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Internal stepping accelerates crosstalk identification rates compared to external stepping. The number of identified multi-PTM peptides versus FAIMS internal stepping, FAIMS external stepping, and standard LC-MS/MS for the PTM combinations: phospho–phospho (A), phospho–acetyl (B), phospho–methyl (C), acetyl–acetyl (D), acetyl–methyl (E), and methyl–methyl (F). Inserted Venn diagrams show overlapping peptides detected across multiple conditions.
