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GenomicsBenchmarking Software for DDA-PASEF Immunopeptidomics
Benchmarking Software for DDA-PASEF Immunopeptidomics
PRJEB98909 | ENA
ProteomicsProtein Contaminants Matter: Building Universal Protein Contaminant Libraries for DDA and DIA Proteomics
Mass spectrometry-based proteomics is challenged by the presence of contaminant background signals. In particular, protein contaminants from reagents and sample handling are often abundant and almost impossible to avoid, reducing the sensitivity, specificity and reproducibility of protein identifica...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) Mus Musculus (ncbitaxon:10090) 
2022-01-21 | MSV000088714 | MassIVE
ProteomicsThunder-DDA-PASEF enables high-coverage immunopeptidomics and is boosted by MS2Rescore with novel MS2PIP timsTOF fragmentation prediction model
Human leukocyte antigen (HLA) class I peptide ligands (HLAIps) are key targets for developing vaccines and immunotherapies against infectious pathogens or cancer cells. Identifying HLAIps is challenging due to their high diversity, low abundance, and patient individuality. Here, we developed a highl...
ORGANISM(S): Homo Sapiens (human) 
2024-03-18 | PXD040385 | JPOST Repository
TranscriptomicsCo-adjuvanting DDA/TDB liposomes with a TLR7 agonist allows for IgG2a/c class-switching in the absence of Th1 cells
Class-switching to IgG2a/c in mice is a hallmark response to intracellular pathogens. T cells can promote class-switching and the predominant pathway for induction of IgG2a/c antibody responses has been suggested to be via stimulation from Th1 cells. We previously formulated CAF®01 (cationic liposom...
ORGANISM(S): Mus musculus 
2023-11-17 | GSE245073 | GEO
UnknownGas-phase fractionation DDA promotes in-depth DIA phosphoproteome analysis.
Not available
S-EPMC11787513 | biostudies-literature
UnknownDda helicase tightly couples translocation on single-stranded DNA to unwinding of duplex DNA: Dda is an optimally active helicase.
Not available
S-EPMC3372602 | biostudies-literature
UnknownDDA-SKF: Predicting Drug-Disease Associations Using Similarity Kernel Fusion.
Not available
S-EPMC8792612 | biostudies-literature
GenomicsCo-adjuvanting DDA/TDB liposomes with a TLR7 agonist allows for IgG2a/c class-switching in the absence of Th1 cells
Co-adjuvanting DDA/TDB liposomes with a TLR7 agonist allows for IgG2a/c class-switching in the absence of Th1 cells
PRJNA1026905 | ENA
UnknownMSFragger-DDA+ Enhances Peptide Identification Sensitivity with Full Isolation Window Search.
Not available
S-EPMC11507693 | biostudies-literature
ProteomicsDDA-PASEF and diaPASEF acquired HCC1806/HS578T proteomic datasets with deliberate batch effects
We generated two comprehensive large-scale proteomics datasets with deliberate batch effects using the latest parallel accumulation-serial fragmentation in both Data-Dependent and Data-Indepentdent Acquisition modes. This dataset contain a balanced two-class design (cell lines: HCC1806 vs HS578T), a...
ORGANISM(S): Homo sapiens (Human) 
2023-11-21 | PXD041391 | Pride
Dda Pasef Dia Hcc1806 Hs578t Batch effects 
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