• Français

Proteomics and Immunopeptidomics Platform

The Proteomics and Immunopeptidomics Platform is equipped with a state-of-the-art Orbitrap Eclipse Tribrid mass spectrometer equipped with a FAIMS module, the first-of-its-kind in Canada, enabling a cutting-edge tumor antigen discovery program for the development of new immunotherapeutic strategies against cancer.

The platform was recently funded with a Canada Foundation for Innovation grant and will be expanding toward a mass spectrometry-based multi-omics platform to foster services and collaborations across the community in the different research themes. The platform delivers high-quality results and provides expertise in planning, designing, execution and data analysis, making the omics field accessible.

Equipement

  • Thermo Orbitrap Eclipse Tribrid- FAIMS module

Services

  • Immunopeptidomics
  • Discovery and targeted proteomics

Clientele

Academic, pharmaceutical or biotechnology industries interested in proteomics/metabolotmics analyses.

Financial partners

  • Fondation Charles-Bruneau
  • Grandir en santé Fund
  • Canada Foundation for Innovation
  • Fondation CHU Sainte-Justine

Team

Contact

Isabelle Sirois PhD 
Manager
514 345-4931, ext.5199 
isabelle.sirois.hsj@ssss.gouv.qc.ca 

Marc-André Déry, PhD
Scientific and Technical Specialist
514 345-4931, ext. 7396
marc-andre.dery.hsj@ssss.gouv.qc.ca 

Christopher Savoie
Bioinformatics Specialist
514 345-4931, ext. 6623
christopher.savoie.hsj@ssss.gouv.qc.ca

Zhaoguan Wu
Mass Spectrometry Specialist
514 345-4931, ext. 7313
zhaoguan.wu.hsj@ssss.gouv.qc.ca

Valérie Villeneuve
Representative, Core facilities
514 345-4931, ext. 2786
valerie.villeneuve.hsj@ssss.gouv.qc.ca

 

Publications

 

