Electro-ultrafiltration to remove sodium dodecyl sulfate in proteins extracted for proteomics

Wang, H. B.; Zhang, Y.; Gui, Shuqi; Feng, Yongrui; Han, Huaiyuan; Mao, Shuhong; Lu, Fuping

doi:10.1039/c7ra02692g

Cited by 6 publications

(2 citation statements)

References 26 publications

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“…Detergents are important factors affecting protein activity, considering their solubilization strength and denaturation severity [ 40 ]. Also, the incomplete removal of detergents during the preparation steps can lead to issues such as ion suppression and reduced trypsin efficiency during MS analysis [ 40 , 41 , 42 , 43 ]. Therefore, we applied the reagents to minimize errors arising from the preparation steps’ efficiency and other factors based on previous research [ 39 ].…”

Section: Discussionmentioning

confidence: 99%

Optimizing MS-Based Multi-Omics: Comparative Analysis of Protein, Metabolite, and Lipid Extraction Techniques

Mok,

Joo,

Cho

et al. 2024

Metabolites

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Multi-omics integrates diverse types of biological information from genomic, proteomic, and metabolomics experiments to achieve a comprehensive understanding of complex cellular mechanisms. However, this approach is also challenging due to technical issues such as limited sample quantities, the complexity of data pre-processing, and reproducibility concerns. Furthermore, existing studies have primarily focused on technical performance assessment and the presentation of modified protocols through quantitative comparisons of the identified protein counts. Nevertheless, the specific differences in these comparisons have been minimally investigated. Here, findings obtained from various omics approaches were profiled using various extraction methods (methanol extraction, the Folch method, and Matyash methods for metabolites and lipids) and two digestion methods (filter-aided sample preparation (FASP) and suspension traps (S-Trap)) for resuspended proteins. FASP was found to be more effective for the identification of membrane-related proteins, whereas S-Trap excelled in isolating nuclear-related and RNA-processing proteins. Thus, FASP may be suitable for investigating the immune response and bacterial infection pathways, whereas S-Trap may be more effective for studies focused on the mechanisms of neurodegenerative diseases. Moreover, regarding the choice of extraction method, the single-phase method identified organic compounds and compounds related to fatty acids, whereas the two-phase extraction method identified more hydrophilic compounds such as nucleotides. Lipids with strong hydrophobicity, such as ChE and TG, were identified in the two-phase extraction results. These findings highlight that significant differences among small molecules are primarily identified due to the varying polarities of extraction solvents. These results, obtained by considering variables such as human error and batch effects in the sample preparation step, offer comprehensive and detailed results not previously provided by existing studies, thereby aiding in the selection of the most suitable pre-processing approach.

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Section: Discussionmentioning

confidence: 99%

Optimizing MS-Based Multi-Omics: Comparative Analysis of Protein, Metabolite, and Lipid Extraction Techniques

Mok,

Joo,

Cho

et al. 2024

Metabolites

View full text Add to dashboard Cite

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“…Most recently, Wang et al . constructed a three‐cell electrodialysis platform to deplete SDS from proteins, terming the process electro‐ultrafiltration . As their starting level of SDS was below the CMC, and residual SDS was not quantified, it is difficult to conclude if Wang's device proved successful.…”

Section: Introductionmentioning

confidence: 99%

Accelerated SDS depletion from proteins by transmembrane electrophoresis: Impacts of Joule heating

Unterlander

Doucette

2018

Electrophoresis

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SDS plays a key role in proteomics workflows, including protein extraction, solubilization and mass-based separations (e.g. SDS-PAGE, GELFrEE). However, SDS interferes with mass spectrometry and so it must be removed prior to analysis. We recently introduced an electrophoretic platform, termed transmembrane electrophoresis (TME), enabling extensive depletion of SDS from proteins in solution with exceptional protein yields. However, our prior TME runs required 1 h to complete, being limited by Joule heating which causes protein aggregation at higher operating currents. Here, we demonstrate effective strategies to maintain lower TME sample temperatures, permitting accelerated SDS depletion. Among these strategies, the use of a magnetic stir bar to continuously agitate a model protein system (BSA) allows SDS to be depleted below 100 ppm (>98% removal) within 10 min of TME operations, while maintaining exceptional protein recovery (>95%). Moreover, these modifications allow TME to operate without any user intervention, improving throughput and robustness of the approach. Through fits of our time-course SDS depletion curves to an exponential model, we calculate SDS depletion half-lives as low as 1.2 min. This promising electrophoretic platform should provide proteomics researchers with an effective purification strategy to enable MS characterization of SDS-containing proteins.

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Sodium dodecyl sulfate removal during electrospray ionization using cyclodextrins as simple sample solution additive for improved mass spectrometric detection of peptides

Quirino

2018

Analytica Chimica Acta

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Electro-ultrafiltration to remove sodium dodecyl sulfate in proteins extracted for proteomics

Abstract: A creative electro-ultrafiltration method was developed to remove sodium dodecyl sulfate (SDS) from proteins extracted for proteomics analysis.

Cited by 6 publications

References 26 publications

Optimizing MS-Based Multi-Omics: Comparative Analysis of Protein, Metabolite, and Lipid Extraction Techniques

Optimizing MS-Based Multi-Omics: Comparative Analysis of Protein, Metabolite, and Lipid Extraction Techniques

Accelerated SDS depletion from proteins by transmembrane electrophoresis: Impacts of Joule heating

Sodium dodecyl sulfate removal during electrospray ionization using cyclodextrins as simple sample solution additive for improved mass spectrometric detection of peptides

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