SUPPLEMENTARY FIGURE LEGENDS Figure S1. Sample glycopeptide fragmentation. MS2 scans of the fragmentation of the triply charged glycopeptide at m/z = 1152.48.

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SUPPLEMENTARY FIGURE LEGENDS Figure S1. Sample glycopeptide fragmentation. MS2 scans of the fragmentation of the triply charged glycopeptide at m/z = The fragmentation was performed in HCD mode with 17% (A), 24% (B), and 30% (C) normalized collision energy. The glycopeptide was also fragmented in CID mode with 35% normalized collision energy (D), as performed in the PIM methodology. The predicted charge states and fragmentation of selected m/z peaks are annotated. Figure S2. Composite MS1 spectra of rKLK6 anion-exchange chromatographic peaks. Combined MS1 spectra over the DCSANTTSCHILGWGK glycopeptide retention time period for recombinant KLK6 from different anion-exchange peaks. Spectra for peaks A-D are shown in Figure S2(A) to S2(D), respectively. The displayed structures reflect the predicted KLK6-attached glycans by composition, not linkage.

z = +2 Y 4 /Y 4 z = +3 0,4 X 1γ /Y 2 z = +3 2,4 X 4 /C 3 z = +2 Y 4 z = +3 Y 4 z = +2 Y 3α z = +2 C 3 FIGURE S1 (A).

z = +2 Y m/z Relative Abundance z = +2 Y 4 /Y z = +2 Y 3α z = +2 Y 3 z = +3 1,5 X 4α /Y 4 z = +3 3,5 X 1γ /Y 2 z = +2 B 4 /Z 4 z = +2 3,5 X 3 /B 3 FIGURE S1 (B).

z = +2 Y 3α /Y m/z Relative Abundance z = +2 Y 4 z = +2 Y 3α z = +2 Y 4 /Y z = +2 Y z = +2 Y 1γ /Y 3 z = +3 1,3 X 3 z = +3 Z 1 z = +1 B 3 /Z 4 FIGURE S1 (C).

m/z Relative Abundance z = +3 Y 1γ /Y 1 z = +2 Y 4 z = +2 Y 4 /Y z = +2 Y 3α z = +2 Y 3 z = +3 Y 1 FIGURE S1 (D).

FIGURE S2 (A).

FIGURE S2 (B).

FIGURE S2 (C).

FIGURE S2 (D).