PMID- 28834231
OWN - NLM
STAT- MEDLINE
DCOM- 20180215
LR  - 20220129
IS  - 1615-9861 (Electronic)
IS  - 1615-9853 (Print)
IS  - 1615-9853 (Linking)
VI  - 17
IP  - 19
DP  - 2017 Oct
TI  - Data-Independent Acquisition of HLA Class I Peptidomes on the Q Exactive Mass 
      Spectrometer Platform.
LID - 10.1002/pmic.201700177 [doi]
AB  - The characterization of peptides presented by human leukocyte antigen (HLA) class 
      I molecules is crucial for understanding immune processes, biomarker discovery, 
      and the development of novel immunotherapies or vaccines. Mass spectrometry 
      allows the direct identification of thousands of HLA-bound peptides from cell 
      lines, blood, or tissue. In recent years, data-independent acquisition (DIA) mass 
      spectrometry methods have evolved, promising to increase reproducibility and 
      sensitivity over classical data-dependent acquisition (DDA) workflows. Here, we 
      describe a DIA setup on the Q Exactive mass spectrometer, optimized regarding the 
      unique properties of HLA class I peptides. The methodology enables sensitive and 
      highly reproducible characterization of HLA peptidomes from individual cell 
      lines. From up to 16 DDA analyses of 100 million human cells, more than 10 000 
      peptides could be confidently identified, serving as basis for the generation of 
      spectral libraries. This knowledge enabled the subsequent interrogation of DIA 
      data, leading to the identification of peptide sets with >90% overlap between 
      replicate samples, a prerequisite for the comparative study of closely related 
      specimens. Furthermore, >3000 peptides could be identified from just one million 
      cells after DIA analysis using a library generated from 300 million cells. The 
      reduction in sample quantity and the high reproducibility of DIA-based HLA 
      peptidome analysis should facilitate personalized medicine applications.
CI  - (c) 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
FAU - Ritz, Danilo
AU  - Ritz D
AD  - Philochem AG, Otelfingen, Switzerland.
FAU - Kinzi, Jonny
AU  - Kinzi J
AD  - Institute of Pharmaceutical Sciences, ETH Zurich, Zurich, Switzerland.
FAU - Neri, Dario
AU  - Neri D
AD  - Institute of Pharmaceutical Sciences, ETH Zurich, Zurich, Switzerland.
FAU - Fugmann, Tim
AU  - Fugmann T
AD  - Philochem AG, Otelfingen, Switzerland.
LA  - eng
GR  - 163479/SNSF_/Swiss National Science Foundation/Switzerland
GR  - 670603/ERC_/European Research Council/International
PT  - Journal Article
PL  - Germany
TA  - Proteomics
JT  - Proteomics
JID - 101092707
RN  - 0 (Histocompatibility Antigens Class I)
RN  - 0 (Peptide Fragments)
SB  - IM
MH  - Data Mining/*methods
MH  - HEK293 Cells
MH  - Histocompatibility Antigens Class I/*analysis
MH  - Humans
MH  - Mass Spectrometry/*methods
MH  - Peptide Fragments/*analysis
PMC - PMC5846733
MID - EMS76517
OTO - NOTNLM
OT  - HLA peptidomics
OT  - antigens
OT  - biomarker
OT  - dia
OT  - immunopeptidomics
COIS- Conflicts of Interest: Dario Neri is co-founder of Philogen, shareholder and 
      member of the board. Tim Fugmann and Danilo Ritz are employees of Philochem AG. 
      The authors declare no additional conflict of interest.
EDAT- 2017/08/24 06:00
MHDA- 2018/02/16 06:00
PMCR- 2018/10/01
CRDT- 2017/08/24 06:00
PHST- 2017/05/12 00:00 [received]
PHST- 2017/07/07 00:00 [revised]
PHST- 2017/08/24 06:00 [pubmed]
PHST- 2018/02/16 06:00 [medline]
PHST- 2017/08/24 06:00 [entrez]
PHST- 2018/10/01 00:00 [pmc-release]
AID - 10.1002/pmic.201700177 [doi]
PST - ppublish
SO  - Proteomics. 2017 Oct;17(19):10.1002/pmic.201700177. doi: 10.1002/pmic.201700177.