PROTOCOLS AND BIO-INFORMATIC TOOLS

  • THE GF-NEO DISCOVERY PLATFORM UNVEILS A [KQE][DG] SEQUENCE MOTIF WITHIN FUSION NEOANTIGENS IN PEDIATRIC CANCER
    iScience, February 20th 2026.
    Christopher Savoie, Zhaoguan Wu*, Frederic Saab*, Tristan St-Laurent, Lou Nielly Thibault, Charles B. Beauparlant, Marc-André Déry, Nehme El-Hachem, Bayrem Gharsallaoui, Samuel-Joseph Tremblay, Anna Sabouret, Nadia Emely Chauca Torres, Mélanie Bilodeau, Éric Bonneil, John Sidney, Alessandro Sette, Arnaud Droit, Pierre Thibault, Sonia Cellot, Étienne Caron, Isabelle Sirois.
  • THE GF-NEO DISCOVERY PLATFORM UNVEILS A [KQE][DG] SEQUENCE MOTIF WITHIN FUSION NEOANTIGENS IN PEDIATRIC CANCER
    iScience, October 30th 2025, Accepted in Principle
    Christopher Savoie, Zhaoguan Wu*, Frederic Saab*, Tristan St-Laurent, Lou Nielly Thibault, Charles B. Beauparlant, Marc-André Déry, Nehme El-Hachem, Bayrem Gharsallaoui, Samuel-Joseph Tremblay, Anna Sabouret, Nadia Emely Chauca Torres, Mélanie Bilodeau, Éric Bonneil, John Sidney, Alessandro Sette, Arnaud Droit, Pierre Thibault, Sonia Cellot, Étienne Caron ET Isabelle Sirois.
  • MHCVIZPIPE: A QUALITY CONTROL SOFTWARE FOR RAPID ASSESSMENT OF SMALL- TO LARGE-SCALE IMMUNOPEPTIDOME DATASETS
    Mol Cell Proteomics. 2022 Jan;21(1):100178
    Kovalchik KA, Ma Q, Wessling L, Saab F, Duquette JD, Kubiniok P, Hamelin DJ, Faridi P, Li C, Purcell AW, Jang A, Paramithiotis E, Tognetti M, Reiter L, Bruderer R, Lanoix J, Bonneil É, Courcelles M, Thibault P, Caron E, Sirois I. doi: 10.1016/j.mcpro.2021.100178. Epub 2021 Nov 17. PMID: 34798331; PMCID: PMC8717601.
  • IMMUNOPEPTIDOMICS: ISOLATION OF MOUSE AND HUMAN MHC CLASS I- AND II-ASSOCIATED PEPTIDES FOR MASS SPECTROMETRY ANALYSIS
    J Vis Exp. 2021 Oct 15;(176).
    Sirois I, Isabelle M, Duquette JD, Saab F, Caron E. doi: 10.3791/63052. PMID:34723952.
  • UNDERSTANDING THE CONSTITUTIVE PRESENTATION OF MHC CLASS I IMMUNOPEPTIDOMES IN PRIMARY TISSUES
    iScience. 2022 Jan 18;25(2)
    Kubiniok P, Marcu A, Bichmann L, Kuchenbecker L, Schuster H, Hamelin D, Duquette JD, Kovalchik KA, Wessling L, Kohlbacher O, Rammensee HG, Neidert MC, Sirois I, Caron E.  103768. doi:10.1016/j.isci.2022.103768. PMID: 35141507; PMCID: PMC8810409.
  • MACHINE LEARNING-ENHANCED IMMUNOPEPTIDOMICS APPLIED TO T-CELL EPITOPE DISCOVERY FOR COVID-19 VACCINES
    Nat Commun. 2024 Nov 28;15(1):10316
    Kovalchik KA, Hamelin DJ, Kubiniok P, Bourdin B, Mostefai F, Poujol R, Paré B, Simpson SM, Sidney J, Bonneil É, Courcelles M, Saini SK, Shahbazy M, Kapoor S, Rajesh V, Weitzen M, Grenier JC, Gharsallaoui B, Maréchal L, Wu Z, Savoie C, Sette A, Thibault P, Sirois I, Smith MA, Decaluwe H, Hussin JG, Lavallée-Adam M, Caron E. doi: 10.1038/s41467-024-54734-9. PMID: 39609459; PMCID: PMC11604954.
  • RHYBRIDFINDER: AN R PACKAGE TO PROCESS IMMUNOPEPTIDOMICS DATA FOR PUTATIVE HYBRID PEPTIDE DISCOVERY
    STAR Protoc. 2021 Oct 21;2(4):100875
    Saab F, Hamelin DJ, Ma Q, Kovalchik KA, Sirois I, Faridi P, Li C, Purcell AW, Kubiniok P, Caron E. doi: 10.1016/j.xpro.2021.100875. PMID: 34746858; PMCID: PMC8551247.

COLLABORATIVE PROJECTS IN IMMUNOPEPTIDOMICS

REVIEWS

About this page
Updated on 7/7/2026
Created on 7/6/2021
Alert or send a suggestion
 

Grow Beyond our wildest dreams

With the support of donors like you, at the heart of the Grow Beyond campaign, we are leading healthcare teams towards the opportunities offered by science and new technologies, so that every child, no matter where in Quebec, has access to the unique expertise and know-how of CHU Sainte-Justine. Together, let's join forces for their future.

Grow Beyond with us.

Contact Us

514 345-4931

Légal

© 2006-2014 CHU Sainte-Justine.
All rights reserved.
Terms of Use, Confidentiality, Security

Avertissement

Les informations contenues dans le site « CHU Sainte-Justine » ne doivent pas être utilisées comme un substitut aux conseils d’un médecin dûment qualifié et autorisé ou d’un autre professionnel de la santé. Les informations fournies ici le sont à des fins exclusivement éducatives et informatives.

Consultez votre médecin si vous croyez être malade ou composez le 911 pour toute urgence médicale.

CHU Sainte-Justine