Thr67 Occupied
108
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 H 2 O loss from primary cleavage products have been omitted for clarity. 1
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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. - PowerPoint PPT Presentation
Transcript of Thr67 Occupied
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.
1
Thr67 Occupied
HEK293 SC
22Supplemental Figure #1
Thr67 Occupied
HEK293 SC
Supplemental Figure #2 3
Thr67 Occupied
HEK293 SC
Supplemental Figure #3 4
Thr67 Occupied
HEK293 SC
Supplemental Figure #4 5
Thr67 Occupied
HEK293 SC
Supplemental Figure #5 6
Thr67 Occupied
HEK293 SC
Supplemental Figure #6 7
Thr67 Occupied
HEK293 SC
Supplemental Figure #7 8
Thr67 Occupied
HEK293 SC
Supplemental Figure #8 9
Thr67 Occupied
HEK293 SC
Supplemental Figure #9 10
Thr67 Occupied
HEK293 SC
Supplemental Figure #10 11
Thr67 Unoccupied
HEK293 SC
Supplemental Figure #11 12
Thr67 Unoccupied
HEK293 SC
Supplemental Figure #12 13
Thr67 Unoccupied
HEK293 SC
Supplemental Figure #13 14
Thr67 Unoccupied
HEK293 SC
Supplemental Figure #14 15
Thr67 Unoccupied
HEK293 SC
Supplemental Figure #15 16
Thr67 Unoccupied
HEK293 SC
Supplemental Figure #16 17
Thr67 Unoccupied
HEK293 SC
Supplemental Figure #17 18
Thr108 Occupied (inferred but not unambiguously determined, due to lack of ETD-MS2)
HEK293 SC
Supplemental Figure #18 19
HEK293 SC
Thr108 Occupied (inferred but not unambiguously determined, due to lack of ETD-MS2)
Supplemental Figure #19 20
HEK293 SC
Thr108 Occupied (inferred but not unambiguously determined, due to lack of ETD-MS2)
Supplemental Figure #20 21
HEK293 SC
Thr108 Occupied (inferred but not unambiguously determined, due to lack of ETD-MS2)
Supplemental Figure #21 22
HEK293 SC
Thr108 Occupied (inferred but not unambiguously determined, due to lack of ETD-MS2)
Supplemental Figure #22 23
HEK293 SC
Thr108 Occupied (inferred but not unambiguously determined, due to lack of ETD-MS2)
Supplemental Figure #23 24
Thr108 Unoccupied
HEK293 SC
Supplemental Figure #24 25
Thr108 Unoccupied
HEK293 SC
Supplemental Figure #25 26
Thr108 Unoccupied
HEK293 SC
Supplemental Figure #26 27
Thr108 Unoccupied
HEK293 SC
Supplemental Figure #27 28
Thr108 Unoccupied
HEK293 SC
Supplemental Figure #28 29
Thr147 Occupied
HEK293 SC
Supplemental Figure #29 30
Thr147 Occupied
HEK293 SC
Supplemental Figure #30 31
Thr147 Occupied
HEK293 SC
Supplemental Figure #31 32
Thr147 Unoccupied
HEK293 SC
Supplemental Figure #32 33
Thr147 Unoccupied
HEK293 SC
Supplemental Figure #33 34
Thr147 Unoccupied
HEK293 SC
Supplemental Figure #34 35
Thr235 Occupied
HEK293 SC
Supplemental Figure #35 36
Thr235 Occupied
HEK293 SC
Supplemental Figure #36 37
Thr235 Occupied
HEK293 SC
Supplemental Figure #37 38
Thr235 Occupied
HEK293 SC
Supplemental Figure #38 39
Thr235 Occupied
HEK293 SC
Supplemental Figure #39 40
Thr235 Occupied
HEK293 SC
Supplemental Figure #40 41
Thr235 Occupied
HEK293 SC
Supplemental Figure #41 42
Thr235 Occupied
HEK293 SC
Supplemental Figure #42 43
Thr235 Occupied
HEK293 SC
Supplemental Figure #43 44
Thr235 Occupied
HEK293 SC
Supplemental Figure #44 45
Thr235 Occupied
HEK293 SC
Supplemental Figure #45 46
Thr235 Occupied
HEK293 SC
Supplemental Figure #46 47
Thr235 Occupied
HEK293 SC
Supplemental Figure #47 48
Thr235 Unoccupied
HEK293 SC
Supplemental Figure #48 49
Thr235 Unoccupied
HEK293 SC
Supplemental Figure #49 50
Thr235 Unoccupied
HEK293 SC
Supplemental Figure #50 51
Thr235 Unoccupied
HEK293 SC
Supplemental Figure #51 52
Thr235 Unoccupied
HEK293 SC
Supplemental Figure #52 53
Thr235 Unoccupied
HEK293 SC
Supplemental Figure #53 54
Thr235 Unoccupied
HEK293 SC
Supplemental Figure #54 55
Thr67 Occupied (Position inferred)
CHO WT
Supplemental Figure #55 56
Thr108 Occupied (Position inferred)
CHO WT
Supplemental Figure #56 57
Thr147 Occupied (Position inferred)
CHO WT
Supplemental Figure #57 58
