PMID- 34391888
OWN - NLM
STAT- MEDLINE
DCOM- 20220324
LR  - 20220716
IS  - 1535-9484 (Electronic)
IS  - 1535-9476 (Print)
IS  - 1535-9476 (Linking)
VI  - 20
DP  - 2021
TI  - Optimized Liquid and Gas Phase Fractionation Increases HLA-Peptidome Coverage for 
      Primary Cell and Tissue Samples.
PG  - 100133
LID - S1535-9476(21)00105-5 [pii]
LID - 10.1016/j.mcpro.2021.100133 [doi]
LID - 100133
AB  - MS is the most effective method to directly identify peptides presented on human 
      leukocyte antigen (HLA) molecules. However, current standard approaches often use 
      500 million or more cells as input to achieve high coverage of the 
      immunopeptidome, and therefore, these methods are not compatible with the often 
      limited amounts of tissue available from clinical tumor samples. Here, we 
      evaluated microscaled basic reversed-phase fractionation to separate HLA peptide 
      samples offline followed by ion mobility coupled to LC-MS/MS for analysis. The 
      combination of these two separation methods enabled identification of 20% to 50% 
      more peptides compared with samples analyzed without either prior fractionation 
      or use of ion mobility alone. We demonstrate coverage of HLA immunopeptidomes 
      with up to 8107 distinct peptides starting with as few as 100 million cells. The 
      increased sensitivity obtained using our methods can provide data useful to 
      improve HLA-binding prediction algorithms as well as to enable detection of 
      clinically relevant epitopes such as neoantigens.
CI  - Copyright (c) 2021 The Authors. Published by Elsevier Inc. All rights reserved.
FAU - Klaeger, Susan
AU  - Klaeger S
AD  - Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA. Electronic 
      address: sklaeger@broadinstitute.org.
FAU - Apffel, Annie
AU  - Apffel A
AD  - Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
FAU - Clauser, Karl R
AU  - Clauser KR
AD  - Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
FAU - Sarkizova, Siranush
AU  - Sarkizova S
AD  - Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
FAU - Oliveira, Giacomo
AU  - Oliveira G
AD  - Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, 
      Massachusetts, USA.
FAU - Rachimi, Suzanna
AU  - Rachimi S
AD  - Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
FAU - Le, Phuong M
AU  - Le PM
AD  - Translational Immunogenomics Laboratory, Dana-Farber Cancer Institute, Boston, 
      Massachusetts, USA.
FAU - Tarren, Anna
AU  - Tarren A
AD  - Translational Immunogenomics Laboratory, Dana-Farber Cancer Institute, Boston, 
      Massachusetts, USA.
FAU - Chea, Vipheaviny
AU  - Chea V
AD  - Translational Immunogenomics Laboratory, Dana-Farber Cancer Institute, Boston, 
      Massachusetts, USA.
FAU - Abelin, Jennifer G
AU  - Abelin JG
AD  - Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
FAU - Braun, David A
AU  - Braun DA
AD  - Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA; Department of 
      Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA; 
      Harvard Medical School, Boston, Massachusetts, USA; Department of Medicine, 
      Brigham and Women's Hospital, Boston, Massachusetts, USA.
FAU - Ott, Patrick A
AU  - Ott PA
AD  - Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA; Department of 
      Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA; 
      Harvard Medical School, Boston, Massachusetts, USA; Department of Medicine, 
      Brigham and Women's Hospital, Boston, Massachusetts, USA.
FAU - Keshishian, Hasmik
AU  - Keshishian H
AD  - Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
FAU - Hacohen, Nir
AU  - Hacohen N
AD  - Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA; Massachusetts 
      General Hospital Cancer Center, Boston, Massachusetts, USA.
FAU - Keskin, Derin B
AU  - Keskin DB
AD  - Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, 
      Massachusetts, USA; Translational Immunogenomics Laboratory, Dana-Farber Cancer 
      Institute, Boston, Massachusetts, USA; Health Informatics Lab, Metropolitan 
      College, Boston University, Boston, Massachusetts, USA.
FAU - Wu, Catherine J
AU  - Wu CJ
AD  - Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA; Department of 
      Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA; 
      Harvard Medical School, Boston, Massachusetts, USA; Department of Medicine, 
      Brigham and Women's Hospital, Boston, Massachusetts, USA.
