Title:
METHOD FOR IDENTIFYING SPLICING PEPTIDE
Document Type and Number:
WIPO Patent Application WO/2023/008321
Kind Code:
A1
Abstract:
Provided is a method for identifying an unknown splicing peptide derived from a known parent peptide included in a biological sample, wherein the method includes: (1) a first step for obtaining mass spectrometry data pertaining to peptides included in the sample by implementing mass spectrometry of the sample; (2) a second step for searching a primary library, which is a database of known amino acid sequences, for an amino acid sequence that matches the mass spectrometry data, and identifying the parent peptide included in the sample; (3) a third step for creating a secondary library including candidates of splicing peptides that can be produced from the identified parent peptide; and (4) a fourth step for searching the secondary library for an amino acid sequence that matches the mass spectrometry data, and identifying the splicing peptide included in the sample.
Inventors:
KOGUCHI YOSHINOBU (US)
IWAMOTO NORIKO (US)
SHIMADA TAKASHI (US)
IWAMOTO NORIKO (US)
SHIMADA TAKASHI (US)
Application Number:
PCT/JP2022/028431
Publication Date:
February 02, 2023
Filing Date:
July 22, 2022
Export Citation:
Assignee:
PROVIDENCE HEALTH & SERVICES OREGON (US)
SHIMADZU CORP (JP)
SHIMADZU CORP (JP)
International Classes:
C07K2/00
Foreign References:
| EP2362225A1 | 2011-08-31 | |||
| EP2362225A1 | 2011-08-31 |
Other References:
ZHANG XIAOMEI; QI YUE; ZHANG QI; LIU WEI: "Application of mass spectrometry-based MHC immunopeptidome profiling in neoantigen identification for tumor immunotherapy", BIOMEDICINE & PHARMACOTHERAPY, ELSEVIER, FR, vol. 120, 16 October 2019 (2019-10-16), FR , XP085902745, ISSN: 0753-3322, DOI: 10.1016/j.biopha.2019.109542
VIGNERON NATHALIE; STROOBANT VINCENT; FERRARI VIOLETTE; ABI HABIB JOANNA; VAN DEN EYNDE BENOIT J.: "Production of spliced peptides by the proteasome", MOLECULAR IMMUNOLOGY, PERGAMON, GB, vol. 113, 9 April 2018 (2018-04-09), GB , pages 93 - 102, XP085827286, ISSN: 0161-5890, DOI: 10.1016/j.molimm.2018.03.030
MISHTO MICHELE, RODRIGUEZ-HERNANDEZ GUILLERMO, NEEFJES JACQUES, URLAUB HENNING, LIEPE JULIANE: "Response: Commentary: An In Silico–In Vitro Pipeline Identifying an HLA-A*02:01+ KRAS G12V+ Spliced Epitope Candidate for a Broad Tumor-Immune Response in Cancer Patients", FRONTIERS IN IMMUNOLOGY, vol. 12, XP093029771, DOI: 10.3389/fimmu.2021.679836
LICHTI CHERYL F., VIGNERON NATHALIE, CLAUSER KARL R., VAN DEN EYNDE BENOIT J., BASSANI-STERNBERG MICHAL: "Navigating Critical Challenges Associated with Immunopeptidomics-Based Detection of Proteasomal Spliced Peptide Candidates", CANCER IMMUNOLOGY RESEARCH, AMERICAN ASSOCIATION FOR CANCER RESEARCH, US, vol. 10, no. 3, 1 March 2022 (2022-03-01), US , pages 275 - 284, XP093029772, ISSN: 2326-6066, DOI: 10.1158/2326-6066.CIR-21-0727
VERKERK TAMARA, KOOMEN SOFIE J. I., FUCHS KYRA J., GRIFFIOEN MARIEKE, SPAAPEN ROBBERT M.: "An unexplored angle: T cell antigen discoveries reveal a marginal contribution of proteasome splicing to the immunogenic MHC class I antigen pool", PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES, NATIONAL ACADEMY OF SCIENCES, vol. 119, no. 29, 19 July 2022 (2022-07-19), XP093029775, ISSN: 0027-8424, DOI: 10.1073/pnas.2119736119
VIGNERON NATHALIE; STROOBANT VINCENT; FERRARI VIOLETTE; ABI HABIB JOANNA; VAN DEN EYNDE BENOIT J.: "Production of spliced peptides by the proteasome", MOLECULAR IMMUNOLOGY, PERGAMON, GB, vol. 113, 9 April 2018 (2018-04-09), GB , pages 93 - 102, XP085827286, ISSN: 0161-5890, DOI: 10.1016/j.molimm.2018.03.030
MISHTO MICHELE, RODRIGUEZ-HERNANDEZ GUILLERMO, NEEFJES JACQUES, URLAUB HENNING, LIEPE JULIANE: "Response: Commentary: An In Silico–In Vitro Pipeline Identifying an HLA-A*02:01+ KRAS G12V+ Spliced Epitope Candidate for a Broad Tumor-Immune Response in Cancer Patients", FRONTIERS IN IMMUNOLOGY, vol. 12, XP093029771, DOI: 10.3389/fimmu.2021.679836
LICHTI CHERYL F., VIGNERON NATHALIE, CLAUSER KARL R., VAN DEN EYNDE BENOIT J., BASSANI-STERNBERG MICHAL: "Navigating Critical Challenges Associated with Immunopeptidomics-Based Detection of Proteasomal Spliced Peptide Candidates", CANCER IMMUNOLOGY RESEARCH, AMERICAN ASSOCIATION FOR CANCER RESEARCH, US, vol. 10, no. 3, 1 March 2022 (2022-03-01), US , pages 275 - 284, XP093029772, ISSN: 2326-6066, DOI: 10.1158/2326-6066.CIR-21-0727
VERKERK TAMARA, KOOMEN SOFIE J. I., FUCHS KYRA J., GRIFFIOEN MARIEKE, SPAAPEN ROBBERT M.: "An unexplored angle: T cell antigen discoveries reveal a marginal contribution of proteasome splicing to the immunogenic MHC class I antigen pool", PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES, NATIONAL ACADEMY OF SCIENCES, vol. 119, no. 29, 19 July 2022 (2022-07-19), XP093029775, ISSN: 0027-8424, DOI: 10.1073/pnas.2119736119
Attorney, Agent or Firm:
FUKAMI PATENT OFFICE, P.C. (JP)
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