PMID- 32359108
OWN - NLM
STAT- MEDLINE
DCOM- 20210607
LR  - 20210607
IS  - 1615-9861 (Electronic)
IS  - 1615-9853 (Linking)
VI  - 20
IP  - 12
DP  - 2020 Jun
TI  - The Choice of HLA-Associated Peptide Enrichment and Purification Strategy Affects 
      Peptide Yields and Creates a Bias in Detected Sequence Repertoire.
PG  - e1900401
LID - 10.1002/pmic.201900401 [doi]
AB  - Understanding the most appropriate workflow for biochemical human leukocyte 
      antigen (HLA)-associated peptide enrichment prior to ligand sequencing is 
      essential to achieve optimal sensitivity in immunopeptidomics experiments. The 
      use of different detergents for HLA solubilization as well as complementary 
      workflows to separate HLA-bound peptides from HLA protein complex components 
      after their immunoprecipitation including HPLC, C18 cartridge, and 5 kDa filter 
      are described. It is observed that all solubilization approaches tested led to 
      similar peptide ligand identification rates; however, a higher number of peptides 
      are identified in samples lysed with CHAPS compared with other methods. The HPLC 
      method is superior in terms of HLA-I peptide recovery compared with 5 kDa filter 
      and C18 cartridge peptide purification methods. Most importantly, it is observed 
      that both the choice of detergent and peptide purification strategy creates a 
      significant bias for the identified peptide sequences, and that allele-specific 
      peptide repertoires are affected depending on the workflow of choice. The results 
      highlight the importance of employing a suitable strategy for HLA peptide 
      enrichment and that the obtained peptide repertoires do not necessarily reflect 
      the true distributions of peptide sequences in the sample.
CI  - (c) 2020 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
FAU - Nicastri, Annalisa
AU  - Nicastri A
AUID- ORCID: 0000-0002-1895-0317
AD  - The Jenner Institute, Nuffield Department of Medicine, University of Oxford, 
      Oxford, OX3 7BN, UK.
FAU - Liao, Hanqing
AU  - Liao H
AD  - The Jenner Institute, Nuffield Department of Medicine, University of Oxford, 
      Oxford, OX3 7BN, UK.
FAU - Muller, Julius
AU  - Muller J
AD  - Molecular Health GmbH, Heidelberg, 69115, Germany.
FAU - Purcell, Anthony W
AU  - Purcell AW
AUID- ORCID: 0000-0003-0532-8331
AD  - Department of Biochemistry and Molecular Biology and Infection and Immunity 
      Program, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, 
      3800, Australia.
FAU - Ternette, Nicola
AU  - Ternette N
AD  - The Jenner Institute, Nuffield Department of Medicine, University of Oxford, 
      Oxford, OX3 7BN, UK.
LA  - eng
PT  - Journal Article
DEP - 20200602
PL  - Germany
TA  - Proteomics
JT  - Proteomics
JID - 101092707
RN  - 0 (Detergents)
RN  - 0 (HLA Antigens)
RN  - 0 (Histocompatibility Antigens Class I)
RN  - 0 (Peptides)
RN  - 0 (Proteome)
SB  - IM
EIN - Proteomics. 2020 Dec;20(24):e2070175. PMID: 33325653
MH  - Amino Acid Sequence
MH  - Chromatography, High Pressure Liquid/methods
MH  - Detergents/chemistry
MH  - HLA Antigens/immunology/isolation & purification/*metabolism
MH  - Histocompatibility Antigens Class I/immunology/isolation & 
      purification/*metabolism
MH  - Humans
MH  - Peptides/immunology/isolation & purification/*metabolism
MH  - Proteome/immunology/*metabolism
MH  - Proteomics/*methods
OTO - NOTNLM
OT  - detergents
OT  - human leukocyte antigen class I molecules
OT  - immunopeptidomics
OT  - purification strategy
EDAT- 2020/05/03 06:00
MHDA- 2021/06/08 06:00
CRDT- 2020/05/03 06:00
PHST- 2019/12/08 00:00 [received]
PHST- 2020/04/14 00:00 [revised]
PHST- 2020/05/03 06:00 [pubmed]
PHST- 2021/06/08 06:00 [medline]
PHST- 2020/05/03 06:00 [entrez]
AID - 10.1002/pmic.201900401 [doi]
PST - ppublish
SO  - Proteomics. 2020 Jun;20(12):e1900401. doi: 10.1002/pmic.201900401. Epub 2020 Jun 
      2.