ArticleProteomics2016
Untargeted, spectral library-free analysis of data-independent acquisition proteomics data generated using Orbitrap mass spectrometers.
Article in Proteomics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
38 citing papers in PubMed.
- Quantitative Proteomic Profiling of Pinctada fucata Shell Nacre Defines a Solubility-Based Type Classification of Shell Matrix Proteins.Marine biotechnology (New York, N.Y.) · 2026Article
- Applications and Prospects of Artificial Intelligence in ProteomicsCurrent protein & peptide science · 2026Review
- Detection and Quantitation of Small Proteins Using Mass Spectrometry.Molecular & cellular proteomics : MCP · 2025Article
- Toward the Development of a Novel Newborn Screening Modality: In-Depth Nontargeted Proteome Analysis of Dried Blood Spots with a Robotic Pipeline Using Low-Cost Iron Powders.Analytical chemistry · 2025Article
- Blood proteome profiling for biomarker discovery in broilers with necrotic enteritis.Scientific reports · 2025Article
- diaTracer enables spectrum-centric analysis of diaPASEF proteomics data.Nature communications · 2025Article
- diaTracer enables spectrum-centric analysis of diaPASEF proteomics data.bioRxiv : the preprint server for biology · 2024Article
- A crustacean neuropeptide spectral library for data-independent acquisition (DIA) mass spectrometry applications.Proteomics · 2024Article
- Network-based elucidation of colon cancer drug resistance mechanisms by phosphoproteomic time-series analysis.Nature communications · 2024Article
- A universal molecular control for DNA, mRNA and protein expression.Nature communications · 2024Article
- Proteomics techniques in protein biomarker discovery.Quantitative biology (Beijing, China) · 2024Review
- An Optimized and High-Throughput Method for Histone Propionylation and Data-Independent Acquisition Analysis for the Identification and Quantification of Histone Post-translational Modifications.Journal of the American Society for Mass Spectrometry · 2023Article
- Definitive Screening Designs to Optimize Library-Free DIA-MS Identification and Quantification of Neuropeptides.Journal of proteome research · 2023Article
- Research Bronchoscopies in Critically Ill Research Participants: An Official American Thoracic Society Workshop Report.Annals of the American Thoracic Society · 2023Article
- Integrated proteomic and phosphoproteomic data-independent acquisition data evaluate the personalized drug responses of primary and metastatic tumors in colorectal cancer.Biophysics reports · 2023Article
- DIA-MS2pep: a library-free framework for comprehensive peptide identification from data-independent acquisition data.Biophysics reports · 2022Article
- Calibr improves spectral library search for spectrum-centric analysis of data independent acquisition proteomics.Scientific reports · 2022Article
- Data-Independent Acquisition Mass Spectrometry-Based Deep Proteome Analysis for Hydrophobic Proteins from Dried Blood Spots Enriched by Sodium Carbonate Precipitation.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Developing mass spectrometry for the quantitative analysis of neuropeptides.Expert review of proteomics · 2021Review
- Discovery-Versus Hypothesis-Driven Detection of Protein-Protein Interactions and Complexes.International journal of molecular sciences · 2021Review
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
We describe an improved version of the data-independent acquisition (DIA) computational analysis tool DIA-Umpire, and show that it enables highly sensitive, untargeted, and direct (spectral library-free) analysis of DIA data obtained using the Orbitrap family of mass spectrometers. DIA-Umpire v2 implements an improved feature detection algorithm with two additional filters based on the isotope pattern and fractional peptide mass analysis. The targeted re-extraction step of DIA-Umpire is updated with an improved scoring function and a more robust, semiparametric mixture modeling of the resulting scores for computing posterior probabilities of correct peptide identification in a targeted setting. Using two publicly available Q Exactive DIA datasets generated using HEK-293 cells and human liver microtissues, we demonstrate that DIA-Umpire can identify similar number of peptide ions, but with better identification reproducibility between replicates and samples, as with conventional data-dependent acquisition. We further demonstrate the utility of DIA-Umpire using a series of Orbitrap Fusion DIA experiments with HeLa cell lysates profiled using conventional data-dependent acquisition and using DIA with different isolation window widths.
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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.