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

2. 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 1545.64 z = +2 C 3 FIGURE S1 (A).

3. z = +2 Y 4 20040060080010001200140016001800 m/z 0 10 20 30 40 50 60 70 80 90 100 Relative Abundance 1626.66 204.09 1444.10 409.82 1025.74 768.10 540.13 366.30 z = +2 Y 4 /Y 4 1524.62 z = +2 Y 3α 1545.64 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).

4. z = +2 Y 3α /Y 3 20040060080010001200140016001800 m/z 0 10 20 30 40 50 60 70 80 90 100 Relative Abundance 204.09 1626.66 1545.64 1444.10 1064.87 713.61 1261.04 875.10 z = +2 Y 4 z = +2 Y 3α z = +2 Y 4 /Y 4 1524.62 z = +2 Y 3 366.30 1371.07 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).

5. 20040060080010001200140016001800 m/z 0 10 20 30 40 50 60 70 80 90 100 Relative Abundance 1626.66 1444.10 1078.97 1005.44 z = +3 Y 1γ /Y 1 z = +2 Y 4 z = +2 Y 4 /Y 4 1524.62 1545.64 z = +2 Y 3α z = +2 Y 3 z = +3 Y 1 FIGURE S1 (D).

6. FIGURE S2 (A).

7. FIGURE S2 (B).

8. FIGURE S2 (C).

9. FIGURE S2 (D).