{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["Grawe C"],"funding":["European Research Council","Stichting Saxum Volutum","KWF Kankerbestrijding"],"pagination":["2683-2693"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC10407929"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["22(8)"],"pubmed_abstract":["In recent years, quantitative mass spectrometry-based interaction proteomics technology has proven very useful in identifying specific DNA-protein interactions using single pull-downs from crude lysates. Here, we applied a SILAC/TMT-based higher-order multiplexing approach to develop an interaction proteomics workflow called Protein-nucleic acid Affinity and Specificity quantification by MAss spectrometry in Nuclear extracts or PASMAN. In PASMAN, DNA pull-downs using a concentration range of specific and control DNA baits are performed in SILAC-labeled nuclear extracts. MS<sup>1</sup>-based quantification to determine specific DNA-protein interactions is then combined with sequential TMT-based quantification of fragmented SILAC peptides, allowing the generation of Hill-like curves and dete"],"journal":["Journal of proteome research"],"pubmed_title":["Determining DNA-Protein Binding Affinities and Specificities from Crude Lysates Using a Combined SILAC/TMT Labeling Strategy."],"pmcid":["PMC10407929"],"funding_grant_id":["771059"],"pubmed_authors":["Hernandez-Quiles M","Jansen PWTC","Grawe C","Vermeulen M","Brimmers A"],"additional_accession":[]},"is_claimable":false,"name":"Determining DNA-Protein Binding Affinities and Specificities from Crude Lysates Using a Combined SILAC/TMT Labeling Strategy.","description":"In recent years, quantitative mass spectrometry-based interaction proteomics technology has proven very useful in identifying specific DNA-protein interactions using single pull-downs from crude lysates. Here, we applied a SILAC/TMT-based higher-order multiplexing approach to develop an interaction proteomics workflow called Protein-nucleic acid Affinity and Specificity quantification by MAss spectrometry in Nuclear extracts or PASMAN. In PASMAN, DNA pull-downs using a concentration range of specific and control DNA baits are performed in SILAC-labeled nuclear extracts. MS<sup>1</sup>-based quantification to determine specific DNA-protein interactions is then combined with sequential TMT-based quantification of fragmented SILAC peptides, allowing the generation of Hill-like curves and dete","dates":{"release":"2023-01-01T00:00:00Z","publication":"2023 Aug","modification":"2025-04-26T06:32:00.442Z","creation":"2025-04-06T11:54:32.437Z"},"accession":"S-EPMC10407929","cross_references":{"pubmed":["37466164"],"doi":["10.1021/acs.jproteome.3c00248"]}}