PMID- 37142057
OWN - NLM
STAT- MEDLINE
DCOM- 20230626
LR  - 20231116
IS  - 1535-9484 (Electronic)
IS  - 1535-9476 (Print)
IS  - 1535-9476 (Linking)
VI  - 22
IP  - 6
DP  - 2023 Jun
TI  - Sensitive, High-Throughput HLA-I and HLA-II Immunopeptidomics Using Parallel 
      Accumulation-Serial Fragmentation Mass Spectrometry.
PG  - 100563
LID - S1535-9476(23)00073-7 [pii]
LID - 10.1016/j.mcpro.2023.100563 [doi]
LID - 100563
AB  - Comprehensive and in-depth identification of the human leukocyte antigen class I 
      (HLA-I) and class II (HLA-II) tumor immunopeptidome can inform the development of 
      cancer immunotherapies. Mass spectrometry (MS) is a powerful technology for 
      direct identification of HLA peptides from patient-derived tumor samples or cell 
      lines. However, achieving sufficient coverage to detect rare and clinically 
      relevant antigens requires highly sensitive MS-based acquisition methods and 
      large amounts of sample. While immunopeptidome depth can be increased by off-line 
      fractionation prior to MS, its use is impractical when analyzing limited amounts 
      of primary tissue biopsies. To address this challenge, we developed and applied a 
      high-throughput, sensitive, and single-shot MS-based immunopeptidomics workflow 
      that leverages trapped ion mobility time-of-flight MS on the Bruker timsTOF 
      single-cell proteomics system (SCP). We demonstrate greater than twofold improved 
      coverage of HLA immunopeptidomes relative to prior methods with up to 15,000 
      distinct HLA-I and HLA-II peptides from 4e7 cells. Our optimized single-shot MS 
      acquisition method on the timsTOF SCP maintains high coverage, eliminates the 
      need for off-line fractionation, and reduces input requirements to as few as 1e6 
      A375 cells for >800 distinct HLA-I peptides. This depth is sufficient to identify 
      HLA-I peptides derived from cancer-testis antigen and noncanonical proteins. We 
      also apply our optimized single-shot SCP acquisition methods to tumor-derived 
      samples, enabling sensitive, high-throughput, and reproducible immunopeptidome 
      profiling with detection of clinically relevant peptides from less than 4e7 cells 
      or 15 mg wet weight tissue.
CI  - Copyright (c) 2023 The Authors. Published by Elsevier Inc. All rights reserved.
FAU - Phulphagar, Kshiti Meera
AU  - Phulphagar KM
FAU - Ctortecka, Claudia
AU  - Ctortecka C
FAU - Jacome, Alvaro Sebastian Vaca
AU  - Jacome ASV
FAU - Klaeger, Susan
AU  - Klaeger S
FAU - Verzani, Eva K
AU  - Verzani EK
FAU - Hernandez, Gabrielle M
AU  - Hernandez GM
FAU - Udeshi, Namrata D
AU  - Udeshi ND
FAU - Clauser, Karl R
AU  - Clauser KR
FAU - Abelin, Jennifer G
AU  - Abelin JG
FAU - Carr, Steven A
AU  - Carr SA
LA  - eng
GR  - P01 CA206978/CA/NCI NIH HHS/United States
GR  - U01 CA271402/CA/NCI NIH HHS/United States
GR  - U24 CA270823/CA/NCI NIH HHS/United States
PT  - Journal Article
DEP - 20230503
PL  - United States
TA  - Mol Cell Proteomics
JT  - Molecular & cellular proteomics : MCP
JID - 101125647
RN  - 0 (Histocompatibility Antigens Class I)
RN  - 0 (Peptides)
SB  - IM
UOF - bioRxiv. 2023 Mar 18;:. PMID: 36993564
MH  - Male
MH  - Humans
MH  - *Histocompatibility Antigens Class I/metabolism
MH  - Mass Spectrometry/methods
MH  - *Neoplasms/metabolism
MH  - Peptides/metabolism
MH  - Cell Line
PMC - PMC10326702
OTO - NOTNLM
OT  - HLA-I and II immunopeptidomics
OT  - high-throughput acquisition
OT  - sensitive single-shot MS analysis
OT  - trapped ion mobility
COIS- Conflict of interest S. A. C. is a member of the scientific advisory boards of 
      Kymera, PTM BioLabs, Seer, and PrognomIQ. A.S.V.J. is an employee of Bruker. All 
      other authors declare no competing interests.
EDAT- 2023/05/05 00:42
MHDA- 2023/06/26 06:41
PMCR- 2023/05/03
CRDT- 2023/05/04 19:25
PHST- 2023/03/10 00:00 [received]
PHST- 2023/04/21 00:00 [revised]
PHST- 2023/04/24 00:00 [accepted]
PHST- 2023/06/26 06:41 [medline]
PHST- 2023/05/05 00:42 [pubmed]
PHST- 2023/05/04 19:25 [entrez]
PHST- 2023/05/03 00:00 [pmc-release]
AID - S1535-9476(23)00073-7 [pii]
AID - 100563 [pii]
AID - 10.1016/j.mcpro.2023.100563 [doi]
PST - ppublish
SO  - Mol Cell Proteomics. 2023 Jun;22(6):100563. doi: 10.1016/j.mcpro.2023.100563. 
      Epub 2023 May 3.