PMID- 38356658
OWN - NLM
STAT- PubMed-not-MEDLINE
LR  - 20240216
IS  - 2001-0370 (Print)
IS  - 2001-0370 (Electronic)
IS  - 2001-0370 (Linking)
VI  - 23
DP  - 2024 Dec
TI  - Enhancing Mass spectrometry-based tumor immunopeptide identification: machine 
      learning filter leveraging HLA binding affinity, aliphatic index and retention 
      time deviation.
PG  - 859-869
LID - 10.1016/j.csbj.2024.01.023 [doi]
AB  - Accurately identifying neoantigens is crucial for developing effective cancer 
      vaccines and improving tumor immunotherapy. Mass spectrometry-based 
      immunopeptidomics has emerged as a promising approach to identifying human 
      leukocyte antigen (HLA) peptides presented on the surface of cancer cells, but 
      false-positive identifications remain a significant challenge. In this study, 
      liquid chromatography-tandem mass spectrometry-based proteomics and 
      next-generation sequencing were utilized to identify HLA-presenting neoantigenic 
      peptides resulting from non-synonymous single nucleotide variations in tumor 
      tissues from 18 patients with renal cell carcinoma or pancreatic cancer. Machine 
      learning was utilized to evaluate Mascot identifications through the prediction 
      of MS/MS spectral consistency, and four descriptors for each candidate sequence: 
      the max Mascot ion score, predicted HLA binding affinity, aliphatic index and 
      retention time deviation, were selected as important features in filtering out 
      identifications with inadequate fragmentation consistency. This suggests that 
      incorporating rescoring filters based on peptide physicochemical characteristics 
      could enhance the identification rate of MS-based immunopeptidomics compared to 
      the traditional Mascot approach predominantly used for proteomics, indicating the 
      potential for optimizing neoantigen identification pipelines as well as clinical 
      applications.
CI  - (c) 2024 The Authors.
FAU - Wei, Feifei
AU  - Wei F
AD  - Division of Cancer Immunotherapy, Kanagawa Cancer Center Research Institute, 
      Yokohama, Japan.
AD  - Cancer Vaccine and Immunotherapy Center, Kanagawa Cancer Center, Yokohama, Japan.
FAU - Kouro, Taku
AU  - Kouro T
AD  - Division of Cancer Immunotherapy, Kanagawa Cancer Center Research Institute, 
      Yokohama, Japan.
AD  - Cancer Vaccine and Immunotherapy Center, Kanagawa Cancer Center, Yokohama, Japan.
FAU - Nakamura, Yuko
AU  - Nakamura Y
AD  - Isotope Science Center, The University of Tokyo, Tokyo, Japan.
FAU - Ueda, Hiroki
AU  - Ueda H
AD  - Research Center for Advanced Science and Technology, The University of Tokyo, 
      Tokyo, Japan.
FAU - Iiizumi, Susumu
AU  - Iiizumi S
AD  - Division of Cancer Immunotherapy, Kanagawa Cancer Center Research Institute, 
      Yokohama, Japan.
AD  - Research & Early Development Division, BrightPath Biotherapeutics Co., Ltd., 
      Kawasaki, Japan.
FAU - Hasegawa, Kyoko
AU  - Hasegawa K
AD  - Division of Cancer Immunotherapy, Kanagawa Cancer Center Research Institute, 
      Yokohama, Japan.
AD  - Research & Early Development Division, BrightPath Biotherapeutics Co., Ltd., 
      Kawasaki, Japan.
FAU - Asahina, Yuki
AU  - Asahina Y
AD  - Division of Cancer Immunotherapy, Kanagawa Cancer Center Research Institute, 
      Yokohama, Japan.
FAU - Kishida, Takeshi
AU  - Kishida T
AD  - Department of Urology, Kanagawa Cancer Center, Yokohama, Japan.
FAU - Morinaga, Soichiro
AU  - Morinaga S
AD  - Department of Hepato-Biliary and Pancreatic Surgery, Kanagawa Cancer Center, 
      Yokohama, Japan.
FAU - Himuro, Hidetomo
AU  - Himuro H
AD  - Division of Cancer Immunotherapy, Kanagawa Cancer Center Research Institute, 
      Yokohama, Japan.
AD  - Cancer Vaccine and Immunotherapy Center, Kanagawa Cancer Center, Yokohama, Japan.
FAU - Horaguchi, Shun
AU  - Horaguchi S
AD  - Division of Cancer Immunotherapy, Kanagawa Cancer Center Research Institute, 
      Yokohama, Japan.
AD  - Cancer Vaccine and Immunotherapy Center, Kanagawa Cancer Center, Yokohama, Japan.
AD  - Department of Pediatric Surgery, Nihon University School of Medicine, Tokyo, 
      Japan.
FAU - Tsuji, Kayoko
AU  - Tsuji K
AD  - Division of Cancer Immunotherapy, Kanagawa Cancer Center Research Institute, 
      Yokohama, Japan.
AD  - Cancer Vaccine and Immunotherapy Center, Kanagawa Cancer Center, Yokohama, Japan.
FAU - Mano, Yasunobu
AU  - Mano Y
AD  - Division of Cancer Immunotherapy, Kanagawa Cancer Center Research Institute, 
      Yokohama, Japan.
AD  - Cancer Vaccine and Immunotherapy Center, Kanagawa Cancer Center, Yokohama, Japan.
FAU - Nakamura, Norihiro
AU  - Nakamura N
AD  - Research & Early Development Division, BrightPath Biotherapeutics Co., Ltd., 
      Kawasaki, Japan.
FAU - Kawamura, Takeshi
AU  - Kawamura T
AD  - Isotope Science Center, The University of Tokyo, Tokyo, Japan.
FAU - Sasada, Tetsuro
AU  - Sasada T
AD  - Division of Cancer Immunotherapy, Kanagawa Cancer Center Research Institute, 
      Yokohama, Japan.
AD  - Cancer Vaccine and Immunotherapy Center, Kanagawa Cancer Center, Yokohama, Japan.
LA  - eng
PT  - Journal Article
DEP - 20240203
PL  - Netherlands
TA  - Comput Struct Biotechnol J
JT  - Computational and structural biotechnology journal
JID - 101585369
PMC - PMC10864759
OTO - NOTNLM
OT  - Aliphatic index
OT  - Immunopeptidomics
OT  - Machine learning
OT  - Mass spectrometry
COIS- Tetsuro Sasada received honoraria from Chugai and Bristol Myers Squibb, and 
      research funds from Taiho.
EDAT- 2024/02/15 06:43
MHDA- 2024/02/15 06:44
PMCR- 2024/02/03
CRDT- 2024/02/15 04:00
PHST- 2023/11/02 00:00 [received]
PHST- 2024/01/31 00:00 [revised]
PHST- 2024/01/31 00:00 [accepted]
PHST- 2024/02/15 06:44 [medline]
PHST- 2024/02/15 06:43 [pubmed]
PHST- 2024/02/15 04:00 [entrez]
PHST- 2024/02/03 00:00 [pmc-release]
AID - S2001-0370(24)00023-0 [pii]
AID - 10.1016/j.csbj.2024.01.023 [doi]
PST - epublish
SO  - Comput Struct Biotechnol J. 2024 Feb 3;23:859-869. doi: 
      10.1016/j.csbj.2024.01.023. eCollection 2024 Dec.