ArticleAnalytical chemistry2021
Rapid Development of Improved Data-Dependent Acquisition Strategies.
Article in Analytical chemistry, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 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.
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Who cites it
27 citing papers in PubMed.
- A One Health Framework for Proteomics Across the Tree of Life to Advance Food Security, Animal Health, and Ecosystem Resilience.Proteomes · 2026Review
- High-resolution sphingolipid analysis in vitro using LC-qToF MS.Methods in enzymology · 2026Article
- The $10 proteome: low-cost, deep and quantitative proteome profiling of limited sample amounts using the Orbitrap Astral and timsTOF Ultra 2 mass spectrometers.bioRxiv : the preprint server for biology · 2025Article
- Nova: A Library for Rapid Development of Mass Spectrometry Software Applications.Journal of the American Society for Mass Spectrometry · 2025Article
- Low-Abundance Serum Protein Biomarker Candidates for HCC in Patients with Liver Cirrhosis.Journal of proteome research · 2025Article
- LC-MS/DIA-based strategy for comprehensive flavonoid profiling: anRSC advances · 2024Article
- Recent Analytical Methodologies in Lipid Analysis.International journal of molecular sciences · 2024Review
- Studying Plant Specialized Metabolites Using Computational Metabolomics Strategies.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Decoding Ubiquitin Modifications by Mass Spectrometry.Advances in experimental medicine and biology · 2024Review
- A complementary approach for detecting biological signals through a semi-automated feature selection tool.Frontiers in chemistry · 2024Article
- Spectra without stories: reporting 94% dark and unidentified ancient proteomes.Open research Europe · 2024Article
- 6-PlexAnalytical chemistry · 2023Article
- Evaluation of Data-Dependent MS/MS Acquisition Parameters for Non-Targeted Metabolomics and Molecular Networking of Environmental Samples: Focus on the Q Exactive Platform.Analytical chemistry · 2023Article
- Optimization of Mass Spectrometric Parameters in Data Dependent Acquisition for Untargeted Metabolomics on the Basis of Putative Assignments.Journal of the American Society for Mass Spectrometry · 2023Article
- TopNEXt: automatic DDA exclusion framework for multi-sample mass spectrometry experiments.Bioinformatics (Oxford, England) · 2023Article
- Article
- Mass spectrometry DDA parameters and global coverage of the metabolome: Spectral molecular networks of momordica cardiospermoides plants.Metabolomics : Official journal of the Metabolomic Society · 2023Article
- Simulated-to-real benchmarking of acquisition methods in untargeted metabolomics.Frontiers in molecular biosciences · 2023Article
- Emerging Computational Methods in Mass Spectrometry Imaging.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2022Review
- Article
Corrections and comments
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Tandem mass spectrometry (LC-MS/MS) is widely used to identify unknown ions in untargeted metabolomics. Data-dependent acquisition (DDA) chooses which ions to fragment based upon intensities observed in MS1 survey scans and typically only fragments a small subset of the ions present. Despite this inefficiency, relatively little work has addressed the development of new DDA methods, partly due to the high overhead associated with running the many extracts necessary to optimize approaches in busy MS facilities. In this work, we first provide theoretical results that show how much improvement is possible over current DDA strategies. We then describe an in silico framework for fast and cost-efficient development of new DDA strategies using a previously developed virtual metabolomics mass spectrometer (ViMMS). Additional functionality is added to ViMMS to allow methods to be used both in simulation and on real samples via an Instrument Application Programming Interface (IAPI). We demonstrate this framework through the development and optimization of two new DDA methods that introduce new advanced ion prioritization strategies. Upon application of these developed methods to two complex metabolite mixtures, our results show that they are able to fragment more unique ions than standard DDA strategies.
Identifiers
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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.