ArticlePatterns (New York, N.Y.)2023
DPHL v.2: An updated and comprehensive DIA pan-human assay library for quantifying more than 14,000 proteins.
Article in Patterns (New York, N.Y.), 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
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- A tri-omics and machine learning framework identifies prognostic biomarkers and metabolic signatures in sepsis.Scientific reports · 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
- DIA-BERT: pre-trained end-to-end transformer models for enhanced DIA proteomics data analysis.Nature communications · 2025Article
- A reference database enabling in-depth proteome and PTM analysis of mouse immune cells.Scientific data · 2025Article
- Integrated View of Baseline Protein Expression in Human Tissues Using Public Data Independent Acquisition Data Sets.Journal of proteome research · 2025Article
- Article
- Comprehensive Mass Spectral Libraries of Human Thyroid Tissues and Cells.Scientific data · 2024Article
- Comprehensive Prostate Fluid-Based Spectral Libraries for Enhanced Protein Detection in Urine.Journal of proteome research · 2024Article
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Authors and funding
35 authors.
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Abstract
A comprehensive pan-human spectral library is critical for biomarker discovery using mass spectrometry (MS)-based proteomics. DPHL v.1, a previous pan-human library built from 1,096 data-dependent acquisition (DDA) MS data of 16 human tissue types, allows quantifying of 10,943 proteins. Here, we generated DPHL v.2 from 1,608 DDA-MS data. The data included 586 DDA-MS data acquired from 18 tissue types, while 1,022 files were derived from DPHL v.1. DPHL v.2 thus comprises data from 24 sample types, including several cancer types (lung, breast, kidney, and prostate cancer, among others). We generated four variants of DPHL v.2 to include semi-tryptic peptides and protein isoforms. DPHL v.2 was then applied to two colorectal cancer cohorts. The numbers of identified and significantly dysregulated proteins increased by at least 21.7% and 14.2%, respectively, compared with DPHL v.1. Our findings show that the increased human proteome coverage of DPHL v.2 provides larger pools of potential protein biomarkers.
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