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UnknownMS2PIP: a tool for MS/MS peak intensity prediction.
Not available
S-EPMC5994937 | biostudies-literature
UnknownMS2Rescore: Data-Driven Rescoring Dramatically Boosts Immunopeptide Identification Rates.
Not available
S-EPMC9411678 | biostudies-literature
UnknownMS2CNN: predicting MS/MS spectrum based on protein sequence using deep convolutional neural networks.
Not available
S-EPMC6929458 | biostudies-literature
ProteomicsBenchmarking DIA data analysis workflows
Data independent acquisition (DIA) has become a well-established method in LC-MS driven proteomics. Nonetheless, there are still a lot of possibilities at the data analysis level. By benchmarking different DIA analysis workflows through a ground truth sample mimicking real differential abundance sam...
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2024-05-06 | PXD044981 | Pride
Shotgun proteomics In silico library Lc-ms Dda library Data analysis Benchmark Dia Library free 
ProteomicsSpectral prediction features as a solution for the search space size problem in proteogenomics
Proteogenomics approaches often struggle with the distinction between right and false peptide-to-spectrum matches as the database size enlarges. However, features extracted from tandem mass spectrometry intensity predictors can enhance the peptide identification rate and can provide extra confidence...
ORGANISM(S): Homo sapiens (Human) 
2021-03-26 | PXD022280 | Pride
Proteogenomics  spectrum predictor  nanopore sequencing  ribosome profiling  rna-seq  ms2pip  prosit  intensity features  machine learning  hct116  percolator  maxquant 
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
UnknownMHCquant2 refines immunopeptidomics tumor antigen discovery.
Not available
S-EPMC12455830 | biostudies-literature
UnknownSpectral Prediction Features as a Solution for the Search Space Size Problem in Proteogenomics.
Not available
S-EPMC8214147 | biostudies-literature
UnknownUpdated MS²PIP web server delivers fast and accurate MS² peak intensity prediction for multiple fragmentation methods, instruments and labeling techniques.
Not available
S-EPMC6602496 | biostudies-literature
ProteomicsProteogenomic analysis of Human acute myeloid leukemia
Here, we used OpenCustomDB, a web-based tool that uses both sample-specific RNAseq data to identify genomic variants and the OpenProt resource that annotates alternative proteins in addition to canonical proteins. We tested OpenCustomDB with a cohort of 17 patients with acute myeloid leukemia and de...
ORGANISM(S): Homo sapiens (Human) 
2023-05-10 | PXD029240 | Pride
Proteogenomics Human Altprot Aml 
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