protein subcellular localization prediction tool (psort ii)  (GenScript corporation)

Journal: Molecular & Cellular Proteomics : MCP

Article Title: Proteomic Analysis of Human Topoisomerases Reveals Their Distinct and Diverse Cellular Functions

doi: 10.1016/j.mcpro.2025.101082

Figure Lengend Snippet: Proteomic analysis of human topoisomerase protein interaction networks. A , schematic representation of human TOP1, TOP2A, TOP2B, TOP3A, and TOP3B proteins, each tagged with the SFB (S protein, FLAG, and streptavidin binding peptide) tag. B , western blot analysis of topoisomerase expression levels in HEK293T stable cell lines. Anti-FLAG antibodies were used to detect ectopically expressed topoisomerases, while antibodies against each topoisomerase were used to detect both ectopic and endogenous proteins. The red arrow indicates the SFB-tagged topoisomerases, and the black arrow indicates the endogenous topoisomerases. C , subcellular localization of human topoisomerases in HEK293T cells stably expressing each SFB-tagged topoisomerase. Immunofluorescence staining was performed using an anti-FLAG antibody, with DAPI staining marking the nucleus. Images for different topoisomerases were captured at different times, so fluorescence intensities are not directly comparable. The scale bar represents 10 μm. D , schematic overview of the major steps in the TAP-MS workflow used to identify human topoisomerase-associated protein complexes. E , summary of TAP-MS results for chromatin-bound topoisomerase complexes, including the total number of peptides and proteins identified. High-confidence interacting proteins (HCIPs) were identified using SAINT analysis with a Bayesian false discovery rate (BFDR) threshold of ≤0.05. F , summary of TAP-MS results for soluble topoisomerase complexes, including the total number of peptides and proteins identified. HCIPs were identified using SAINT analysis with a Bayesian FDR threshold of <0.05. DAPI, 4′,6-diamidino-2-phenylindole; LC-MS/MS, liquid chromatography-tandem mass spectrometry; SAINT, Significance Analysis of INTeractome; TAP-MS, tandom affinity purification–mass spectrometry.

Article Snippet: Protein subcellular localization information was downloaded from The Human Protein Atlas ( https://www.proteinatlas.org/ ).

Techniques: Binding Assay, Western Blot, Expressing, Stable Transfection, Immunofluorescence, Staining, Fluorescence, Liquid Chromatography with Mass Spectroscopy, Liquid Chromatography, Mass Spectrometry, Affinity Purification

Journal: Molecular & Cellular Proteomics : MCP

Article Title: Proteomic Analysis of Human Topoisomerases Reveals Their Distinct and Diverse Cellular Functions

doi: 10.1016/j.mcpro.2025.101082

Figure Lengend Snippet: Overview of the topoisomerase protein interaction landscape. A , heatmap showing the averaged and normalized PSM (peptide spectrum match) numbers for each topoisomerase, for each bait protein in the chromatin fractions. B , heatmap showing the averaged and normalized PSM numbers for each topoisomerase, for each bait protein in the soluble fractions. C , subcellular localization of HCIPs for each topoisomerase. Data were obtained from The Human Protein Atlas ( https://www.proteinatlas.org ). D , Gene Ontology (GO) analysis results for the biological processes associated with HCIPs for each topoisomerase. Only terms with p values less than 0.01 are presented. E , GO analysis results for the molecular functions associated with HCIPs for each topoisomerase. Only terms with p values less than 0.01 are presented. HCIP, high-confidence interacting protein.

Article Snippet: Protein subcellular localization information was downloaded from The Human Protein Atlas ( https://www.proteinatlas.org/ ).

Techniques:

Journal: Molecular & Cellular Proteomics : MCP

Article Title: Proteomic Analysis of Human Topoisomerases Reveals Their Distinct and Diverse Cellular Functions

doi: 10.1016/j.mcpro.2025.101082

Figure Lengend Snippet: Overview of the TOP1 interaction network. A , heatmap showing the normalized PSM numbers for TOP1 HCIPs for each bait protein in the chromatin fractions. B , heatmap showing the PSM numbers for TOP1 HCIPs for each bait protein in the soluble fractions. C , an integrated interaction map of the TOP1 HCIPs protein visualized using Cytoscape software. Proteins were clustered based on the biological processes they are involved in. D , the subcellular localization of HCIPs for TOP1. Data were downloaded from The Human Protein Atlas ( https://www.proteinatlas.org ). E , results of GO analysis of the biological processes associated with HCIPs for TOP1. HCIPs, high-confidence interacting proteins; PSM, peptide spectrum match.

