ArticleAnalytical chemistry2015
Multiplexed quantification for data-independent acquisition.
Article in Analytical chemistry, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 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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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
28 citing papers in PubMed.
- Implementation of Nonisobaric TMT Analogs for Accurate Precursor-Level Quantification by plexDIA.Rapid communications in mass spectrometry : RCM · 2026Article
- The proteomics and phosphoproteomics landscape of melanoma under T cell attack.Cell reports. Medicine · 2026Article
- Accurate quantification in proteomics with QuantUMS.Nature biotechnology · 2026Article
- Multiplexed Data-Independent Acquisition-Based Proteomics Enabled by TMTpro Complementary Ions.Analytical chemistry · 2025Article
- Combining Data Independent Acquisition With Spike-In SILAC (DIA-SiS) Improves Proteome Coverage and Quantification.Molecular & cellular proteomics : MCP · 2024Article
- Evaluation of Protein Identification and Quantification by the diaPASEF Method on timsTOF SCP.Journal of the American Society for Mass Spectrometry · 2024Article
- Instrumentation at the Leading Edge of Proteomics.Analytical chemistry · 2024Review
- MS-Based Proteomics of Body Fluids: The End of the Beginning.Molecular & cellular proteomics : MCP · 2023Article
- Strategies for Increasing the Depth and Throughput of Protein Analysis by plexDIA.Journal of proteome research · 2023Review
- Chemical isotope labeling for quantitative proteomics.Mass spectrometry reviews · 2023Review
- Making single-cell proteomics biologically relevant.Nature methods · 2023Article
- Increasing the throughput of sensitive proteomics by plexDIA.Nature biotechnology · 2023Article
- Advances in stable isotope labeling: dynamic labeling for spatial and temporal proteomic analysis.Molecular omics · 2022Review
- On the Road to Accurate Protein Biomarkers in Prostate Cancer Diagnosis and Prognosis: Current Status and Future Advances.International journal of molecular sciences · 2021Review
- The Isotopic Ac-IP Tag Enables Multiplexed Proteome Quantification in Data-Independent Acquisition Mode.Analytical chemistry · 2021Article
- Improved SILAC Quantification with Data-Independent Acquisition to Investigate Bortezomib-Induced Protein Degradation.Journal of proteome research · 2021Article
- A Versatile Isobaric Tag Enables Proteome Quantification in Data-Dependent and Data-Independent Acquisition Modes.Analytical chemistry · 2020Article
- Mass Defect-Based DiLeu Tagging for Multiplexed Data-Independent Acquisition.Analytical chemistry · 2020Article
- Mass Spectrometry Advances and Perspectives for the Characterization of Emerging Adoptive Cell Therapies.Molecules (Basel, Switzerland) · 2020Review
- Comparative Proteomic Analysis of Adhesion/Invasion Related Proteins inFrontiers in microbiology · 2020Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
Data-independent acquisition (DIA) strategies provide a sensitive and reproducible alternative to data-dependent acquisition (DDA) methods for large-scale quantitative proteomic analyses. Unfortunately, DIA methods suffer from incompatibility with common multiplexed quantification methods, specifically stable isotope labeling approaches such as isobaric tags and stable isotope labeling of amino acids in cell culture (SILAC). Here we expand the use of neutron-encoded (NeuCode) SILAC to DIA applications (NeuCoDIA), producing a strategy that enables multiplexing within DIA scans without further convoluting the already complex MS(2) spectra. We demonstrate duplex NeuCoDIA analysis of both mixed-ratio (1:1 and 10:1) yeast and mouse embryo myogenesis proteomes. Analysis of the mixed-ratio yeast samples revealed the strong accuracy and precision of our NeuCoDIA method, both of which were comparable to our established MS(1)-based quantification approach. NeuCoDIA also uncovered the dynamic protein changes that occur during myogenic differentiation, demonstrating the feasibility of this methodology for biological applications. We consequently establish DIA quantification of NeuCode SILAC as a useful and practical alternative to DDA-based approaches.
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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.