TY - JOUR
T1 - MHC-I Ligand Discovery Using Targeted Database Searches of Mass Spectrometry Data
T2 - Implications for T-Cell Immunotherapies
AU - Murphy, J. Patrick
AU - Konda, Prathyusha
AU - Kowalewski, Daniel J.
AU - Schuster, Heiko
AU - Clements, Derek
AU - Kim, Youra
AU - Cohen, Alejandro M.
AU - Sharif, Tanveer
AU - Nielsen, Morten
AU - Stevanovic, Stefan
AU - Lee, Patrick W.
AU - Gujar, Shashi
N1 - Publisher Copyright:
© 2017 American Chemical Society.
PY - 2017/4/7
Y1 - 2017/4/7
N2 - Class I major histocompatibility complex (MHC-I)-bound peptide ligands dictate the activation and specificity of CD8+ T cells and thus are important for devising T-cell immunotherapies. In recent times, advances in mass spectrometry (MS) have enabled the precise identification of these MHC-I peptides, wherein MS spectra are compared against a reference proteome. Unfortunately, matching these spectra to reference proteome databases is hindered by inflated search spaces attributed to a lack of enzyme restriction in the searches, limiting the efficiency with which MHC ligands are discovered. Here we offer a solution to this problem whereby we developed a targeted database search approach and accompanying tool SpectMHC, that is based on a priori-predicted MHC-I peptides. We first validated the approach using MS data from two different allotype-specific immunoprecipitates for the C57BL/6 mouse background. We then developed allotype-specific HLA databases to search previously published MS data sets of human peripheral blood mononuclear cells (PBMCs). This targeted search strategy improved peptide identifications for both mouse and human ligandomes by greater than 2-fold and is superior to traditional "no enzyme" searches of reference proteomes. Our targeted database search promises to uncover otherwise missed novel T-cell epitopes of therapeutic potential.
AB - Class I major histocompatibility complex (MHC-I)-bound peptide ligands dictate the activation and specificity of CD8+ T cells and thus are important for devising T-cell immunotherapies. In recent times, advances in mass spectrometry (MS) have enabled the precise identification of these MHC-I peptides, wherein MS spectra are compared against a reference proteome. Unfortunately, matching these spectra to reference proteome databases is hindered by inflated search spaces attributed to a lack of enzyme restriction in the searches, limiting the efficiency with which MHC ligands are discovered. Here we offer a solution to this problem whereby we developed a targeted database search approach and accompanying tool SpectMHC, that is based on a priori-predicted MHC-I peptides. We first validated the approach using MS data from two different allotype-specific immunoprecipitates for the C57BL/6 mouse background. We then developed allotype-specific HLA databases to search previously published MS data sets of human peripheral blood mononuclear cells (PBMCs). This targeted search strategy improved peptide identifications for both mouse and human ligandomes by greater than 2-fold and is superior to traditional "no enzyme" searches of reference proteomes. Our targeted database search promises to uncover otherwise missed novel T-cell epitopes of therapeutic potential.
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U2 - 10.1021/acs.jproteome.6b00971
DO - 10.1021/acs.jproteome.6b00971
M3 - Article
C2 - 28244318
AN - SCOPUS:85017135077
SN - 1535-3893
VL - 16
SP - 1806
EP - 1816
JO - Journal of Proteome Research
JF - Journal of Proteome Research
IS - 4
ER -