Tool for Rapid Analysis of glycopeptide by Permethylation (TRAP) via one-pot site mapping and glycan analysis.

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Horatio Richardson
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1 Tool for Rapid Analysis of glycopeptide by Permethylation (TRAP) via one-pot site mapping and glycan analysis. Asif Shajahan, Nitin T. Supekar, Christian Heiss, Mayumi Ishihara, and Parastoo Azadi* Complex Carbohydrate Research Center, The University of Georgia, 315 Riverbend Road, Athens, GA Corresponding Author*: Supplementary Materials Table of Contents Page No. Supp. Figure S1 - Cluster of peaks and cleaved products were observed for the S-2 acetylated and permethylated angiotensin on MALDI-MS Supp. Figure S2 - Analysis of pronase digest of RNase B by permethylation S-2 Supp. Figure S3 - Evaluation of reproducibility and extraction efficiency of S-3 to S-4 TRAP Supp. Figure S4 - Analysis of tryptic digest of RNase B (25 µg) by TRAP S-5 followed by SPE sample clean up without organic extraction Supp. Figure S5 - Structures of glycoforms of permethylated glycopeptides of S-5 pronase digest of human transferrin. Supp. Figure S6 - Structures of glycoforms of permethylated glycopeptides of S-6 pronase digest of bovine fetuin. Supp. Figure S7 - CID MS 2 of permethylated -glycan released from the S-6 glycopeptides of bovine fetuin Modifications observed on amino acids of peptides during permethylation. S-7 to S-42 Supp. Table S1 S17 Supp. Figure S8 S25 Supp. Figure S26 - Identification of terminal sialic acid linkage isomers on S-44 transferrin by MS n analysis. S-1

2 Supp. Figure S1: Cluster of peaks and cleaved products were observed for the acetylated and permethylated angiotensin on MALDI-MS, which could be due to partial acetylation of histidine and tyrosine. A. B. Supp. Figure S2. Analysis of pronase digest of RNase B by permethylation of glycopeptides and mass spectrometry; MALDI-MS spectra of multiple glycoforms of permethylated glycopeptide from the pronase digest of RNase B; A. at 1/20 pronase glycoprotein ratio; B. at 1/30 pronase glycoprotein ratio; S*RNL. * loss of NMe 3. S-2

3 A. rganic layer B. Water layer C. D. S-3

4 Supp. Figure S3. Evaluation of reproducibility and extraction efficiency of TRAP (the figure is a representative of triplicate experiments); A. MALDI-MS spectrum of multiple glycoforms of permethylated glycopeptide N*LTK from the tryptic digest of RNase B extracted on organic layer, B. MALDI-MS spectrum of permethylated tryptic digest of RNase B extracted on water layer, C & D. monosaccharide composition analysis by GC-MS of organic and water layer, respectively. The figures demonstrate complete recovery of permethylated glycopeptide on organic layer during liquid-liquid extraction (LLE) since no peak corresponding to glycopeptides was observed in water layer. * loss of NMe 3, # non-glycopeptide peak. Results and discussion on the evaluation of reproducibility and liquid-liquid extraction efficiency of TRAP In order to evaluate the liquid-liquid extraction efficiency after the permethylation of glycopeptides, we have compared the presence of permethylated glycopeptide species in both organic and water layer. The organic dichloromethane layer was directly analyzed by MALDI-MS after evaporation (Supp. Figure 3A). The aqueous layer was desalted by C18 SPE, dried and analyzed by MALDI-MS (Supp. Figure 3B). The organic and aqueous layers were also analyzed for the presence of monosaccharides by GC-MS method (Supp. Figures 3C and 3D). In both analysis, almost complete recovery of permethylated glycopeptides towards the organic layer was observed. The experiment was conducted in triplicate and consistent results were observed in all cases. To evaluate the efficient retention of permethylated glycopeptide on C18 SPE cartridge, we have performed direct C18 SPE of permethylation reaction mixture after quenching the reaction with ddh 2 without dichloromethane extraction. Efficient retention of permethylated glycopeptide on C18 SPE cartridge was observed as shown in Supp. Figure S4, even with TRAP performed on 25 µg of RNase B tryptic digest. Experimental procedure Evaluation of LLE of permethylated glycopeptides. The permethylated glycopeptides mixture (250 µg, permethylated in triplicate) was vortexed thoroughly for 10 min with CH 2 Cl 2 and the organic and aqueous layer was separated. The organic layer was washed five times with 2 ml ddh 2. The organic layer was removed carefully and transferred to a clean glass tube and subsequently dried under a stream of nitrogen gas. The aqueous layer and the water washes was mixed, desalted by passing through C18 SPE and lyophilized. The efficiency of the extraction was evaluated by MALDI-MS and gas chromatography (GC) of both organic and water layers (Supp. Figure S3). S-4

