova N, Kozhinov AN, Virta P, Holm P, Menin L, et al. Anal Chem. 2021;93(38):12930-7.

The Human Proteoform Project: Defining the human proteome, Smith LM, Agar JN, Chamot-Rooke J, Danis PO, Ge Y, Loo JA, et al., Sci Adv. 2021;7(46):eabk0734.

TDFragMapper: a visualization tool for evaluating experimental parameters in top-down proteomics, Dhenin J, Lima DB, Dupre M, Chamot-Rooke J. Bioinformatics. 2021;38(4):1136-8.

Structural Analysis of Monoclonal Antibodies with Top-down and Middle-down Electron Transfer Dissociation Mass Spectrometry: The First Decade, Fornelli L, Ayoub D, Srzentic K, Nagornov KO, Kozhinov AN, Gasilova N, et al.Chimia. 2022;76(1-2):114-26.

Papanastasiou D, Kounadis D, Lekkas A, Orfanopoulos I, Mpozatzidis A, Smyrnakis A, et al. The Omnitrap Platform: A Versatile Segmented Linear Ion Trap for Multidimensional Multiple-Stage Tandem Mass Spectrometry. J Am Soc Mass Spectrom. 2022;33(10):1990-2007.

Other articles:

A Novel Family of Quadrupole-Orbitrap Mass Spectrometers for a Broad Range of Analytical Applications, Preprints.org, 08 Jun 2020

Next-generation precision antibody profiling; from science fiction to reality, Project Repository Journal. Zubarev, R.A. et al. Vol 15, 38-41, 07 Nov 2022

Adding colour to mass spectra: Charge Determination Analysis (CHARDA) assigns charge state to every ion peak, ChemRxiv, 17 Sept 2021

The TopSpec system: new levels in antibody charecterisation by top-down mass spectrometry, Project Repository Journal, Zubarev R.A. et al. Vol 16, Vol 16, 42-46, 23 Feb 2023

Post-project articles (published after project due date, January 2023)

The TopSpec system: new levels in antibody characterisation by top-down mass spectrometry (Project Repository Journal, Feb 2023).

Software:

Free:

Method development for top-down proteomics: FDFragMapper
TDFragMapper: a visualization tool for evaluating experimental parameters in top-down proteomics, Dhenin J, Lima DB, Dupre M, Chamot-Rooke J. Bioinformatics. 2021;38(4):1136-8.

New analysis tool for charge state determination in complex datasets: CHARDA
Adding colour to mass spectra: Charge Determination Analysis (CHARDA) assigns charge state to every ion peak, ChemRxiv, 17 Sept 2021

Other:

Autovectis:

Data repositories:

TDFragMapper: Evaluating experimental parameters for confident intact protein characterization in top-down proteomics

TopSpec platform (pI-trap/Orbitrap/Omnitrap) combined data

Omnitrap MS2 and MS3 data of Herceptin

TopSpec media

Posters:

ASMS_2020_FTMS_Simulator_Spectroswiss_Th553

ASMS_2020_Top_down_analysis_of_intact_mAb_on_the_omni-orbitrap_MS

ASMS_2022_Metaflows_Spectroswiss

ASMS_2022 _ poster_309295_OMNITRAP

IMSC22 Poster _ Top-down of mAbs

Presentations:

RZubarev TopSpec Ventura Feb 2019

IMSF Tsybin 16 March 2021 5 PM CET final

ASMS 2021 ADC Proteoforms Tsybin

2022_EUPA_ChamotRooke

2022_Proteovillamoura-ChamotRooke_Proteoforms and their expanding role
in biomedical research

EFTMS 2022 Tsybin FT Mass Spectra Simulation: Fundamentals and Applications

IMSC_2022_The Exclusive Ion Activation Arsenal of the Omnitrap

IMSC_2022_Omnitrap ExD in DDA mode

IMSC 2022 Targeted deconvolution feature extraction and annotation via time-domain transient modelling in Orbitrap FTMS for biopharma applications

EPIC-XS-workshop-Chamot-Rooke Intact protein analysis The expanding role of proteoforms in health and disease

20221024-update_TopSpec-IP-ChamotRooke

Other media:

Banner

TopSpec project video

With subtitles