PMID- 36627305
OWN - NLM
STAT- MEDLINE
DCOM- 20230117
LR  - 20240210
IS  - 2052-4463 (Electronic)
IS  - 2052-4463 (Linking)
VI  - 10
IP  - 1
DP  - 2023 Jan 10
TI  - InvitroSPI and a large database of proteasome-generated spliced and non-spliced 
      peptides.
PG  - 18
LID - 10.1038/s41597-022-01890-6 [doi]
LID - 18
AB  - Noncanonical epitopes presented by Human Leucocyte Antigen class I (HLA-I) 
      complexes to CD8(+) T cells attracted the spotlight in the research of novel 
      immunotherapies against cancer, infection and autoimmunity. Proteasomes, which 
      are the main producers of HLA-I-bound antigenic peptides, can catalyze both 
      peptide hydrolysis and peptide splicing. The prediction of proteasome-generated 
      spliced peptides is an objective that still requires a reliable (and large) 
      database of non-spliced and spliced peptides produced by these proteases. Here, 
      we present an extended database of proteasome-generated spliced and non-spliced 
      peptides, which was obtained by analyzing in vitro digestions of 80 unique 
      synthetic polypeptide substrates, measured by different mass spectrometers. 
      Peptides were identified through invitroSPI method, which was validated through 
      in silico and in vitro strategies. The peptide product database contains 16,631 
      unique peptide products (5,493 non-spliced, 6,453 cis-spliced and 4,685 
      trans-spliced peptide products), and a substrate sequence variety that is a 
      valuable source for predictors of proteasome-catalyzed peptide hydrolysis and 
      splicing. Potential artefacts and skewed results due to different identification 
      and analysis strategies are discussed.
CI  - (c) 2023. The Author(s).
FAU - Roetschke, Hanna P
AU  - Roetschke HP
AUID- ORCID: 0000-0001-7272-6677
AD  - Max-Planck-Institute for Multidisciplinary Sciences (MPI-NAT), 37077, Gottingen, 
      Germany.
AD  - Centre for Inflammation Biology and Cancer Immunology (CIBCI) & Peter Gorer 
      Department of Immunobiology, King's College London (KCL), SE1 1UL, London, UK.
FAU - Rodriguez-Hernandez, Guillermo
AU  - Rodriguez-Hernandez G
AD  - Centre for Inflammation Biology and Cancer Immunology (CIBCI) & Peter Gorer 
      Department of Immunobiology, King's College London (KCL), SE1 1UL, London, UK.
AD  - Francis Crick Institute, NW1 1AT, London, UK.
FAU - Cormican, John A
AU  - Cormican JA
AD  - Max-Planck-Institute for Multidisciplinary Sciences (MPI-NAT), 37077, Gottingen, 
      Germany.
FAU - Yang, Xiaoping
AU  - Yang X
AD  - Proteomics Core Facility, James Black Centre, King's College London (KCL), SE5 
      9NU, London, UK.
FAU - Lynham, Steven
AU  - Lynham S
AD  - Proteomics Core Facility, James Black Centre, King's College London (KCL), SE5 
      9NU, London, UK.
FAU - Mishto, Michele
AU  - Mishto M
AUID- ORCID: 0000-0003-3042-2792
AD  - Centre for Inflammation Biology and Cancer Immunology (CIBCI) & Peter Gorer 
      Department of Immunobiology, King's College London (KCL), SE1 1UL, London, UK. 
      michele.mishto@kcl.ac.uk.
AD  - Francis Crick Institute, NW1 1AT, London, UK. michele.mishto@kcl.ac.uk.
FAU - Liepe, Juliane
AU  - Liepe J
AD  - Max-Planck-Institute for Multidisciplinary Sciences (MPI-NAT), 37077, Gottingen, 
      Germany. jliepe@mpinat.mpg.de.
LA  - eng
GR  - 29686/CRUK_/Cancer Research UK/United Kingdom
PT  - Dataset
PT  - Journal Article
DEP - 20230110
PL  - England
TA  - Sci Data
JT  - Scientific data
JID - 101640192
RN  - 0 (Histocompatibility Antigens Class I)
RN  - 0 (Peptides)
RN  - EC 3.4.25.1 (Proteasome Endopeptidase Complex)
SB  - IM
MH  - Humans
MH  - *CD8-Positive T-Lymphocytes
MH  - Cytoplasm
MH  - Histocompatibility Antigens Class I
MH  - Peptides/chemistry
MH  - *Proteasome Endopeptidase Complex
PMC - PMC9832164
COIS- The authors have no conflicts of interest.
EDAT- 2023/01/11 06:00
MHDA- 2023/01/13 06:00
PMCR- 2023/01/10
CRDT- 2023/01/10 23:15
PHST- 2021/08/25 00:00 [received]
PHST- 2022/12/01 00:00 [accepted]
PHST- 2023/01/10 23:15 [entrez]
PHST- 2023/01/11 06:00 [pubmed]
PHST- 2023/01/13 06:00 [medline]
PHST- 2023/01/10 00:00 [pmc-release]
AID - 10.1038/s41597-022-01890-6 [pii]
AID - 1890 [pii]
AID - 10.1038/s41597-022-01890-6 [doi]
PST - epublish
SO  - Sci Data. 2023 Jan 10;10(1):18. doi: 10.1038/s41597-022-01890-6.