ArticleJournal of proteome research2019
DO-MS: Data-Driven Optimization of Mass Spectrometry Methods.
Article in Journal of proteome research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers, 1 of them a synthesis that pooled it.
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.
The trial behind it
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Who cites it
36 citing papers in PubMed, 1 synthesis or guideline pooled it, 68 citations in OpenAlex.
- Initial recommendations for performing, benchmarking and reporting single-cell proteomics experiments.Nature methods · 2023Guideline
- Mass Spectrometry-based Solutions for Single-cell Proteomics.Genomics, proteomics & bioinformatics · 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
- Towards a Treatment for Leukodystrophy Using Cell-Based Interception and Precision Medicine.Biomolecules · 2024Review
- Improved Data Acquisition Settings on Q Exactive HF-X and Fusion Lumos Tribrid Orbitrap-Based Mass Spectrometers for Proteomic Analysis of Limited Samples.Journal of proteome research · 2024Article
- Observations from the Proteomics Bench.Proteomes · 2024Article
- Mass Spectrometry-Based Proteogenomics: New Therapeutic Opportunities for Precision Medicine.Annual review of pharmacology and toxicology · 2024Review
- Metabolomic, Proteomic, and Single-Cell Proteomic Analysis of Cancer Cells Treated with the KRASJournal of proteome research · 2023Article
- 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
- Metabolomic, proteomic and single cell proteomic analysis of cancer cells treated with the KRASbioRxiv : the preprint server for biology · 2023Article
- Data-Driven Optimization of DIA Mass Spectrometry by DO-MS.bioRxiv : the preprint server for biology · 2023Article
- Uncovering biology by single-cell proteomics.Communications biology · 2023Review
- Strategies for Increasing the Depth and Throughput of Protein Analysis by plexDIA.Journal of proteome research · 2023Review
- Fiber-Type Shifting in Sarcopenia of Old Age: Proteomic Profiling of the Contractile Apparatus of Skeletal Muscles.International journal of molecular sciences · 2023Review
- Increasing the throughput of sensitive proteomics by plexDIA.Nature biotechnology · 2023Article
- Exploring functional protein covariation across single cells using nPOP.Genome biology · 2022Article
- Single-Cell Proteomics Preparation for Mass Spectrometry Analysis Using Freeze-Heat Lysis and an Isobaric Carrier.Journal of visualized experiments : JoVE · 2022Article
- Insights into protein post-translational modification landscapes of individual human cells by trapped ion mobility time-of-flight mass spectrometry.Nature communications · 2022Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
The performance of ultrasensitive liquid chromatography and tandem mass spectrometry (LC-MS/MS) methods, such as single-cell proteomics by mass spectrometry (SCoPE-MS), depends on multiple interdependent parameters. This interdependence makes it challenging to specifically pinpoint the sources of problems in the LC-MS/MS methods and approaches for resolving them. For example, a low signal at the MS2 level can be due to poor LC separation, ionization, apex targeting, ion transfer, or ion detection. We sought to specifically diagnose such problems by interactively visualizing data from all levels of bottom-up LC-MS/MS analysis. Many software packages, such as MaxQuant, already provide such data, and we developed an open source platform for their interactive visualization and analysis: Data-driven Optimization of MS (DO-MS). We found that in many cases DO-MS not only specifically diagnosed LC-MS/MS problems but also enabled us to rationally optimize them. For example, by using DO-MS to optimize the sampling of the elution peak apexes, we increased ion accumulation times and apex sampling, which resulted in a 370% more efficient delivery of ions for MS2 analysis. DO-MS is easy to install and use, and its GUI allows for interactive data subsetting and high-quality figure generation. The modular design of DO-MS facilitates customization and expansion. DO-MS v1.0.8 is available for download from GitHub: https://github.com/SlavovLab/DO-MS . Additional documentation is available at https://do-ms.slavovlab.net .
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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.