PMID- 34303857
OWN - NLM
STAT- MEDLINE
DCOM- 20220324
LR  - 20240214
IS  - 1535-9484 (Electronic)
IS  - 1535-9476 (Print)
IS  - 1535-9476 (Linking)
VI  - 20
DP  - 2021
TI  - The Choice of Search Engine Affects Sequencing Depth and HLA Class I 
      Allele-Specific Peptide Repertoires.
PG  - 100124
LID - S1535-9476(21)00096-7 [pii]
LID - 10.1016/j.mcpro.2021.100124 [doi]
LID - 100124
AB  - Standardization of immunopeptidomics experiments across laboratories is a 
      pressing issue within the field, and currently a variety of different methods for 
      sample preparation and data analysis tools are applied. Here, we compared 
      different software packages to interrogate immunopeptidomics datasets and found 
      that Peaks reproducibly reports substantially more peptide sequences (~30-70%) 
      compared with Maxquant, Comet, and MS-GF+ at a global false discovery rate (FDR) 
      of <1%. We noted that these differences are driven by search space and spectral 
      ranking. Furthermore, we observed differences in the proportion of peptides 
      binding the human leukocyte antigen (HLA) alleles present in the samples, 
      indicating that sequence-related differences affected the performance of each 
      tested engine. Utilizing data from single HLA allele expressing cell lines, we 
      observed significant differences in amino acid frequency among the peptides 
      reported, with a broadly higher representation of hydrophobic amino acids L, I, 
      P, and V reported by Peaks. We validated these results using data generated with 
      a synthetic library of 2000 HLA-associated peptides from four common HLA alleles 
      with distinct anchor residues. Our investigation highlights that search engines 
      create a bias in peptide sequence depth and peptide amino acid composition, and 
      resulting data should be interpreted with caution.
CI  - Copyright (c) 2021 The Authors. Published by Elsevier Inc. All rights reserved.
FAU - Parker, Robert
AU  - Parker R
AD  - Nuffield Department of Medicine, Centre for Cellar and Medical Physiology, 
      University of Oxford, Oxford, UK. Electronic address: robert.parker@ndm.ox.ac.uk.
FAU - Tailor, Arun
AU  - Tailor A
AD  - Nuffield Department of Medicine, Centre for Cellar and Medical Physiology, 
      University of Oxford, Oxford, UK.
FAU - Peng, Xu
AU  - Peng X
AD  - Nuffield Department of Medicine, Centre for Cellar and Medical Physiology, 
      University of Oxford, Oxford, UK.
FAU - Nicastri, Annalisa
AU  - Nicastri A
AD  - Nuffield Department of Medicine, Centre for Cellar and Medical Physiology, 
      University of Oxford, Oxford, UK.
FAU - Zerweck, Johannes
AU  - Zerweck J
AD  - JPT Peptide Technologies GmbH, Berlin, Germany.
FAU - Reimer, Ulf
AU  - Reimer U
AD  - JPT Peptide Technologies GmbH, Berlin, Germany.
FAU - Wenschuh, Holger
AU  - Wenschuh H
AD  - JPT Peptide Technologies GmbH, Berlin, Germany.
FAU - Schnatbaum, Karsten
AU  - Schnatbaum K
AD  - JPT Peptide Technologies GmbH, Berlin, Germany.
FAU - Ternette, Nicola
AU  - Ternette N
AD  - Nuffield Department of Medicine, Centre for Cellar and Medical Physiology, 
      University of Oxford, Oxford, UK. Electronic address: 
      nicola.ternette@ndm.ox.ac.uk.
LA  - eng
GR  - 28736/CRUK_/Cancer Research UK/United Kingdom
GR  - C328/A21998/CRUK_/Cancer Research UK/United Kingdom
GR  - C6078/A28736/CRUK_/Cancer Research UK/United Kingdom
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20210723
PL  - United States
TA  - Mol Cell Proteomics
JT  - Molecular & cellular proteomics : MCP
JID - 101125647
RN  - 0 (Histocompatibility Antigens Class I)
RN  - 0 (Peptide Library)
RN  - 0 (Peptides)
SB  - IM
MH  - Alleles
MH  - Amino Acid Sequence
MH  - Histocompatibility Antigens Class I/*chemistry/genetics
MH  - Humans
MH  - Mass Spectrometry
MH  - Peptide Library
MH  - Peptides/*chemistry/genetics
MH  - Proteomics/methods
MH  - *Search Engine
PMC - PMC8724928
OTO - NOTNLM
OT  - HLA
OT  - MHC
OT  - MS search engine
OT  - database search
OT  - de novo sequencing
OT  - human leukocyte antigen
OT  - immunopeptidomics
OT  - major histocompatibility complex
OT  - peptide sequence annotation
OT  - peptide spectrum match
COIS- Conflict of interest N. T. is directing immunopeptidomics research at Enara Bio 
      part-time and serves on the Scientific Advisory Boards of Enara Bio and T-Cypher 
      Bio. N. T. is consultant to Hoffman-La Roche and Grey Wolf Therapeutics. All 
      other authors declare no conflict of interest.
EDAT- 2021/07/26 06:00
MHDA- 2022/03/25 06:00
PMCR- 2021/07/23
CRDT- 2021/07/25 20:32
PHST- 2020/12/18 00:00 [received]
PHST- 2021/07/09 00:00 [revised]
PHST- 2021/07/12 00:00 [accepted]
PHST- 2021/07/26 06:00 [pubmed]
PHST- 2022/03/25 06:00 [medline]
PHST- 2021/07/25 20:32 [entrez]
PHST- 2021/07/23 00:00 [pmc-release]
AID - S1535-9476(21)00096-7 [pii]
AID - 100124 [pii]
AID - 10.1016/j.mcpro.2021.100124 [doi]
PST - ppublish
SO  - Mol Cell Proteomics. 2021;20:100124. doi: 10.1016/j.mcpro.2021.100124. Epub 2021 
      Jul 23.