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GenomicsBenchmarking Software for DDA-PASEF Immunopeptidomics
Benchmarking Software for DDA-PASEF Immunopeptidomics
PRJEB98909 | ENA
ProteomicsImmunopeptidomics-based identification of naturally presented non-canonical circRNA-derived peptides
Circular RNAs (circRNAs) are covalently closed non-coding RNAs lacking the 5’ cap and the poly-A tail. Nevertheless, it has been demonstrated that certain circRNAs can undergo active translation. Therefore, aberrantly expressed circRNAs in human cancers could be an unexplored source of tumor-specifi...
ORGANISM(S): Homo sapiens (Human) 
2024-03-20 | PXD043989 | Pride
Immunopeptidomics Circrna Antigen discovery 
ProteomicsSensitive neoantigen discovery by real-time mutanome-guided immunopeptidomics
Targeting cancer-specific HLA-peptide complexes is a promising immunotherapy approach, with mutated neoantigens offering high value for their immunogenicity and cancer-specificity. Selecting immunogenic targets requires personalized prioritization of cancer-specific immunopeptides. Mass spectrometry...
ORGANISM(S): Homo sapiens (Human) 
2025-06-20 | PXD059824 | Pride
Immunopeptidomics Real-time searches Antigen discovery 
ProteomicsSAPrIm 2.0: A semi-automated protocol for mid-throughput soluble HLA immunopeptidomics
Human leukocyte antigen (HLA) molecules are pivotal in guiding human adaptive immune responses through their presentation of peptide ligands, collectively known as the immunopeptidome. This process is central to the development of cancer immunotherapies, such as vaccines and T-cell therapies. Profil...
ORGANISM(S): Homo sapiens (Human) 
2025-05-26 | PXD058880 | Pride
Shla Hla Mass spectrometry Mhc Saprim Immunopeptidomics Soluble hla Plasma immunopeptidomics 
UnknownImmunopeptidomics toolkit library (IPTK): a python-based modular toolbox for analyzing immunopeptidomics data.
Not available
S-EPMC8369717 | biostudies-literature
ProteomicsImmunepeptidome of Coxsackievirus B3 infection models of human enterocyte and antigen presenting cell lines
Coxsackieviruses B (CVBs) emerge as candidate environmental triggers for the autoimmunity against pancreatic islet β cells leading to type 1 diabetes. Persistent CVB infections in the gut and pancreas correlate with islet autoantibody seroconversion, suggesting defective antiviral control in predisp...
ORGANISM(S): Homo sapiens (Human) 
2026-05-07 | PXD070471 | Pride
Coxsackievirus b Autoimmunity Human leukocyte antigen (hla) Immunopeptidomics Intestinal immunity Type 1 diabetes 
ProteomicsBenchmarking Software for DDA-PASEF Immunopeptidomics
Mass spectrometry (MS) is the method of choice for high-throughput identification of immunopeptides, which are generated by intracellular proteases, unlike proteomics peptides that are typically derived from trypsin-digested proteins. This distinction necessitates searching without the constraints o...
ORGANISM(S): Homo Sapiens (human) 
2026-06-26 | PXD065501 | JPOST Repository
ProteomicsImmunopeptidomics of colorectal cancer organoids
Background: Patient derived organoids (PDOs) can be established from colorectal cancers as in vitro models to interrogate cancer biology and its clinical relevance. We applied mass spectrometry (MS) immunopeptidomics to investigate neoantigen presentation and whether this can be augmented through in...
ORGANISM(S): Homo sapiens (Human) 
2019-11-27 | PXD014017 | Pride
Organoids Colorectal cancer Mass spectrometry Immunopeptidomics 
ProteomicsImproved sensitivity of immunopeptidomics by leveraging available large-scale pan-HLA spectral libraries and data-independent acquisition
Mass spectrometry is the state-of-the-art methodology for capturing the breadth and depth of the immunopeptidome across HLA allotypes and cell types. The majority of studies in the immunopeptidomics field are discovery-driven and data-dependent tandem mass spectrometry acquisition is commonly used, ...
ORGANISM(S): Homo sapiens (Human) 
2021-04-13 | PXD022950 | Pride
Pan-hla Immunopeptidomics Dia 
UnknownData-Independent Immunopeptidomics Discovery of Low-Abundant Bacterial Epitopes.
Not available
S-EPMC12687359 | biostudies-literature
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