ArticleJournal of proteome research2023
Data-Driven Optimization of DIA Mass Spectrometry by DO-MS.
Article 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 10 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
10 citing papers in PubMed.
- Nitrate-Sialin2 axis couples ER-mitochondrial calcium signaling with fatty acid metabolism to drive white adipose browning.Nature communications · 2026Article
- Single-Cell Proteomic Technologies: Tools in the Quest for Principles.Annual review of biophysics · 2026Review
- Principles of protein abundance regulation across single cells in a mammalian tissue.bioRxiv : the preprint server for biology · 2025Article
- Trends in Mass Spectrometry-Based Single-Cell Proteomics.Analytical chemistry · 2025Review
- Standard operating procedure combined with comprehensive quality control system for multiple LC-MS platforms urinary proteomics.Nature communications · 2025Article
- Massively parallel sample preparation for multiplexed single-cell proteomics using nPOP.Nature protocols · 2024Article
- PeakQC: A Software Tool for Omics-Agnostic Automated Quality Control of Mass Spectrometry Data.Journal of the American Society for Mass Spectrometry · 2024Article
- Single-cell proteomics reveals decreased abundance of proteostasis and meiosis proteins in advanced maternal age oocytes.Molecular human reproduction · 2024Article
- Massively parallel sample preparation for multiplexed single-cell proteomics using nPOP.bioRxiv : the preprint server for biology · 2023Article
- Strategies for Increasing the Depth and Throughput of Protein Analysis by plexDIA.Journal of proteome research · 2023Review
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
Mass spectrometry (MS) enables specific and accurate quantification of proteins with ever-increasing throughput and sensitivity. Maximizing this potential of MS requires optimizing data acquisition parameters and performing efficient quality control for large datasets. To facilitate these objectives for data-independent acquisition (DIA), we developed a second version of our framework for data-driven optimization of MS methods (DO-MS). The DO-MS app v2.0 (do-ms.slavovlab.net) allows one to optimize and evaluate results from both label-free and multiplexed DIA (plexDIA) and supports optimizations particularly relevant to single-cell proteomics. We demonstrate multiple use cases, including optimization of duty cycle methods, peptide separation, number of survey scans per duty cycle, and quality control of single-cell plexDIA data. DO-MS allows for interactive data display and generation of extensive reports, including publication of quality figures that can be easily shared. The source code is available at github.com/SlavovLab/DO-MS.
Indexed as
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What OpenQuestion holds
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.