Thr67 Occupied

1. Supplemental Figures 1-101: Compilation of MS2 spectra for all detected peptides relating to the four O-glycosites in LDLR class A repeat linker regions, in three cell lines, with annotations by Proteome Discoverer 1.4. Figures include ”CID-MS2” and, where available, ETD-MS2 spectra for peptides in linker regions with occupied O-glycosites, and HCD-MS2 spectra for peptides with unoccupied O-glycosites. In some cases peptides with unoccupied O-glycosites are represented by ETD-MS2 or ”CID-MS2” spectra. Cell lines represented are HEK293 SC, HEK293 SC T11-KO, and CHO WT. O-glycosites include Thr67, Thr108, Thr147, and Thr235. Annotations of fragments derived by H2O loss from primary cleavage products have been omitted for clarity.

2. HEK293 SC Thr67 Occupied Supplemental Figure #1 2

3. HEK293 SC Thr67 Occupied Supplemental Figure #2

4. HEK293 SC Thr67 Occupied Supplemental Figure #3

5. HEK293 SC Thr67 Occupied Supplemental Figure #4

6. HEK293 SC Thr67 Occupied Supplemental Figure #5

7. HEK293 SC Thr67 Occupied Supplemental Figure #6

8. HEK293 SC Thr67 Occupied Supplemental Figure #7

9. HEK293 SC Thr67 Occupied Supplemental Figure #8

10. HEK293 SC Thr67 Occupied Supplemental Figure #9

11. HEK293 SC Thr67 Occupied Supplemental Figure #10

12. HEK293 SC Thr67 Unoccupied Supplemental Figure #11

13. HEK293 SC Thr67 Unoccupied Supplemental Figure #12

14. HEK293 SC Thr67 Unoccupied Supplemental Figure #13

15. HEK293 SC Thr67 Unoccupied Supplemental Figure #14

16. HEK293 SC Thr67 Unoccupied Supplemental Figure #15

17. HEK293 SC Thr67 Unoccupied Supplemental Figure #16

18. HEK293 SC Thr67 Unoccupied Supplemental Figure #17

19. HEK293 SC Thr108 Occupied (inferred but not unambiguously determined, due to lack of ETD-MS2) Supplemental Figure #18

20. HEK293 SC Thr108 Occupied (inferred but not unambiguously determined, due to lack of ETD-MS2) Supplemental Figure #19

21. HEK293 SC Thr108 Occupied (inferred but not unambiguously determined, due to lack of ETD-MS2) Supplemental Figure #20

22. HEK293 SC Thr108 Occupied (inferred but not unambiguously determined, due to lack of ETD-MS2) Supplemental Figure #21

23. HEK293 SC Thr108 Occupied (inferred but not unambiguously determined, due to lack of ETD-MS2) Supplemental Figure #22

24. HEK293 SC Thr108 Occupied (inferred but not unambiguously determined, due to lack of ETD-MS2) Supplemental Figure #23

25. HEK293 SC Thr108 Unoccupied Supplemental Figure #24

26. HEK293 SC Thr108 Unoccupied Supplemental Figure #25

27. HEK293 SC Thr108 Unoccupied Supplemental Figure #26

28. HEK293 SC Thr108 Unoccupied Supplemental Figure #27

29. HEK293 SC Thr108 Unoccupied Supplemental Figure #28

30. HEK293 SC Thr147 Occupied Supplemental Figure #29

31. HEK293 SC Thr147 Occupied Supplemental Figure #30

32. HEK293 SC Thr147 Occupied Supplemental Figure #31

33. HEK293 SC Thr147 Unoccupied Supplemental Figure #32

34. HEK293 SC Thr147 Unoccupied Supplemental Figure #33

35. HEK293 SC Thr147 Unoccupied Supplemental Figure #34

36. HEK293 SC Thr235 Occupied Supplemental Figure #35

37. HEK293 SC Thr235 Occupied Supplemental Figure #36

38. HEK293 SC Thr235 Occupied Supplemental Figure #37

39. HEK293 SC Thr235 Occupied Supplemental Figure #38

40. HEK293 SC Thr235 Occupied Supplemental Figure #39

41. HEK293 SC Thr235 Occupied Supplemental Figure #40

42. HEK293 SC Thr235 Occupied Supplemental Figure #41

43. HEK293 SC Thr235 Occupied Supplemental Figure #42

44. HEK293 SC Thr235 Occupied Supplemental Figure #43

45. HEK293 SC Thr235 Occupied Supplemental Figure #44

46. HEK293 SC Thr235 Occupied Supplemental Figure #45

47. HEK293 SC Thr235 Occupied Supplemental Figure #46

48. HEK293 SC Thr235 Occupied Supplemental Figure #47

49. HEK293 SC Thr235 Unoccupied Supplemental Figure #48

50. HEK293 SC Thr235 Unoccupied Supplemental Figure #49