ArticleJournal of the American Society for Mass Spectrometry2019
Improving Precursor Selectivity in Data-Independent Acquisition Using Overlapping Windows.
Article in Journal of the American Society for Mass Spectrometry, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 88 papers.
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Who cites it
88 citing papers in PubMed, 160 citations in OpenAlex.
- Identification and characterization of a novel aldehyde metabolite of WIN18,446 and associated WIN18,446-ALDH1A2 protein adducts using mass spectrometry.Drug metabolism reviews · 2026Article
- Revisiting resonance-excitation collision-induced dissociation for data-independent acquisition.bioRxiv : the preprint server for biology · 2026Article
- A quantitative proteomics dataset for assessment and prediction of low dose X-ray radiation exposure in mice.bioRxiv : the preprint server for biology · 2026Article
- Multimodal analysis of molecular remodeling in aging spleen identified global and cell type specific changes.bioRxiv : the preprint server for biology · 2026Article
- Hepatocyte growth factor in biosheets promotes autonomous regeneration of cutaneous tissue after transplantation onto a full-thickness skin defect.Materials today. Bio · 2026Article
- Proteomic profiling of human omental and subcutaneous adipose tissue in individuals with a broad range of BMI.Scientific data · 2026Article
- Advances in Mass Spectrometry Instrumentation and Methodology for Analysis of Alternative Protein Isoforms.Journal of mass spectrometry : JMS · 2026Review
- Is Protein Quantification and Physical Normalization Always Necessary in Proteomics?bioRxiv : the preprint server for biology · 2026Article
- Mistranslating tRNA variants impact the proteome and phosphoproteome of Saccharomyces cerevisiae.G3 (Bethesda, Md.) · 2026Article
- Proteomic Profiling of Human Omental and Subcutaneous Adipose Tissue in Individuals with a Broad Range of BMI.bioRxiv : the preprint server for biology · 2026Article
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- Mass spectrometry-based proteomics of FFPE tissues: progress, limitations, and clinical translation barriers.Clinical proteomics · 2025Review
- Scoring information integration with statistical quality control enhanced cross-run analysis of data-independent acquisition proteomics data.Communications chemistry · 2025Article
- Improving Proteomic Dynamic Range with Multiple Accumulation Precursor Mass Spectrometry.Journal of proteome research · 2025Article
- Mistranslating tRNA variants impact the proteome and phosphoproteome ofbioRxiv : the preprint server for biology · 2025Article
- Slice-PASEF: Maximising Ion Utilisation in LC-MS Proteomics.bioRxiv : the preprint server for biology · 2025Article
- The impact of exercise on skeletal muscle proteome of prediabetic subjects analyzed with data independent mass spectrometry.Scientific reports · 2025Article
- Enrichment of extracellular vesicles using Mag-Net for the analysis of the plasma proteome.Nature communications · 2025Article
- Data Independent Acquisition to Inform the Development of Targeted Proteomics Assays Using a Triple Quadrupole Mass Spectrometer.Journal of proteome research · 2025Article
28 more citing papers are in PubMed but not listed here.
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Authors and funding
10 authors at 3 institutions in 1 country.
Funding
Abstract
A major goal of proteomics research is the accurate and sensitive identification and quantification of a broad range of proteins within a sample. Data-independent acquisition (DIA) approaches that acquire MS/MS spectra independently of precursor information have been developed to overcome the reproducibility challenges of data-dependent acquisition and the limited breadth of targeted proteomics strategies. Typical DIA implementations use wide MS/MS isolation windows to acquire comprehensive fragment ion data. However, wide isolation windows produce highly chimeric spectra, limiting the achievable sensitivity and accuracy of quantification and identification. Here, we present a DIA strategy in which spectra are collected with overlapping (rather than adjacent or random) windows and then computationally demultiplexed. This approach improves precursor selectivity by nearly a factor of 2, without incurring any loss in mass range, mass resolution, chromatographic resolution, scan speed, or other key acquisition parameters. We demonstrate a 64% improvement in sensitivity and a 17% improvement in peptides detected in a 6-protein bovine mix spiked into a yeast background. To confirm the method's applicability to a realistic biological experiment, we also analyze the regulation of the proteasome in yeast grown in rapamycin and show that DIA experiments with overlapping windows can help elucidate its adaptation toward the degradation of oxidatively damaged proteins. Our integrated computational and experimental DIA strategy is compatible with any DIA-capable instrument. The computational demultiplexing algorithm required to analyze the data has been made available as part of the open-source proteomics software tools Skyline and msconvert (Proteowizard), making it easy to apply as part of standard proteomics workflows. Graphical Abstract.
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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.