Chinese Journal of Chromatography ›› 2024, Vol. 42 ›› Issue (4): 333-344.DOI: 10.3724/SP.J.1123.2023.04025
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LI Yanan1,2,3, LIU Xiaoyan3, WANG Yan3, LIU Zhen3, YE Mingliang3,*(), WANG Hailin1,2,*(
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Received:
2023-04-25
Online:
2024-04-08
Published:
2024-04-03
Supported by:
CLC Number:
LI Yanan, LIU Xiaoyan, WANG Yan, LIU Zhen, YE Mingliang, WANG Hailin. Deciphering cellular processes responding to lethality of 17β-estradiol by quantitative phosphoproteomics[J]. Chinese Journal of Chromatography, 2024, 42(4): 333-344.
Fig. 1 Effect of high-dose 17β-estradiol (E2) on HeLa cell viability (n=6) Dose-dependent and time-dependent cell cytotoxicity analysis of E2 in micromolar range by Cell Counting Kit-8 (CCK-8) assay. HeLa cells treated with equal volume of dimethyl sulfoxide (DMSO) were prepared as control samples. ns: no significance, p>0.05. p<0.05, 0.01, 0.001 were shown as *, **, ***, respectively.
Fig. 4 Ti4+-IMAC coupled with DIA-based quantitative method for in-depth identification of phosphorylation sites a. workflow of quantitative phosphoproteomics for temporal profiling of phosphoproteomics responding to E2 stimulation; b. the number of quantified phosphorylation sites and phosphoproteins in each sample; assessment of quantification reproducibility of the phosphorylation site abundances by (c) Pearson correlation analysis and (d) coefficient of variation analysis within each treatment. Each treatment was performed for four biological replicates (bio. rep.1, 2, 3, 4). Ti4+-IMAC: immobilized titanium ion affinity chromatography; DIA: data-independent acquisition; FASP: filter aided sample preparation; SPE: solid-phase extraction; bio.rep.: biological replicate; Pearson’s r: Pearson correlation coefficient.
Fig. 5 Quantitative screening of high-dose E2 regulating phosphorylation sites Comparison of the phosphorylation site abundance changes in E2 versus DMSO treated HeLa cells; FC: fold change; a threshold of p<0.01 and |log2(FC)|≥1 for significantly up- (red) or down-regulated (blue) phosphorylation site by E2.
Fig. 6 Biological information analysis of high-dose E2-regulated phosphoproteins (a, c) Gene Ontology (GO) analysis according to biological process and (b, d) Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway for the E2-regulated phosphoproteins. Upper: the 599 E2-regulated phosphoproteins were quantified by t-test analysis ( |log2(FC)|≥1, p<0.05); lower: the 325 2 E2-regulated phosphoproteins were found to be phosphorylated or dephosphorylated upon high-dose E2 treatment. e. Gene Set Enrichment Analysis (GSEA) enrichment analysis according to KEGG/WikiPathway of E2 treated cell samples. NES: normalized enrichment score; NOM p: nominal p value; FDR: false discovery rate; FDR q: a p value that has been adjusted for the FDR.
Fig. 7 Quantification information of E2 regulating phosphorylation sites Phosphorylation site intensities of each replicate were converted to fold changes over averaged control intensities. Four biological replicates were employed for each treatment. □?: not quantified; M: the maximum multiplicity observed for this phosphorylation site. Singly phosphorylated parent peptides (multiplicity 1, M1) and doubly phosphorylated (multiplicity 2, M2) will undergo site collapse separately.
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