Thr147 Occupied (Position inferred)
CHO WT
Supplemental Figure #58 59
Thr235 Occupied
CHO WT
Supplemental Figure #59 60
Thr235 Occupied
CHO WT
Supplemental Figure #60 61
Thr235 Occupied
CHO WT
Supplemental Figure #61 62
Thr235 Occupied
CHO WT
Supplemental Figure #62 63
Thr235 Occupied
CHO WT
Supplemental Figure #63 64
Thr235 Occupied
CHO WT
Supplemental Figure #64 65
Thr235 Occupied
CHO WT
Supplemental Figure #65 66
Thr235 Occupied
CHO WT
Supplemental Figure #66 67
Thr235 Occupied
CHO WT
Supplemental Figure #67 68
Thr235 Occupied
CHO WT
Supplemental Figure #68 69
Thr235 Occupied
CHO WT
Supplemental Figure #69 70
Thr235 Occupied
CHO WT
Supplemental Figure #70 71
Thr235 Occupied
CHO WT
Supplemental Figure #71 72
Thr235 Occupied
CHO WT
Supplemental Figure #72 73
Thr235 Occupied
CHO WT
Supplemental Figure #73 74
Thr235 Unoccupied
CHO WT
Supplemental Figure #74 75
Thr235 Unoccupied
CHO WT
Supplemental Figure #75 76
Thr235 Unoccupied
CHO WT
Supplemental Figure #76 77
Thr235 Unoccupied
CHO WT
Supplemental Figure #77 78
Thr235 Unoccupied
CHO WT
Supplemental Figure #78 79
Thr235 Unoccupied
CHO WT
Supplemental Figure #79 80
Thr235 Unoccupied
CHO WT
Supplemental Figure #80 81
Thr235 Unoccupied
CHO WT
Supplemental Figure #81 82
Thr235 Unoccupied
CHO WT
Supplemental Figure #82 83
Thr235 Unoccupied
CHO WT
Supplemental Figure #83 84
Thr235 Unoccupied
CHO WT
Supplemental Figure #84 85
Thr235 Unoccupied
CHO WT
Supplemental Figure #85 86
Thr235 Unoccupied
CHO WT
Supplemental Figure #86 87
Thr67 Unoccupied
HEK293 SC T11 KO
Supplemental Figure #87 88
Thr67 Unoccupied
HEK293 SC T11 KO
Supplemental Figure #88 89
Thr108 Unoccupied
HEK293 SCHEK293 SC T11 KO
Supplemental Figure #89 90
Thr108 Unoccupied
HEK293 SC T11 KO
Supplemental Figure #90 91
Thr108 Unoccupied
HEK293 SC T11 KO
Supplemental Figure #91 92
Thr108 Unoccupied
HEK293 SC T11 KO
Supplemental Figure #92 93
Thr108 Unoccupied
HEK293 SC T11 KO
Supplemental Figure #93 94
Thr147 Unoccupied
HEK293 SC T11 KO
Supplemental Figure #94 95
Thr235 Occupied
HEK293 SC T11 KO
Supplemental Figure #95 96
Thr235 Occupied
HEK293 SC T11 KO
Supplemental Figure #96 97
Thr235 Unoccupied
HEK293 SC T11 KO
Supplemental Figure #97 98
Thr235 Unoccupied
HEK293 SC T11 KO
Supplemental Figure #98 99
Thr235 Unoccupied
HEK293 SC T11 KO
Supplemental Figure #99 100
Thr235 Unoccupied
HEK293 SC T11 KO
Supplemental Figure #100 101
Thr235 Unoccupied
HEK293 SC T11 KO
Supplemental Figure #101 102
Supplemental Figures 102-106: MS2 spectra for detected peptides covering potential N-glycosites of the LDLR
ectodomain determined to be occupied using O18-labeled H2O in two cell lines, with annotations by Proteome
Discoverer 1.4.
Figures include HCD-MS2 spectra for peptides covering potential N-glycosites demonstrated to be glycosylated by detection of 18O-Asp. Cell lines represented are HEK293 SC and CHO WT. The 97NGSD site was not found labeled in either cell line; unlabeled peptides from HEK293 SC were characterized (not shown). One 18O-Asp peptide covering the 156NSST site was characterized from HEK293 SC (Fig. 102). No unlabeled peptides covering the 156NSST site was characterized for either cell line. Two 18O-Asp peptides covering the 272NVTL site was characterized from CHO WT (Fig. 104-5) but none from HEK293 SC. No unlabeled peptides covering the 272NVTL site were characterized for either cell line. The 515NGSK site was not found labeled in either cell line, but was conservely represented by unlabeled peptides from both cell lines (not shown). The 657NLTQ site was well covered by multiple 18O-Asp peptides from both cell lines (representative examples in Fig. 103+106).
103
156NSST (Hek293)
Supplemental Figure #102 104
657NLTQ (Hek293)
Supplemental Figure #103 105
272NVTL (CHO)
Supplemental Figure #104 106
272NVTL (CHO)
Supplemental Figure #105 107
657NLTQ (CHO)
Supplemental Figure #106 108
