ReviewJournal of proteome research2023
Strategies for Increasing the Depth and Throughput of Protein Analysis by plexDIA.
Review in Journal of proteome research, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers, 1 of them a synthesis that pooled it.
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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
22 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Initial recommendations for performing, benchmarking and reporting single-cell proteomics experiments.Nature methods · 2023Guideline
- Implementation of Nonisobaric TMT Analogs for Accurate Precursor-Level Quantification by plexDIA.Rapid communications in mass spectrometry : RCM · 2026Article
- Proteomics in bone malignancies: from bulk profiling to single-cell and ultra-low-input technologies.Journal of translational medicine · 2026Review
- Single-Cell Proteomic Technologies: Tools in the Quest for Principles.Annual review of biophysics · 2026Review
- Multiplexed Data-Independent Acquisition-Based Proteomics Enabled by TMTpro Complementary Ions.Analytical chemistry · 2025Article
- Principles of protein abundance regulation across single cells in a mammalian tissue.bioRxiv : the preprint server for biology · 2025Article
- Slice-PASEF: Maximising Ion Utilisation in LC-MS Proteomics.bioRxiv : the preprint server for biology · 2025Article
- Proteomic landscape of Alzheimer's disease: emerging technologies, advances and insights (2021 - 2025).Molecular neurodegeneration · 2025Review
- Ubiquitin-Proteasome System Dysregulation in Alzheimer's Disease Impacts Protein Abundance.bioRxiv : the preprint server for biology · 2025Article
- Increasing mass spectrometry throughput using time-encoded sample multiplexing.bioRxiv : the preprint server for biology · 2025Article
- Dynamics of Single-Cell Protein Covariation during Epithelial-Mesenchymal Transition.Journal of proteome research · 2025Article
- Data acquisition approaches for single cell proteomics.Proteomics · 2025Review
- Massively parallel sample preparation for multiplexed single-cell proteomics using nPOP.Nature protocols · 2024Article
- Inferring post-transcriptional regulation within and across cell types in human testis.bioRxiv : the preprint server for biology · 2024Article
- Single-cell proteomics reveals decreased abundance of proteostasis and meiosis proteins in advanced maternal age oocytes.Molecular human reproduction · 2024Article
- Single-nucleus proteomics identifies regulators of protein transport.bioRxiv : the preprint server for biology · 2024Article
- Dynamics of single-cell protein covariation during epithelial-mesenchymal transition.bioRxiv : the preprint server for biology · 2024Article
- A critical evaluation of ultrasensitive single-cell proteomics strategies.Analytical and bioanalytical chemistry · 2024Review
- Massively parallel sample preparation for multiplexed single-cell proteomics using nPOP.bioRxiv : the preprint server for biology · 2023Article
- Data-Driven Optimization of DIA Mass Spectrometry by DO-MS.Journal of proteome research · 2023Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
Accurate protein quantification is key to identifying protein markers, regulatory relationships between proteins, and pathophysiological mechanisms. Realizing this potential requires sensitive and deep protein analysis of a large number of samples. Toward this goal, proteomics throughput can be increased by parallelizing the analysis of both precursors and samples using multiplexed data independent acquisition (DIA) implemented by the plexDIA framework: https://plexDIA.slavovlab.net. Here we demonstrate the improved precisions of retention time estimates within plexDIA and how this enables more accurate protein quantification. plexDIA has demonstrated multiplicative gains in throughput, and these gains may be substantially amplified by improving the multiplexing reagents, data acquisition, and interpretation. We discuss future directions for advancing plexDIA, which include engineering optimized mass-tags for high-plexDIA, introducing isotopologous carriers, and developing algorithms that utilize the regular structures of plexDIA data to improve sensitivity, proteome coverage, and quantitative accuracy. These advances in plexDIA will increase the throughput of functional proteomic assays, including quantifying protein conformations, turnover dynamics, modifications states and activities. The sensitivity of these assays will extend to single-cell analysis, thus enabling functional single-cell protein analysis.
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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.