Peptide centric detection of cross-linked peptides using PASEF, MeroX, and Skyline

Cross-linking mass spectrometry (XL-MS) has evolved into a pivotal technique for probing protein interactions, with recent ad-vancements significantly enhancing its analytical potential. This technical note presents advancements in cross-linking mass spec-trometry (XL-MS) through the implementation of Parallel Accumulation-Serial Fragmentation (PASEF) on timsTOF instruments, enhancing the detection and analysis of protein interactions. Addressing the challenges in XL-MS, such as the interpretation of complex spectra, low abundance of cross-linked peptides (XL-peptides), and data acquisition biases, the 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 method is described for processing DDA-PASEF data using Bruker software, enabling the conversion of this data into a format compatible with MeroX and Skyline tools. This approach, demonstrated with a bovine serum albumin (BSA) case study, significantly improves the identification and understanding of protein interactions, equipping the cross-linking community to overcome current analytical limitations.