5 Supp. Figure S4. Analysis of tryptic digest of RNase B (25 µg) by TRAP followed by SPE sample clean up without organic extraction; MALDI-MS spectrum of multiple glycoforms of permethylated glycopeptide NLTK from the tryptic digest of RNase B. * loss of NMe 3. The spectrum also demonstrates that the sensitivity of TRAP method is 25 µg for RNase B. Supp. Figure S5. Structures of glycoforms of permethylated glycopeptides N*K (Me), N*VT+Me and N*KS+Me detected from the MS analysis of pronase digest of human transferrin. S-5

6 Supp. Figure S6. Structures of glycoforms of permethylated glycopeptides N*C $ S (Me), N*DS (Me) R (Me) and N*GSYL detected from the MS analysis pronase digest of bovine fetuin. Supp. Figure S7. CID MS 2 of permethylated -glycan (unreduced) from the glycopeptides of bovine fetuin upon permethylation (lithium adduct). S-6

7 Modifications observed on amino acids of peptides during permethylation. A peptide library with various peptides which comprises all 20 natural amino acids were permethylated individually and characterized by MS and MS n experiments. In order to deduce a general rule, modifications observed on the amino acids during permethylation reaction was observed and tabulated as shown in Supp. Tables Supp. Table S1. Modifications observed on the amino acids upon permethylation of the peptides and glycopeptides No. Common name of amino acid Structure of methylated amino acids observed Mass difference of permethylated amino acids observed in peptides 1 Glycine Alanine R R' N Me PerMe - A Serine Threonine Cysteine Valine S-7

8 7 Leucine R R' N Me PerMe - L Isoleucine Methionine Proline Phenyl alanine Tyrosine Tryptophan Aspartic acid S-8

9 15 Glutamic acid R Me N R' Me PerMe - E 16 Asparagine Glutamine Histidine Lysine Arginine # - loss of - loss of NMe 3, $ - loss of SMe Elimination of N-terminal α-amine group (after quarternization) was also observed on the peptides during permethylation S-9

10 Relative Abundance z1 Me, Me (K # ) b2 (CH 2 ) 4 NMe 3 NMe 3 (N*K #(Me) ) b2 2 NMe 3 (N*K* #(Me) ) N*K* (Me) c1 (N*) N*K* (Me) m/z Supp. Figure S8: CID MS 3 fragmentation spectra of peptide N*K (Me) (generated from the MS 2 of transferrin glycopeptide) at m/z (1 + ). Supp. Table S2. N*K (Me) Predicted fragment structure Amino acid sequence Fragment type N* c1 K # z1 Me, Me N*K #(Me) - (CH 2 ) 4 NMe 3 b2 - (CH 2 ) 4 NMe 3 S-10

11 N*K* # (Me) b2-2 NMe 3 N*K* (Me) N*K #(Me) N*K (Me) * loss of NMe 3 # loss of Me S-11

12 Relative Abundance a2 NMe 3 (N*V) b2 NMe 3 (N*V) c2 NMe 3 (N*V) N*VT $(Me) a3 - CMe, Me, NMe 3 (N*VT #(Me) - CMe) N*VT ##(Me) N*VT #(Me) m/z Supp. Figure S9: CID MS 3 fragmentation spectra of peptide N*VT #(Me) (generated from the MS 2 of transferrin glycopeptide) at m/z (1 + ). Supp. Table S3. N*VT #(Me) Predicted fragment structure Amino acid sequence N*V Fragment type a2 N*V b2 S-12

13 N*V c2 N*VT #(Me) - CMe a3 - CMe - Me N*VT $(Me) N*VT ##(Me) N*VT #(Me) * loss of NMe 3 # loss of Me $ loss of CH(Me)CH 3 S-13

