ArticleNature communications2022
A streamlined platform for analyzing tera-scale DDA and DIA mass spectrometry data enables highly sensitive immunopeptidomics.
Article in Nature communications, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 50 papers.
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Who cites it
50 citing papers in PubMed.
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- NetMHCIIphosPan: A Machine Learning Tool for Predicting HLA Class II Antigen Presentation of Phosphorylated Peptides.Journal of proteome research · 2026Article
- Benchmarking Software for DDA-PASEF Immunopeptidomics.Molecular & cellular proteomics : MCP · 2026Article
- Identification of molecularly targeted therapy-induced immunopeptidome in diffuse midline glioma (DMG).Neoplasia (New York, N.Y.) · 2026Article
- NetMHCIIphosPan: a machine learning tool for predicting HLA class II antigen presentation of phosphorylated peptides.bioRxiv : the preprint server for biology · 2026Article
- C/EBPβ-induced alternative splicing of RCAN1 generates a potent TCR-T target in mesenchymal glioblastoma.Cellular & molecular immunology · 2026Article
- In-depth analysis of data characteristics and comparative evaluation of dda and dia accuracy in label-free quantitative proteomics of biological samples.Clinical proteomics · 2025Article
- Benchmarking informatics workflows for data-independent acquisition single-cell proteomics.Nature communications · 2025Article
- DigDig: A Software for In-Depth Analysis and Comparison of Proteolytic Digestion.Analytical chemistry · 2025Article
- MHCquant2 refines immunopeptidomics tumor antigen discovery.Genome biology · 2025Article
- Deciphering the MHC immunopeptidome of human cancers with Ligand.MHC atlas.Briefings in bioinformatics · 2025Article
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- Analysis of p53-Independent Functions of the Mdm2-MdmX Complex Using Data-Independent Acquisition-Based Profiling.Proteomes · 2025Article
- Engineered Proteins and Chemical Tools to Probe the Cell Surface Proteome.Chemical reviews · 2025Review
- InstaNovo enables diffusion-powered de novo peptide sequencing in large-scale proteomics experiments.Nature machine intelligence · 2025Article
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Authors and funding
11 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Integrating data-dependent acquisition (DDA) and data-independent acquisition (DIA) approaches can enable highly sensitive mass spectrometry, especially for imunnopeptidomics applications. Here we report a streamlined platform for both DDA and DIA data analysis. The platform integrates deep learning-based solutions of spectral library search, database search, and de novo sequencing under a unified framework, which not only boosts the sensitivity but also accurately controls the specificity of peptide identification. Our platform identifies 5-30% more peptide precursors than other state-of-the-art systems on multiple benchmark datasets. When evaluated on immunopeptidomics datasets, we identify 1.7-4.1 and 1.4-2.2 times more peptides from DDA and DIA data, respectively, than previously reported results. We also discover six T-cell epitopes from SARS-CoV-2 immunopeptidome that might represent potential targets for COVID-19 vaccine development. The platform supports data formats from all major instruments and is implemented with the distributed high-performance computing technology, allowing analysis of tera-scale datasets of thousands of samples for clinical applications.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.