ArticleAnalytical chemistry2023
Optimized Suspension Trapping Method for Phosphoproteomics Sample Preparation.
Article in Analytical chemistry, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- (Phospho)proteomic Profiling Reveals Mutation-Specific Adaptive Signaling to PI3Kα Inhibition inJournal of proteome research · 2026Article
- MLMarker: a machine learning framework for tissue inference and biomarker discovery.Genome biology · 2026Article
- Mass Spectrometry Proteomics: A Key to Faster Drug Discovery.Journal of medicinal chemistry · 2026Review
- Endogenous Phosphopeptidomics Analysis by Using Mesoporous IMAC Materials.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Inhibition of TBK1/IKKε mediated RIPK1 phosphorylation sensitizes tumors to immune cell killing.Cell death discovery · 2025Article
- FAS Inhibited Proteomics and Phosphoproteomics Profiling of Colorectal Cancer Spheroids Shows Activation of Ferroptotic Death Mechanism.Journal of proteome research · 2024Article
- Chloroform/Methanol Protein Extraction and In-solution Trypsin Digestion Protocol for Bottom-up Proteomics Analysis.Bio-protocol · 2024Article
- Analysis of Protein Cysteine Acylation Using a Modified Suspension Trap (Acyl-Trap).Journal of proteome research · 2024Article
- Analysis of Protein Cysteine Acylation Using a Modified Suspension Trap (Acyl-Trap).bioRxiv : the preprint server for biology · 2024Article
- In-Depth Endogenous Phosphopeptidomics of Serum with Zirconium(IV)-Grafted Mesoporous Silica Enrichment.Analytical chemistry · 2024Article
- Optimized Workflow for Proteomics and Phosphoproteomics With Limited Tissue Samples.Current protocols · 2024Article
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Authors and funding
5 authors.
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Abstract
A successful mass spectrometry-based phosphoproteomics analysis relies on effective sample preparation strategies. Suspension trapping (S-Trap) is a novel, rapid, and universal method of sample preparation that is increasingly applied in bottom-up proteomics studies. However, the performance of the S-Trap protocol for phosphoproteomics studies is unclear. In the existing S-Trap protocol, the addition of phosphoric acid (PA) and methanol buffer creates a fine protein suspension to capture proteins on a filter and is a critical step for subsequent protein digestion. Herein, we demonstrate that this addition of PA is detrimental to downstream phosphopeptide enrichment, rendering the standard S-Trap protocol suboptimal for phosphoproteomics. In this study, the performance of the S-Trap digestion for proteomics and phosphoproteomics is systematically evaluated in large-scale and small-scale samples. The results of this comparative analysis show that an optimized S-Trap approach, where trifluoroacetic acid is substituted for PA, is a simple and effective method to prepare samples for phosphoproteomics. Our optimized S-Trap protocol is applied to extracellular vesicles to demonstrate superior sample preparation workflow for low-abundance, membrane-rich samples.
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