ArticleMolecular & cellular proteomics : MCP2021
Feasibility of Phosphoproteomics on Leftover Samples After RNA Extraction With Guanidinium Thiocyanate.
Article in Molecular & cellular proteomics : MCP, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed, 15 citations in OpenAlex.
- Trial
- Scalable clinical proteomics from DNA/RNA extraction flowthroughs enables integrated proteogenomic profiling from a single cancer biopsy.Clinical proteomics · 2026Article
- PhosSight: A Unified Deep Learning Framework Boosting and Accelerating Phosphoproteome Identification to Enable Biological Discoveries.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- π-SeqOmics: A Sequential Workflow for Genomic, Transcriptomic, Proteomic, and Phosphoproteomic Profiling From Biopsy-Scale Samples.Molecular & cellular proteomics : MCP · 2026Article
- Finding coexisting combinations of posttranslational modifications with HomMTM spectra.Briefings in bioinformatics · 2025Article
- The translatome of glioblastoma.Molecular oncology · 2025Article
- Advancements in Global Phosphoproteomics Profiling: Overcoming Challenges in Sensitivity and Quantification.Proteomics · 2025Review
- Rummagene: massive mining of gene sets from supporting materials of biomedical research publications.Communications biology · 2024Article
- Deep Learning Prediction Boosts Phosphoproteomics-Based Discoveries Through Improved Phosphopeptide Identification.Molecular & cellular proteomics : MCP · 2024Article
- The 2022 Report on the Human Proteome from the HUPO Human Proteome Project.Journal of proteome research · 2023Review
- Phosphoproteomics After Guanidinium Thiocyanate Extraction of Tissue Biopsies.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Relationship between miRNA-433 and SPP1 in the presence of fracture and traumatic brain injury.Experimental and therapeutic medicine · 2021Article
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In daily practice, different types of biomolecules are usually extracted for large-scale "omics" analysis with tailored protocols. However, when sample material is limited, an all-in-one strategy is preferable. Although lysis of cells and tissues with urea is widely used for phosphoproteomic applications, DNA, RNA, and proteins can be simultaneously extracted from small samples using acid guanidinium thiocyanate-phenol-chloroform (AGPC). Use of AGPC for mass spectrometry-based phosphoproteomics was reported but has not yet been thoroughly evaluated against a classical phosphoproteomic protocol. Here we compared urea- with AGPC-based protein extraction, profiling phosphorylations in the DNA damage response pathway after ionizing irradiation of U2OS cells as proof of principle. On average we identified circa 9000 phosphosites per sample with both extraction methods. Moreover, we observed high similarity of phosphosite characteristics (e.g., 94% shared class 1 identifications) and deduced kinase activities (e.g., ATM, ATR, CHEK1/2, PRKDC). We furthermore extended our comparison to murine and human tissue samples yielding similar and highly correlated results for both extraction protocols. AGPC-based sample extraction can thus replace common cell lysates for phosphoproteomic workflows and may thus be an attractive way to obtain input material for multiple omics workflows, yielding several data types from a single sample.
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Registered trials
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