ArticleNature communications2018
Chromatogram libraries improve peptide detection and quantification by data independent acquisition mass spectrometry.
Article in Nature communications, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 339 papers, 1 of them a synthesis that pooled it.
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Who cites it
339 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Mass Spectral Feature Analysis of Ubiquitylated Peptides Provides Insights into Probing the Dark Ubiquitylome.Journal of the American Society for Mass Spectrometry · 2024Pooled it
- Trial
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- Development and Validation of a Streamlined Workflow for Proteomic Analysis of Proteins and Post-translational Modifications from Dried Blood.Journal of proteome research · 2026Article
- ELAVL1 and ELAVL4 are required for Musashi-dependent translational activation.bioRxiv : the preprint server for biology · 2026Article
- AlphaDIA enables DIA transfer learning for feature-free proteomics.Nature biotechnology · 2026Article
- Comparative Evaluation of DDA- and DIA-Based Proteomic Workflows in Beryllium-Related Lung Disease.bioRxiv : the preprint server for biology · 2026Article
- Revisiting resonance-excitation collision-induced dissociation for data-independent acquisition.bioRxiv : the preprint server for biology · 2026Article
- Timed secreted proteomes reveal regulation of hepatokines by the liver circadian clock.Nature communications · 2026Article
- Accurate quantification in proteomics with QuantUMS.Nature biotechnology · 2026Article
- A Multiplexed Quantitative Analysis of Germline Single Amino Acid Variants by Targeted Proteomics in Nondepleted Human Plasma.Journal of proteome research · 2026Article
279 more citing papers are in PubMed but not listed here.
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Authors and funding
8 authors.
Funding
Abstract
Data independent acquisition (DIA) mass spectrometry is a powerful technique that is improving the reproducibility and throughput of proteomics studies. Here, we introduce an experimental workflow that uses this technique to construct chromatogram libraries that capture fragment ion chromatographic peak shape and retention time for every detectable peptide in a proteomics experiment. These coordinates calibrate protein databases or spectrum libraries to a specific mass spectrometer and chromatography setup, facilitating DIA-only pipelines and the reuse of global resource libraries. We also present EncyclopeDIA, a software tool for generating and searching chromatogram libraries, and demonstrate the performance of our workflow by quantifying proteins in human and yeast cells. We find that by exploiting calibrated retention time and fragmentation specificity in chromatogram libraries, EncyclopeDIA can detect 20-25% more peptides from DIA experiments than with data dependent acquisition-based spectrum libraries alone.
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Registered trials
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.