Improving MHC-I Ligand Identification by Incorporating Targeted Searches of Mass Spectrometry Data.
Methods Mol Biol
; 2120: 161-171, 2020.
Article
em En
| MEDLINE
| ID: mdl-32124318
ABSTRACT
Effective immunotherapies rely on specific activation of immune cells. Class I major histocompatibility complex (MHC-I) bound peptide ligands play a major role in dictating the specificity and activation of CD8+ T cells and hence are important in developing T cell-based immunotherapies. Mass spectrometry-based approaches are most commonly used for identifying these MHC-bound peptides, wherein the MS/MS spectra are compared against a reference proteome database. Unfortunately, the effectiveness of matching the immunopeptide MS/MS spectra to a reference proteome database is hindered by inflated search spaces attributed to a lack of enzyme restriction in searches. These large search spaces limit the efficiency with which MHC-I peptides are identified. Here, we describe the implementation of a targeted database search approach and accompanying tool, SpectMHC, that is based on a priori-predicted MHC-I peptides. We have previously shown that this targeted search strategy improved peptide identifications for both mouse and human MHC ligands by greater than two-fold and is superior to traditional "no enzyme" search of reference proteomes (Murphy et al. J Res Proteome 161806-1816, 2017).
Palavras-chave
Texto completo:
1
Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Peptídeos
/
Antígenos de Histocompatibilidade Classe I
/
Proteômica
/
Espectrometria de Massas em Tandem
Tipo de estudo:
Diagnostic_studies
Limite:
Animals
/
Humans
Idioma:
En
Revista:
Methods Mol Biol
Assunto da revista:
BIOLOGIA MOLECULAR
Ano de publicação:
2020
Tipo de documento:
Article
País de afiliação:
Canadá