ArticleNature biotechnology2021
MaxDIA enables library-based and library-free data-independent acquisition proteomics.
Article in Nature biotechnology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 126 papers.
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Who cites it
126 citing papers in PubMed.
- Preprocessing Large-Scale Proteomics Data.Methods in molecular biology (Clifton, N.J.) · 2027Article
- De novo synthesis of cardiolipin controls respiratory chain biogenesis in neonatal mouse hearts.EMBO reports · 2026Article
- PhosSight: A Unified Deep Learning Framework Boosting and Accelerating Phosphoproteome Identification to Enable Biological Discoveries.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- A single-domain antibody targets aggregation-prone region of α-synuclein to reduce synucleinopathy, rescue neurodegeneration and improve function.bioRxiv : the preprint server for biology · 2026Article
- AlphaDIA enables DIA transfer learning for feature-free proteomics.Nature biotechnology · 2026Article
- Efferocytosis of apoptotic bodies drives SARS-CoV-2 infection and macrophage inflammation.Nature communications · 2026Article
- pmultiqc: An Open-Source, Lightweight, and Metadata-Oriented QC Reporting Library for MS Proteomics.Molecular & cellular proteomics : MCP · 2026Article
- Evaluation of Data-Independent Acquisition-Based Phosphoproteomics Analysis in Mammalian and Bacterial Systems.Journal of proteome research · 2026Article
- Proximity Labeling Reveals How Lrp2 Interacts with the Endocytic Machine.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
- Multi-omics analyses of the Alviniconcha holobiont reveal multi-faceted adaptations to deep-sea hydrothermal vents.Science China. Life sciences · 2026Article
- Complete Data Analysis Workflow for Quantitative DIA Mass Spectrometry Using Nextflow.Journal of proteome research · 2026Article
- Advances in Mass Spectrometry Instrumentation and Methodology for Analysis of Alternative Protein Isoforms.Journal of mass spectrometry : JMS · 2026Review
- The stroke risk gene Foxf2 maintains brain endothelial cell function via Tie2 signaling.Nature neuroscience · 2026Article
- The State of Peptide Detectability in Computational Proteomics and Guidelines for AI Applications.Computational and structural biotechnology journal · 2026Article
- Methods for the Investigation of Protein-Ligands Interactions.Advances in experimental medicine and biology · 2026Review
- Advances and Applications of Spatial Proteomics: From Organellar Maps to Clinical Translation.Chembiochem : a European journal of chemical biology · 2026Review
- Article
- Data-independent acquisition-based quantitative proteomics in plants.Frontiers in plant science · 2026Review
- Proteome-Wide Analysis and Surface Protein Isolation for Secretome Characterization Reveal Insights into the Biology of the Leaf-Cutter AntAnalytical chemistry · 2025Article
66 more citing papers are in PubMed but not listed here.
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18 authors.
Funding
Abstract
MaxDIA is a software platform for analyzing data-independent acquisition (DIA) proteomics data within the MaxQuant software environment. Using spectral libraries, MaxDIA achieves deep proteome coverage with substantially better coefficients of variation in protein quantification than other software. MaxDIA is equipped with accurate false discovery rate (FDR) estimates on both library-to-DIA match and protein levels, including when using whole-proteome predicted spectral libraries. This is the foundation of discovery DIA-hypothesis-free analysis of DIA samples without library and with reliable FDR control. MaxDIA performs three- or four-dimensional feature detection of fragment data, and scoring of matches is augmented by machine learning on the features of an identification. MaxDIA's bootstrap DIA workflow performs multiple rounds of matching with increasing quality of recalibration and stringency of matching to the library. Combining MaxDIA with two new technologies-BoxCar acquisition and trapped ion mobility spectrometry-both lead to deep and accurate proteome quantification.
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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.