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ProteomicsSynthetic peptide library
Synthetic peptides are commonly used in biomedical science for many applications in basic and translational research. Here, we assembled a large dataset of synthetic peptides whose identity was validated using mass spectrometry. We analyzed the mass spectra and used them for method validation as wel...
ORGANISM(S): Homo sapiens (Human) 
2022-10-11 | PXD031812 | Pride
Peptide synthesis Mass spectrometry Predictor 
ProteomicsDigestion of TSN2 and TSN89 synthetic peptides by proteasomes
Proteasomes are large multi-subunit enzymes that act as the main producers of antigenic peptides presented at the cell surface to CD8+ T cells. They can simply cut proteins or ligate non-contiguous peptide fragments thereby generating novel sequences, i.e. spliced peptides via a process called prote...
ORGANISM(S): Homo sapiens (Human) 
2022-12-19 | PXD025995 | Pride
Synthetic peptides Proteasome Digestion Lc-ms/ms 
ProteomicsinSPIRE Spectral Rescoring Tool
inSPIRE is an open-source tool for spectral rescoring of mass spectrometry search results. For this project, inSPIRE was applied to MaxQuant, PEAKS DB, and Mascot search results from a tryptic digestion of the K562 proteome. Here we provide the RAW files and search results using MaxQuant, PEAKS DB, ...
ORGANISM(S): Homo sapiens (Human) 
2022-10-26 | PXD034056 | Pride
Rescoring Mass spectrometry 
ProteomicsiBench Ground Truth Validation Tool 2.0
iBench is an open-source tool that provides enhanced validation of Mass Spectrometry identification methods. In this updated version, iBench 2.0 takes high confidence peptide identifications from previously measured MS data and embeds the sequences in an in silico-only proteome as spliced or non-spl...
ORGANISM(S): Homo sapiens (Human) 
2023-12-21 | PXD044451 | Pride
Mass spectrometry 20s proteasomes Benchmarking Mhc-i presentation Pcps 
ProteomicsiBench Ground Truth Validation Tool
iBench is an open-source tool that provides enhanced validation of Mass Spectrometry identification methods. For this project, iBench was applied to Percolator rescored results from Mascot searches from a tryptic digestion of the K562 proteome, HLA-I immunopeptidome experiment, and synthetic peptide...
ORGANISM(S): Homo sapiens (Human) 
2022-10-11 | PXD034968 | Pride
Mascot Proteomics Mass spectrometry Benchmarking 
ProteomicsKRAS G12V spliced neoepitope is produced by proteasomes
This dataset contains further evidence that the HLA-A*02:01+ KRAS G12V+ spliced neoepitope we previously identified (Mishto et al., Front. Immunol. 2019) is produced by proteasomes in various experimental conditions
ORGANISM(S): Homo sapiens (Human) 
2022-09-05 | PXD024528 | Pride
Mass spectrometry Epitope discovery Peptide splicing Proteasome Cis-spliced peptides Kras 
ProteomicsDigestion of a variety of synthetic peptides by proteasomes
Proteasomes are large multi-subunit enzymes that act as the main producers of antigenic peptides presented at the cell surface to CD8+ T cells. They can simply cut proteins or recombine their fragments thereby generating novel sequences, i.e. spliced peptides via a process called proteasome-catalyse...
ORGANISM(S): Homo sapiens (Human) 
2020-04-14 | PXD016782 | Pride
Synthetic peptides Proteasome Digestion Lc-ms/ms 
ProteomicsSPI-ART and the features of cis-spliced peptides in HLA class I immunopeptidomes
The identification of peptides presented by HLA class I molecules to CD8+ T cells – i.e. the HLA-I immunopeptidome - is a useful tool to fish epitopes suitable for vaccinations and immunotherapies against cancer, infection and autoimmunity. These peptides are mainly generated by proteasomes through ...
ORGANISM(S): Homo sapiens (Human) 
2022-08-12 | PXD025346 | Pride
K562 cell line Mass spectrometry Peptide splicing Immunopeptidome Hla-i Cis-spliced peptides 
ProteomicsDatabase search engines and target database features impinge upon the identification of post-translationally cis-spliced peptides in HLA class I immunopeptidomes
Unconventional epitopes presented by HLA class I complexes are emerging targets for T cell targeted immunotherapies. Their identification by mass spectrometry required development of novel methods to cope with the large number of theoretical candidates. Methods to identify post-translationally splic...
ORGANISM(S): Homo sapiens (Human) 
2022-04-06 | PXD031709 | Pride
K562 cell line Mass spectrometry Peptide splicing Immunopeptidome Hla-i Cis-spliced peptides 
UnknownIdentification of a class of non-conventional ER-stress-response-derived immunogenic peptides.
Not available
S-EPMC8278487 | biostudies-literature
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