{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["Rojas Echeverri JC"],"funding":["Martin-Luther-Universit?t Halle-Wittenberg","Deutsche Forschungsgemeinschaft","University of Washington","Bundesministerium f?r Wirtschaft und Energie","National Institute of General Medical Sciences","Region of Saxony-Anhalt","NIGMS NIH HHS"],"pagination":["7373-7379"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC11099889"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["96(19)"],"pubmed_abstract":["Cross-linking mass spectrometry (XL-MS) has evolved into a pivotal technique for probing protein interactions. This study describes the implementation of Parallel Accumulation-Serial Fragmentation (PASEF) on timsTOF instruments, enhancing the detection and analysis of protein interactions by XL-MS. Addressing the challenges in XL-MS, such as the interpretation of complex spectra, low abundant cross-linked peptides, and a data acquisition bias, our current study integrates a peptide-centric approach for the analysis of XL-MS data and presents the foundation for integrating data-independent acquisition (DIA) in XL-MS with a vendor-neutral and open-source platform. A novel workflow is described for processing data-dependent acquisition (DDA) of PASEF-derived information. For this, software by"],"journal":["Analytical chemistry"],"pubmed_title":["A Workflow for Improved Analysis of Cross-Linking Mass Spectrometry Data Integrating Parallel Accumulation-Serial Fragmentation with MeroX and Skyline."],"pmcid":["PMC11099889"],"funding_grant_id":["INST 271/404-1 FUGG","RTG 2467 - 391498659","UWPR95794","R24 GM141156","CRC 1423 - 421152132","KK5096401SK0","INST 271/405-1 FUGG"],"pubmed_authors":["Tanzler D","Shulman N","Riffle M","MacLean BX","Hause F","Ihling CH","Iacobucci C","Sinz A","Rojas Echeverri JC"],"additional_accession":[]},"is_claimable":false,"name":"A Workflow for Improved Analysis of Cross-Linking Mass Spectrometry Data Integrating Parallel Accumulation-Serial Fragmentation with MeroX and Skyline.","description":"Cross-linking mass spectrometry (XL-MS) has evolved into a pivotal technique for probing protein interactions. This study describes the implementation of Parallel Accumulation-Serial Fragmentation (PASEF) on timsTOF instruments, enhancing the detection and analysis of protein interactions by XL-MS. Addressing the challenges in XL-MS, such as the interpretation of complex spectra, low abundant cross-linked peptides, and a data acquisition bias, our current study integrates a peptide-centric approach for the analysis of XL-MS data and presents the foundation for integrating data-independent acquisition (DIA) in XL-MS with a vendor-neutral and open-source platform. A novel workflow is described for processing data-dependent acquisition (DDA) of PASEF-derived information. For this, software by","dates":{"release":"2024-01-01T00:00:00Z","publication":"2024 May","modification":"2026-04-08T19:50:50.619Z","creation":"2026-04-08T14:33:42.723Z"},"accession":"S-EPMC11099889","cross_references":{"pubmed":["38696819"],"doi":["10.1021/acs.analchem.4c00829"]}}