ArticleJournal of proteome research2022
In Search of a Universal Method: A Comparative Survey of Bottom-Up Proteomics Sample Preparation Methods.
Article in Journal of proteome research, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 52 papers.
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Who cites it
52 citing papers in PubMed.
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- Comparison of In-Gel and SP3 Based Sample Preparation Protocols for LC-MS/MS Based Proteomics.Proteomics · 2026Article
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- Targeted Quantitative Analysis of Specific Proteins in Cytosolic, Mitochondrial, and Nuclear Fractions Using PRM.Journal of proteome research · 2026Article
- Extracellular Vesicle-Mediated Nucleolin Transfer in Glioblastoma: A Targetable Axis Driving Blood-Tumour Barrier Formation.Journal of extracellular vesicles · 2026Article
- Stroke in persistent chronic kidney disease condition alters innate-immunity to escalate mitochondrial dysfunction and aging.npj aging · 2026Article
- High-Throughput Proteomics Sample Preparation Using a 96-Channel Pipettor and Magnetic Pin Device.Journal of proteome research · 2026Article
- Comparative Analysis of Lysis Buffers for Enhanced Proteomic and Glycoproteomic Profiling.Biomolecules · 2026Article
- The effects of alcohol dependence on the CSF proteome in mice: Evidence for blood-brain barrier dysfunction and neuroinflammation.Neurobiology of disease · 2026Article
- Blood Matrices and Sample Preparation Influence Blood Marker Discovery.Journal of proteome research · 2026Article
- Proteogenomic detection of tumor-specific somatic mutant proteins in urinary extracellular vesicles for non-invasive monitoring of bladder cancer.Frontiers in oncology · 2026Article
- An Overview of Mass Spectrometry-Based Methods to Analyze Post-Translational Modifications.Methods in molecular biology (Clifton, N.J.) · 2026Review
- Major toxin composition of particulate matter from a coal-fired power plant and its proteomics-associated toxicological profiles in the lungs of balb/c mice.Toxicology reports · 2025Article
- From Identification to Insight: Making Full Use of the Diagnostic Potential of MS/MS Proteotyping in Clinical Microbiology Using Efficient Bioinformatics.Journal of proteome research · 2025Review
- Sample Preparation for Multi-Omics Analysis: Considerations and Guidance for Identifying the Ideal Workflow.Proteomics · 2025Review
- A Flexible End-to-End Automated Sample Preparation Workflow Enables Standardized and Scalable Bottom-up Proteomics.Analytical chemistry · 2025Article
- Impact of Sample Preparation Strategies on the Quantitative Accuracy of Low-Abundance Serum Proteins in Shotgun Proteomics.Journal of proteome research · 2025Article
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Robust, efficient, and reproducible protein extraction and sample processing is a key step for bottom-up proteomics analyses. While many sample preparation protocols for mass spectrometry have been described, selecting an appropriate method remains challenging since some protein classes may require specialized solubilization, precipitation, and digestion procedures. Here, we present a comprehensive comparison of the 16 most widely used sample preparation methods, covering in-solution digests, device-based methods, and commercially available kits. We find a remarkably good performance of the majority of the protocols with high reproducibility, little method dependency, and low levels of artifact formation. However, we revealed method-dependent differences in the recovery of specific protein features, which we summarized in a descriptive guide matrix. Our work thereby provides a solid basis for the selection of MS sample preparation strategies for a given proteomics project.
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