ArticleNature communications2022
Benchmarking of analysis strategies for data-independent acquisition proteomics using a large-scale dataset comprising inter-patient heterogeneity.
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 52 papers.
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Who cites it
52 citing papers in PubMed, 115 citations in OpenAlex.
- Extracellular Vesicles in Cardiovascular Disease: Intercellular Signaling, Liquid Biopsy Biomarkers, and Therapeutic Translation.Circulation research · 2026Review
- Ground Truth-Based Evaluation of False Discovery Rate and Statistical Power in DIA Proteomics.bioRxiv : the preprint server for biology · 2026Article
- Clarifying the scope and capabilities of ROTS in differential expression analysis.Bioinformatics (Oxford, England) · 2026Article
- REACTOR: REgulon Activity analysis and Comparison Tool for single-cell transcriptOmics Research.Bioinformatics (Oxford, England) · 2026Article
- Evaluation of Data-Independent Acquisition-Based Phosphoproteomics Analysis in Mammalian and Bacterial Systems.Journal of proteome research · 2026Article
- Clinical peptidomics for respiratory diseases: matrices, workflows, and translation towards treatable traits, with a focus on COPD.Clinical proteomics · 2026Review
- Proteomic characterization of intrahepatic cholangiocarcinoma identifies risk-stratifying subgroups and EIF4A1 as a therapeutic target.Nature communications · 2026Article
- Generation of High-Quality Succinyl Spectral Libraries for Improved Proteome-Wide Succinylome Analysis Using Data-Independent Acquisition.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Integrating endogenous TurboID and data-independent acquisition mass spectrometry for in vivo proximity labeling.The EMBO journal · 2026Article
- Advances and Applications of Spatial Proteomics: From Organellar Maps to Clinical Translation.Chembiochem : a European journal of chemical biology · 2026Review
- Performance Characteristics of Zeno Trap Scanning DIA for Sensitive and Quantitative Proteomics at High Throughput.Proteomics · 2026Article
- Mitochondrial metabolic remodeling and multi-omics profiling identify plasma biomarkers of myocardial infarction.Journal of molecular and cellular cardiology plus · 2025Article
- Benchmarking informatics workflows for data-independent acquisition single-cell proteomics.Nature communications · 2025Article
- Real-Time Eco-AI, Electrophoresis-Correlative Data-Dependent Acquisition with AI-Based Data Processing Broadens Access to Single-Cell Mass Spectrometry Proteomics.Angewandte Chemie (International ed. in English) · 2025Article
- Multicenter evaluation of label-free quantification in human plasma on a high dynamic range benchmark set.Nature communications · 2025Article
- Proteomic characterization of the pseudocapsule of clear cell renal cell carcinoma in VHL disease reveals a distinct microenvironment at the tumor boundary zone.Neoplasia (New York, N.Y.) · 2025Article
- QuickProt: A Bioinformatics and Visualization Tool for DIA and PRM Mass Spectrometry-Based Proteomics Datasets.Proteomics · 2025Article
- Enhancing Tandem MS Sensitivity and Peptide Identification via Ion Preaccumulation in an Orbitrap Mass Spectrometer.Journal of proteome research · 2025Article
- Article
- Multicenter Longitudinal Quality Assessment of MS-Based Proteomics in Plasma and Serum.Journal of proteome research · 2025Article
Corrections and comments
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Authors and funding
12 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Numerous software tools exist for data-independent acquisition (DIA) analysis of clinical samples, necessitating their comprehensive benchmarking. We present a benchmark dataset comprising real-world inter-patient heterogeneity, which we use for in-depth benchmarking of DIA data analysis workflows for clinical settings. Combining spectral libraries, DIA software, sparsity reduction, normalization, and statistical tests results in 1428 distinct data analysis workflows, which we evaluate based on their ability to correctly identify differentially abundant proteins. From our dataset, we derive bootstrap datasets of varying sample sizes and use the whole range of bootstrap datasets to robustly evaluate each workflow. We find that all DIA software suites benefit from using a gas-phase fractionated spectral library, irrespective of the library refinement used. Gas-phase fractionation-based libraries perform best against two out of three reference protein lists. Among all investigated statistical tests non-parametric permutation-based statistical tests consistently perform best.
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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.