ArticleJournal of proteome research2018
Comparison of In-Solution, FASP, and S-Trap Based Digestion Methods for Bottom-Up Proteomic Studies.
Article in Journal of proteome research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 90 papers.
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Who cites it
90 citing papers in PubMed, 181 citations in OpenAlex.
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- Multiomics analysis to evaluate the enrichment of extracellular vesicles from human plasma.Journal of lipid research · 2025Article
- Proteome-Wide Investigation of Proline Hydroxylation in Pancreatic Ductal Adenocarcinoma Using DiLeu Isobaric Labeling Strategy.Molecular & cellular proteomics : MCP · 2025Article
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- Salivary Proteome Insights: Evaluation of Saliva Preparation Methods in Mucopolysaccharidoses Research.Biomedicines · 2025Article
- The proteomic landscape of stool-derived extracellular vesicles in patients with pre-cancerous lesions and colorectal cancer.Communications biology · 2025Article
- Metabolic Responses, Cell Recoverability, and Protein Signatures of Three Extremophiles: Sustained Life During Long-Term Subzero Incubations.Microorganisms · 2025Article
- Widespread release of translational repression across Plasmodium's host-to-vector transmission event.PLoS pathogens · 2025Article
- Challenges of MS-based small extracellular vesicles proteomics.Journal of extracellular vesicles · 2024Review
- Recurrent somatic mutations of FAT family cadherins induce an aggressive phenotype and poor prognosis in anaplastic large cell lymphoma.British journal of cancer · 2024Article
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- Quantitative proteomics and multi-omics analysis identifies potential biomarkers and the underlying pathological molecular networks in Chinese patients with multiple sclerosis.BMC neurology · 2024Article
- Generational Diet-Induced Obesity Remodels the Omental Adipose Proteome in Female Mice.Nutrients · 2024Article
- Comprehensive Overview of Bottom-Up Proteomics Using Mass Spectrometry.ACS measurement science au · 2024Review
30 more citing papers are in PubMed but not listed here.
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
Abstract
Bottom-up proteomic strategies rely on efficient digestion of proteins into peptides for mass spectrometry analysis. In-solution and filter-based strategies are commonly used for proteomic analysis. In recent years, filter-aided sample preparation (FASP) has become the dominant filter-based method due to its ability to remove SDS prior to mass spectrometry analysis. However, the time-consuming nature of FASP protocols have led to the development of new filter-based strategies. Suspension traps (S-Traps) were recently reported as an alternative to FASP and in-solution strategies as they allow for high concentrations of SDS in a fraction of the time of a typical FASP protocol. In this study, we compare the yields from in-solution, FASP, and S-Trap based digestions of proteins extracted in SDS and urea-based lysis buffers. We performed label-free quantification to analyze the differences in the portions of the proteome identified using each method. Overall, our results show that each digestion method had a high degree of reproducibility within the method type. However, S-Traps outperformed FASP and in-solution digestions by providing the most efficient digestion with the greatest number of unique protein identifications. This is the first work to provide a direct quantitative comparison of two filter-based digestion methods and a traditional in-solution approach to provide information regarding the most efficient proteomic preparation.
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Registered trials
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