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ProteomicsHalf decimal place rule
Many MS2 spectra in bottom-up proteomics experiments remain unassigned. To improve proteome coverage, we applied the half decimal place rule (HDPR) to remove non-peptidic molecules. The HDPR considers the ratio of the first digit after the decimal point to the full molecular mass and results in a re...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2017-03-29 | MSV000080727 | MassIVE
ProteomicsLarge scale intact glycopeptide identification by Mascot database search
We present the adaptability of Mascot search engine for automated identification of intact glycopeptide mass spectra. The steps involved in adopting Mascot for intact glycopeptide analysis include: i) assigning unique one letter codes for monosaccharides, ii) linearizing glycan sequences and iii) pr...
ORGANISM(S): Homo sapiens (Human) 
2018-02-08 | PXD005931 | Pride
Mascot Glycoproteomics Higher-energy collisional induced dissociation (hcd) Prostate cancer Serum 
ProteomicsPublic T cell epitopes shared among SARS-CoV-2 Public T cell epitopes shared among SARS-CoV-2 variants are presented on prevalent HLA class I alleles variants are presented on prevalent HLA class I alleles
In this project, we used MS-based immunopeptidomics and T-cell screening assays to identify SARS-CoV-2 epitopes. The MS identified epitopes were further valdiated for CD8 T cell immunogenecity. PBMC from a large number of patients infected with SARS-CoV-2 were used for valdiation of MS identifed and...
ORGANISM(S): Homo sapiens (Human) 
2023-03-11 | PXD028862 | Pride
Sars-cov-2 Lc-ms Immunopeptidomics 
ProteomicsRestoration of defective nuclear-mitochondrial DNA damage signaling suppresses neuropathology and extends healthspan in Ataxia telangiectasia across species
Ataxia-telangiectasia (A-T) is a disease characterized by genomic instability and severe neurodegeneration. It is caused by mutation in Ataxia-telangiectasia mutated gene (ATM) which encodes ATM, a key player in DNA double-strand break (DSB) repair. While many major symptoms of A-T (including hyper...
ORGANISM(S): Caenorhabditis elegans 
2018-06-25 | PXD003380 | Pride
Aging Mass spectrometry Liquid chromatography C.elegans 
ProteomicsA T-cell receptor targeting a shared neoantigen mediates elimination of primary human acute myeloid leukemia in vivo
This paper presents a T-cell receptor (TCR) reactive to the recurrent D835Y driver mutation in the FLT3 tyrosine-kinase domain. TCRFLT3D/Y-redirected T cells selectively eliminated primary human AML cells harboring the D835Y mutation in vitro and in vivo. The TCRFLT3D/Y cells rejected both CD34+ and...
ORGANISM(S): Homo sapiens (Human) 
2023-08-28 | PXD043908 | Pride
Human Prm Lc-ms Acute myeloid leukemia Cellular immunotherapy 
ProteomicsLarge scale intact glycopeptide identification by Mascot database search
We present the adaptability of Mascot search engine for automated identification of intact glycopeptide mass spectra. The steps involved in adopting Mascot for intact glycopeptide analysis include: i) assigning unique one letter codes for monosaccharides, ii) linearizing glycan sequences and iii) pr...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2018-07-02 | MSV000082567 | MassIVE
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