4D-diaXLMS: Proteome-wide Four-Dimensional Data-Independent Acquisition Workflow for Cross-Linking Mass Spectrometry

Cross-linking mass spectrometry (XL-MS) is a powerful tool for examining protein structures and interactions. Nevertheless, analysis of low-abundance cross-linked peptides is often limited in the data-dependent acquisition (DDA) mode due to its semistochastic nature. To address this issue, we introduced a workflow called 4D-diaXLMS, representing the first-ever application of four-dimensional data-independent acquisition for proteome-wide cross-linking analysis. Cross-linking studies of the HeLa cell proteome were evaluated using the classical cross-linker disuccinimidyl suberate as an example. Compared with the DDA analysis, 4D-diaXLMS exhibited marked improvement in the identification coverage of cross-linked peptides, with a total increase of 36% in single-shot analysis across all 16 SCX fractions. This advantage was further amplified when reducing the fraction number to 8 and 4, resulting in 125 and 149% improvements, respectively. Using 4D-diaXLMS, up to 83% of the cross-linked peptides were repeatedly identified in three replicates, more than twice the 38% in the DDA mode. Furthermore, 4D-diaXLMS showed good performance in the quantitative analysis of yeast cross-linked peptides even in a 15-fold excess amount of HeLa cell matrix, with a low coefficient of variation and high quantitative accuracies in all concentrations. Overall, 4D-diaXLMS was proven to have high coverage, good reproducibility, and accurate quantification for in-depth XL-MS analysis in complex samples, demonstrating its immense potential for advances in the field.