PMID- 37334365
OWN - NLM
STAT- MEDLINE
DCOM- 20230620
LR  - 20230623
IS  - 1664-3224 (Electronic)
IS  - 1664-3224 (Linking)
VI  - 14
DP  - 2023
TI  - SAPrIm, a semi-automated protocol for mid-throughput immunopeptidomics.
PG  - 1107576
LID - 10.3389/fimmu.2023.1107576 [doi]
LID - 1107576
AB  - Human leukocyte antigen (HLA) molecules play a crucial role in directing adaptive 
      immune responses based on the nature of their peptide ligands, collectively 
      coined the immunopeptidome. As such, the study of HLA molecules has been of major 
      interest in the development of cancer immunotherapies such as vaccines and T-cell 
      therapies. Hence, a comprehensive understanding and profiling of the 
      immunopeptidome is required to foster the growth of these personalised solutions. 
      We herein describe SAPrIm, an Immunopeptidomics tool for the Mid-Throughput era. 
      This is a semi-automated workflow involving the KingFisher platform to isolate 
      immunopeptidomes using anti-HLA antibodies coupled to a hyper-porous magnetic 
      protein A microbead, a variable window data independent acquisition (DIA) method 
      and the ability to run up to 12 samples in parallel. Using this workflow, we were 
      able to concordantly identify and quantify ~400 - 13000 unique peptides from 5e5 
      - 5e7 cells, respectively. Overall, we propose that the application of this 
      workflow will be crucial for the future of immunopeptidome profiling, especially 
      for mid-size cohorts and comparative immunopeptidomics studies.
CI  - Copyright (c) 2023 Lim Kam Sian, Goncalves, Steele, Shamekhi, Bramberger, Jin, 
      Shahbazy, Purcell, Ramarathinam, Stoychev and Faridi.
FAU - Lim Kam Sian, Terry C C
AU  - Lim Kam Sian TCC
AD  - Department of Medicine, School of Clinical Sciences, Faculty of Medicine, Nursing 
      & Health Sciences, Monash University, Clayton, VIC, Australia.
AD  - Monash Proteomics and Metabolomics Platform, Department of Biochemistry and 
      Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, 
      Clayton, VIC, Australia.
FAU - Goncalves, Gabriel
AU  - Goncalves G
AD  - Department of Medicine, School of Clinical Sciences, Faculty of Medicine, Nursing 
      & Health Sciences, Monash University, Clayton, VIC, Australia.
AD  - Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery 
      Institute, Monash University, Clayton, VIC, Australia.
FAU - Steele, Joel R
AU  - Steele JR
AD  - Monash Proteomics and Metabolomics Platform, Department of Biochemistry and 
      Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, 
      Clayton, VIC, Australia.
FAU - Shamekhi, Tima
AU  - Shamekhi T
AD  - Department of Medicine, School of Clinical Sciences, Faculty of Medicine, Nursing 
      & Health Sciences, Monash University, Clayton, VIC, Australia.
FAU - Bramberger, Liesl
AU  - Bramberger L
AD  - Department of Medicine, School of Clinical Sciences, Faculty of Medicine, Nursing 
      & Health Sciences, Monash University, Clayton, VIC, Australia.
FAU - Jin, Dongbin
AU  - Jin D
AD  - Department of Medicine, School of Clinical Sciences, Faculty of Medicine, Nursing 
      & Health Sciences, Monash University, Clayton, VIC, Australia.
FAU - Shahbazy, Mohammad
AU  - Shahbazy M
AD  - Department of Medicine, School of Clinical Sciences, Faculty of Medicine, Nursing 
      & Health Sciences, Monash University, Clayton, VIC, Australia.
AD  - Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery 
      Institute, Monash University, Clayton, VIC, Australia.
FAU - Purcell, Anthony W
AU  - Purcell AW
AD  - Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery 
      Institute, Monash University, Clayton, VIC, Australia.
FAU - Ramarathinam, Sri
AU  - Ramarathinam S
AD  - Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery 
      Institute, Monash University, Clayton, VIC, Australia.
FAU - Stoychev, Stoyan
AU  - Stoychev S
AD  - ReSyn Biosciences (Pty) Ltd., Pretoria, South Africa.
FAU - Faridi, Pouya
AU  - Faridi P
AD  - Department of Medicine, School of Clinical Sciences, Faculty of Medicine, Nursing 
      & Health Sciences, Monash University, Clayton, VIC, Australia.
AD  - Monash Proteomics and Metabolomics Platform, Department of Biochemistry and 
      Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, 
      Clayton, VIC, Australia.
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20230602
PL  - Switzerland
TA  - Front Immunol
JT  - Frontiers in immunology
JID - 101560960
RN  - 0 (Histocompatibility Antigens Class I)
RN  - 0 (Peptides)
RN  - 0 (HLA Antigens)
RN  - 0 (Histocompatibility Antigens Class II)
SB  - IM
MH  - Humans
MH  - *Histocompatibility Antigens Class I
MH  - *Peptides
MH  - HLA Antigens
MH  - Histocompatibility Antigens Class II
MH  - Immunotherapy
PMC - PMC10272402
OTO - NOTNLM
OT  - DIA
OT  - HLA-bound peptides
OT  - cancer antigen
OT  - human leukocyte antigen
OT  - immunopeptidomics
COIS- Author SS was employed by ReSyn Biosciences. The remaining authors declare that 
      the research was conducted in the absence of any commercial or financial 
      relationships that could be construed as a potential conflict of interest.
EDAT- 2023/06/19 06:42
MHDA- 2023/06/20 06:42
PMCR- 2023/01/01
CRDT- 2023/06/19 03:06
PHST- 2022/11/25 00:00 [received]
PHST- 2023/05/10 00:00 [accepted]
PHST- 2023/06/20 06:42 [medline]
PHST- 2023/06/19 06:42 [pubmed]
PHST- 2023/06/19 03:06 [entrez]
PHST- 2023/01/01 00:00 [pmc-release]
AID - 10.3389/fimmu.2023.1107576 [doi]
PST - epublish
SO  - Front Immunol. 2023 Jun 2;14:1107576. doi: 10.3389/fimmu.2023.1107576. 
      eCollection 2023.