Article Snippet: Protein subcellular localization information was downloaded from The Human Protein Atlas ( https://www.proteinatlas.org/ ).

Techniques: Software

Journal: Molecular & Cellular Proteomics : MCP

Article Title: Proteomic Analysis of Human Topoisomerases Reveals Their Distinct and Diverse Cellular Functions

doi: 10.1016/j.mcpro.2025.101082

Figure Lengend Snippet: Overview of the TOP2A and TOP2B interaction network. A , heatmap showing the normalized PSM numbers for TOP2A HCIPs for each bait protein in the chromatin and soluble fractions. B , heatmap showing the normalized PSM numbers for TOP2B HCIPs for each bait protein in the chromatin and soluble fractions. C , an integrated interaction map of TOP2A and TOP2B HCIPs proteins visualized using Cytoscape software. D , the subcellular localization of HCIPs for TOP2A. Data were downloaded from The Human Protein Atlas ( https://www.proteinatlas.org ). E , the subcellular localization of HCIPs for TOP2B. Data were downloaded from The Human Protein Atlas ( https://www.proteinatlas.org ). F , results of GO analysis of the biological processes associated with HCIPs for TOP2A and TOP2B. GO, Gene Ontology; PSM, peptide spectrum match; HCIPs, high-confidence interacting proteins.

Article Snippet: Protein subcellular localization information was downloaded from The Human Protein Atlas ( https://www.proteinatlas.org/ ).

Techniques: Software

Journal: Molecular & Cellular Proteomics : MCP

Article Title: Proteomic Analysis of Human Topoisomerases Reveals Their Distinct and Diverse Cellular Functions

doi: 10.1016/j.mcpro.2025.101082

Figure Lengend Snippet: Overview of the TOP3A interaction network. A , heatmap showing the normalized PSM numbers for TOP3A HCIPs for each bait protein in the chromatin fractions. B , heatmap showing the normalized PSM numbers for TOP3A HCIPs for each bait protein in the soluble fractions. C , an integrated interaction map of TOP3A protein visualized using Cytoscape software. Proteins were clustered based on the biological processes they are involved in. D , the subcellular localization of HCIPs for TOP3A. Data were downloaded from The Human Protein Atlas ( https://www.proteinatlas.org ). E , results of GO analysis of the biological processes associated with HCIPs for TOP3A. GO, Gene Ontology; PSM, peptide spectrum match; HCIP, high-confidence interacting protein.

Article Snippet: Protein subcellular localization information was downloaded from The Human Protein Atlas ( https://www.proteinatlas.org/ ).

Techniques: Software

Journal: Molecular & Cellular Proteomics : MCP

Article Title: Proteomic Analysis of Human Topoisomerases Reveals Their Distinct and Diverse Cellular Functions

doi: 10.1016/j.mcpro.2025.101082

Figure Lengend Snippet: Overview of the TOP3B interaction network. A , heatmap showing the normalized PSM numbers for TOP3B HCIPs for each bait protein in the chromatin fractions. B , heatmap showing the normalized PSM numbers for TOP3B HCIPs for each bait protein in the soluble fractions. C , an integrated interaction map of the TOP3B protein visualized using Cytoscape software. Proteins were clustered based on the biological processes they are involved in. D , the subcellular localization of HCIPs for TOP3B. Data were downloaded from The Human Protein Atlas ( https://www.proteinatlas.org ). E , results of GO analysis of the biological processes associated with HCIPs for TOP3B. HCIP, high-confidence interacting protein; PSM, peptide spectrum match.

Article Snippet: Protein subcellular localization information was downloaded from The Human Protein Atlas ( https://www.proteinatlas.org/ ).

Techniques: Software