Fig. 6: DIA-based XL-MS analysis based on predicted spectral libraries.
From: XL-MSDigger: a deep learning-based, versatile solution for cross-linking mass spectrometry
a Distribution of Cα-Cα distances between cross-linking sites of intra-protein cross-linked peptides uniquely identified in DIA analysis among 100 proteins with known structures, with the red line representing the theoretical distance constraint of the DSS cross-linker. b Distribution of Cα-Cα distances between cross-linking sites of intra-protein cross-linked peptides identified in DDA analysis among 100 proteins with known structures. c Mapping schematic of identified cross-linked peptides in DDA results (yellow) and those unique in DIA results (blue) on two proteins (GMPS and RUVBL1) crystal structures. d Interactions between the HSP90AA1 protein and other 10 proteins identified in both DIA and DDA analyses, with lines indicating identified cross-linked peptides between two proteins, brown for DIA results, and green for DDA results. Source data are provided as a Source Data file.