FAU - Carr, Steven A
AU  - Carr SA
AD  - Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA. Electronic 
      address: scarr@broad.mit.edu.
LA  - eng
GR  - P50 CA101942/CA/NCI NIH HHS/United States
GR  - U24 CA210986/CA/NCI NIH HHS/United States
GR  - T32 HG002295/HG/NHGRI NIH HHS/United States
GR  - U24 CA224331/CA/NCI NIH HHS/United States
GR  - R21 CA216772/CA/NCI NIH HHS/United States
GR  - R01 CA155010/CA/NCI NIH HHS/United States
GR  - R01 CA229261/CA/NCI NIH HHS/United States
GR  - U01 CA214125/CA/NCI NIH HHS/United States
PT  - Journal Article
PT  - Research Support, N.I.H., Extramural
PT  - Research Support, Non-U.S. Gov't
PT  - Research Support, U.S. Gov't, Non-P.H.S.
DEP - 20210812
PL  - United States
TA  - Mol Cell Proteomics
JT  - Molecular & cellular proteomics : MCP
JID - 101125647
RN  - 0 (Antigens, Neoplasm)
RN  - 0 (Histocompatibility Antigens Class I)
RN  - 0 (Peptides)
SB  - IM
MH  - Antigens, Neoplasm/*analysis
MH  - Cell Line
MH  - Chemical Fractionation
MH  - Chromatography, Liquid
MH  - Histocompatibility Antigens Class I/*analysis
MH  - Humans
MH  - Ion Mobility Spectrometry
MH  - Neoplasms/chemistry
MH  - Peptides/*analysis
MH  - Tandem Mass Spectrometry
PMC - PMC8724927
OTO - NOTNLM
OT  - FAIMS
OT  - HLA
OT  - basic reversed-phase fractionation
OT  - immunopeptidomics
OT  - ion mobility
COIS- Conflict of interest D. A. B. reported nonfinancial support from Bristol-Myers 
      Squibb, honoraria from LM Education/Exchange Services, and personal fees from 
      Octane Global, Defined Health, Dedham Group, Adept Field Solutions, Slingshot 
      Insights, Blueprint Partnerships, Charles River Associates, Trinity Group, and 
      Insight Strategy, outside the submitted work. P. A. O. has received research 
      funding from and has advised Neon Therapeutics, Bristol-Meyers Squibb, Merck, 
      CytomX, Pfizer, Novartis, Celldex, Amgen, Array, AstraZeneca/MedImmune, Armo 
      BioSciences, and Roche/Genentech, outside the submitted work. D. B. K. has 
      previously advised Neon Therapeutics and has received consulting fees from Neon 
      Therapeutics. D. B. K. owns equity in Agenus, Armata Pharmaceuticals, Breakbio, 
      BioMarin Pharmaceutical, Bristol Myers Squibb, Celldex Therapeutics, Chinook 
      Therapeutics, Editas Medicine, Exelixis, Gilead Sciences, IMV, Lexicon 
      Pharmaceuticals, Moderna, and Regeneron Pharmaceuticals. BeiGene, a Chinese 
      biotech company, supports unrelated research at TIGL. C. J. W. holds equity in 
      BioNTech, Inc and receives research funding from Pharmacyclics, Inc. S. A. C. is 
      a member of the scientific advisory boards of Kymera, PTM BioLabs, and Seer and 
      an ad hoc scientific advisor to Pfizer and Biogen. All the other authors declare 
      no competing interests.
EDAT- 2021/08/16 06:00
MHDA- 2022/03/25 06:00
PMCR- 2021/08/12
CRDT- 2021/08/15 20:39
PHST- 2021/02/22 00:00 [received]
PHST- 2021/07/08 00:00 [revised]
PHST- 2021/08/01 00:00 [accepted]
PHST- 2021/08/16 06:00 [pubmed]
PHST- 2022/03/25 06:00 [medline]
PHST- 2021/08/15 20:39 [entrez]
PHST- 2021/08/12 00:00 [pmc-release]
AID - S1535-9476(21)00105-5 [pii]
AID - 100133 [pii]
AID - 10.1016/j.mcpro.2021.100133 [doi]
PST - ppublish
SO  - Mol Cell Proteomics. 2021;20:100133. doi: 10.1016/j.mcpro.2021.100133. Epub 2021 
      Aug 12.