February 24, 2023 @ 2:00 p.m. (JST)

Feb 24 @ 7 AM (CEST) / Feb 23 @ 9 PM (PDT) / Feb 23 @ 11 PM (CST) 


Dr. Si Wu

(Oklahoma University, U.S.A.)


Dr. Rachel R. Ogorzalek Loo

(University of California, Los Angeles, U.S.A.) 


Dr. Julia Chamot-Rooke 

(Pasteur Institute, France)

About the webinar

Nobuaki Takemori, Organizer

(Ehime University, Japan) 


Top-down proteomics, which enables large-scale analysis of proteoforms in vivo, is a cutting-edge field of proteomics. JPrOS held its first webinar last summer, inviting five leading researchers to share their expertise with the up-and-coming generation of scientists who will one day be at the forefront of proteomics technology in Japan. In this long-awaited second webinar, three distinguished researchers will present exciting lectures further deepen our understanding of top-down proteomics.


Quantitative Analysis Techniques in Top-Down Proteomics

Top-down proteomics enables highly accurate identification of intact proteoforms, but how can we obtain quantitative information on proteoforms? Are the quantitative analysis techniques used in bottom-up proteomics, such as multiplex quantification using isobaric reagents, applicable in top-down proteomics? Dr. Si Wu will explain the principles of quantitative analysis in top-down proteomics and also introduce the TMT labelling technique for intact proteoforms developed by her group.


References for this lecture

Optimization of Higher-Energy Collisional Dissociation Fragmentation Energy for Intact Protein-Level Tandem Mass Tag Labeling.

Guo Y, Chowdhury T, Seshadri M, Cupp-Sutton KA, Wang Q, Yu D, Wu S.

J Proteome Res. 2023 (doi: 10.1021/acs.jproteome.2c00549)


Optimization of protein-level tandem mass tag (TMT) labeling conditions in complex samples with top-down proteomics.

Guo Y, Yu D, Cupp-Sutton KA, Liu X, Wu S.

Anal Chim Acta. 2022 (doi: 10.1016/j.aca.2022.340037)

Gel Electrophoresis in Top-Down Proteomics

In the history of proteomics, protein electrophoresis such as two-dimensional gel electrophoresis and SDS-PAGE have always been important proteome separation techniques. Then what is the role of gel electrophoresis in top-down proteomics? Dr. Rachel R. Ogorzalek Loo, a pioneer in combined gel electrophoresis and mass spectrometry research, explains the role of gel electrophoresis in the era of top-down proteomics.


References for this lecture

The Acyl-Proteome of Syntrophus aciditrophicus Reveals Metabolic Relationships in Benzoate Degradation.

Muroski JM, Fu JY, Nguyen HH, Wofford NQ, Mouttaki H, James KL, McInerney MJ, Gunsalus RP, Loo JA, Ogorzalek Loo RR.

Mol Cell Proteomics. 2022 (doi: 10.1016/j.mcpro.2022.100215)


Dynamic acylome reveals metabolite driven modifications in Syntrophomonas wolfei.

Fu JY, Muroski JM, Arbing MA, Salguero JA, Wofford NQ, McInerney MJ, Gunsalus RP, Loo JA, Ogorzalek Loo RR.

Front Microbiol. 2022 (doi: 10.3389/fmicb.2022.1018220) 

Biological Research using Top-Down Proteomics

In addition to understanding the technical features of top-down proteomics, it is also necessary to master the specific experimental strategies for using these techniques to interpret biological phenomena. Dr. Julia Chamot-Rooke will give a lecture on the importance of top-down proteomics in the life sciences by presenting excellent practical examples of using proteoform information obtained by top-down proteomics using state-of-the-art mass spectrometry systems for the discrimination of bacterial pathogens.


References for this lecture

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

Dupré M, Duchateau M, Malosse C, Borges-Lima D, Calvaresi V, Podglajen I, Clermont D, Rey M, Chamot-Rooke J.

J Proteome Res. 2021 (doi: 10.1021/acs.jproteome.0c00351) 


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

Borges Lima D, Dupré M, Mariano Santos MD, Carvalho PC, Chamot-Rooke J.

J Am Soc Mass Spectrom. 2021 (doi: 10.1021/jasms.1c00014) 

time table

Time (JST) 








Nobuaki Takemori

(Ehime Univ.)

Opening Remarks


Si Wu

(Oklahoma Univ.)

Quantitative Analysis Techniques in Top-Down Proteomics

Rachel Loo


Proteomics: Top-Down, Bottom-Up, and Side-to-Side

Julia Chamot-Rooke

(Pasteur Inst.)

The Expanding Role of Proteoforms in Infectious Diseases

register now!!

This zoom webinar is free of charge and open all, including non-members!


A link to participate in the JPrOS webinar will be sent to your registered e-mail address. If you do not receive the link on that day, please contact us.


For inquiries about the webinar: takemori(at)m.ehime-u.ac.jp  


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previous webinar (August 7, 2022)

JPROS Webinar Part 1.pdf
Adobe Acrobat Document 2.0 MB