ArticleNature communications2022
dia-PASEF data analysis using FragPipe and DIA-NN for deep proteomics of low sample amounts.
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 249 papers.
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Who cites it
249 citing papers in PubMed.
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- Identification of a conserved gene family with an essential role inProceedings of the National Academy of Sciences of the United States of America · 2026Article
- From patient to tumor organoid: Culture protocol choice controls glioblastoma tumor architecture and identity.Brain pathology (Zurich, Switzerland) · 2026Article
- Induction of Oxidative Stress on Retinal Pigment Epithelial Cells Triggered a Proangiogenic Environment.International journal of molecular sciences · 2026Article
- Aryl Aldehyde-Anchored Small Molecules Recruit FBXO22 for Targeted Degradation of NSD2.Journal of medicinal chemistry · 2026Article
- Mechanistic Exploration of Half-Sandwich Iridium(III) Anticancer Compounds through Integrated Cellular, Proteomic, and In Vivo Analyses.Journal of medicinal chemistry · 2026Article
- AlphaDIA enables DIA transfer learning for feature-free proteomics.Nature biotechnology · 2026Article
- An inflammasome-driven differentiation program in intestinal stem cells protects against Salmonella infection.Nature immunology · 2026Article
189 more citing papers are in PubMed but not listed here.
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Authors and funding
13 authors.
Funding
Abstract
The dia-PASEF technology uses ion mobility separation to reduce signal interferences and increase sensitivity in proteomic experiments. Here we present a two-dimensional peak-picking algorithm and generation of optimized spectral libraries, as well as take advantage of neural network-based processing of dia-PASEF data. Our computational platform boosts proteomic depth by up to 83% compared to previous work, and is specifically beneficial for fast proteomic experiments and those with low sample amounts. It quantifies over 5300 proteins in single injections recorded at 200 samples per day throughput using Evosep One chromatography system on a timsTOF Pro mass spectrometer and almost 9000 proteins in single injections recorded with a 93-min nanoflow gradient on timsTOF Pro 2, from 200 ng of HeLa peptides. A user-friendly implementation is provided through the incorporation of the algorithms in the DIA-NN software and by the FragPipe workflow for spectral library generation.
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