PMID- 29314742
OWN - NLM
STAT- MEDLINE
DCOM- 20190816
LR  - 20240328
IS  - 1615-9861 (Electronic)
IS  - 1615-9853 (Print)
IS  - 1615-9853 (Linking)
VI  - 18
IP  - 12
DP  - 2018 Jun
TI  - The Role of Mass Spectrometry and Proteogenomics in the Advancement of HLA 
      Epitope Prediction.
PG  - e1700259
LID - 10.1002/pmic.201700259 [doi]
LID - 1700259
AB  - A challenge in developing personalized cancer immunotherapies is the prediction 
      of putative cancer-specific antigens. Currently, predictive algorithms are used 
      to infer binding of peptides to human leukocyte antigen (HLA) heterodimers to aid 
      in the selection of putative epitope targets. One drawback of current epitope 
      prediction algorithms is that they are trained on datasets containing biochemical 
      HLA-peptide binding data that may not completely capture the rules associated 
      with endogenous processing and presentation. The field of MS has made great 
      improvements in instrumentation speed and sensitivity, chromatographic 
      resolution, and proteogenomic database search strategies to facilitate the 
      identification of HLA-ligands from a variety of cell types and tumor tissues. As 
      such, these advances have enabled MS profiling of HLA-binding peptides to be a 
      tractable, orthogonal approach to lower throughput biochemical assays for 
      generating comprehensive datasets to train epitope prediction algorithms. In this 
      review, we will highlight the progress made in the field of HLA-ligand profiling 
      enabled by MS and its impact on current and future epitope prediction strategies.
CI  - (c) 2018 Neon Therapeutics. Proteomics Published by WILEY-VCH Verlag GmbH & Co. 
      KGaA, Weinheim.
FAU - Creech, Amanda L
AU  - Creech AL
AD  - Neon Therapeutics, Cambridge, MA, USA.
FAU - Ting, Ying S
AU  - Ting YS
AD  - Neon Therapeutics, Cambridge, MA, USA.
FAU - Goulding, Scott P
AU  - Goulding SP
AD  - Neon Therapeutics, Cambridge, MA, USA.
FAU - Sauld, John F K
AU  - Sauld JFK
AD  - Neon Therapeutics, Cambridge, MA, USA.
FAU - Barthelme, Dominik
AU  - Barthelme D
AD  - Neon Therapeutics, Cambridge, MA, USA.
FAU - Rooney, Michael S
AU  - Rooney MS
AD  - Neon Therapeutics, Cambridge, MA, USA.
FAU - Addona, Terri A
AU  - Addona TA
AD  - Neon Therapeutics, Cambridge, MA, USA.
FAU - Abelin, Jennifer G
AU  - Abelin JG
AD  - Neon Therapeutics, Cambridge, MA, USA.
LA  - eng
PT  - Journal Article
PT  - Review
DEP - 20180223
PL  - Germany
TA  - Proteomics
JT  - Proteomics
JID - 101092707
RN  - 0 (Epitopes)
RN  - 0 (HLA Antigens)
MH  - Computational Biology/*methods
MH  - Epitopes/*immunology/metabolism
MH  - HLA Antigens/*immunology/metabolism
MH  - Humans
MH  - Mass Spectrometry/*methods
MH  - Proteogenomics/*methods
PMC - PMC6033110
OTO - NOTNLM
OT  - cancer
OT  - epitope prediction
OT  - immunoproteomics
OT  - neoantigens
OT  - peptidomics
EDAT- 2018/01/10 06:00
MHDA- 2019/08/17 06:00
PMCR- 2018/07/05
CRDT- 2018/01/10 06:00
PHST- 2017/09/26 00:00 [received]
PHST- 2017/12/12 00:00 [revised]
PHST- 2018/01/10 06:00 [pubmed]
PHST- 2019/08/17 06:00 [medline]
PHST- 2018/01/10 06:00 [entrez]
PHST- 2018/07/05 00:00 [pmc-release]
AID - PMIC12795 [pii]
AID - 10.1002/pmic.201700259 [doi]
PST - ppublish
SO  - Proteomics. 2018 Jun;18(12):e1700259. doi: 10.1002/pmic.201700259. Epub 2018 Feb 
      23.