14 Relative Abundance a2 NMe 3 (N*L) b2 NMe 3 (N*L) b3 NMe 3, Me (N*LT # ) Supp. Figure S10: CID MS 3 fragmentation spectra of peptide N*LTK (generated from the MS 2 of RNase B glycopeptide) at m/z (1 + ) Supp. Table S4: N*LTK (From Glycopeptide) m/z N*LTK N*LT # K b3 NMe 3 (N*LT) N*LT # K* Predicted fragment structure Amino acid sequence Fragment type N*L a2 - NMe 3 NHMe Me N Exact Mass: N*L b2 - NMe 3 NHMe Me N Exact Mass: N Me N*LT b3 - Me, S-14

15 N*LT b3 - NMe 3 N*LT # K* N*LT* NHMe Exact Mass: N*LT # K Me N N Me Me N Me NMe 3 N*LTK * loss of NMe 3 # loss of Me S-15

16 Relative Abundance a2 NMe 3 (N*L) b3 NMe 3, Me (N*LT # ) b2 NMe 3 (N*L) b3 NMe 3 (N*LT) N*LT # K* (Me) N*LTK* (Me) m/z N*LT # K (Me) Supp. Figure S11: CID MS 3 fragmentation spectra of peptide N*LTK (Me) (generated from the MS 2 of RNase B glycopeptide) at m/z (1 + ) Supp. Table S5: N*LTK (Me) (From Glycopeptide) Predicted fragment structure Amino acid sequence Fragment type N*L a2 - NMe 3 N*L b2 - NMe 3 N*LT # b3 - Me, S-16

17 N*LT b3 - NMe 3 N*LT # K* (Me) N*LTK* (Me) N*LT # K (Me) N*LTK (Me) * loss of NMe 3 # loss of Me S-17

18 Synthetic peptides Relative Abundance y2a2 (Y) m/z Supp. Figure S12: CID MS 2 fragmentation spectra of peptide VYV at m/z (1 + ) Supp. Table S6: VYV z2 (Y # V) z2-cme ) a2 NMe 3 (V*Y) V*YV y2 (YV) VYV Predicted fragment structure Amino acid sequence Y Fragment type y2a2 V*Y z2 CMe a2 Y # V z2 - Me S-18

19 YV y2 V*YV VYV * loss of NMe 3 # loss of loss of CMe 100 V*TC (Me) G (Me) Relative Abundance b3 - MeH - CH 2 SCH 2 CNMe 2 (V*T # C $ ) b3z2 (C (Me) ) b2 (V*T) z2 Me z2 (C (Me) G (Me) ) (C (Me) G* (Me) ) V * T # C (Me) G (Me) - MeH V * C (Me) G (Me) - CH(Me)CH m/z VTC (Me) G (Me) Supp. Figure S13: HCD MS 2 fragmentation spectra of peptide VTC (Me) G (Me) at m/z (1 + ) S-19

20 Supp. Table S7: VTC (Me) G (Me) Predicted fragment structure Amino acid sequence C (Me) Fragment type b3z2 V*T b2 V*T # C $ - MeH - CH 2 SCH 2 CNMe 2 b3 - MeH - CH 2 SCH 2 - CNMe 2 C (Me) G* (Me) - Me z2 - Me C (Me) G (Me) z2 S-20

21 V * C (Me) G (Me)\ - CH(Me)CH 3 V * T # C (Me) G (Me) - MeH V * TC (Me) G (Me) VTC (Me) G (Me) * loss of NMe 3 # loss of loss of side chain (-CH(Me)-CH 3 ) $ loss of side chain (-CH 2 -S-CH 2 -C-NMe 2 ) S-21

22 Relative Abundance b3z2 (C (Me) ) b3 - MeH - CH 2 SCH 2 CNMe 2 (V*T # C $ ) b2 (V*T) z2 Me (C (Me) G* (2Me) ) z2 (C (Me) G (2Me) ) V * C (Me) G (2Me) - CH(Me)CH 3 V * T # C (Me) G (2Me) - MeH m/z V*TC (Me) G (2Me) VTC (Me) G (2Me) Supp. Figure S14: HCD MS 2 fragmentation spectra of peptide VTC (Me) G (2Me) at m/z (1 + ) Supp. Table S8: VTC (Me) G (2Me) Predicted fragment structure Amino acid sequence C (Me) Fragment type b3z2 V*T b2 S-22

23 V*T # C $ - MeH - CH 2 SCH 2 CNMe 2 b3 - MeH - CH 2 SCH 2 - CNMe 2 C (Me) G* (Me 2 ) - Me z2 - Me C (Me) G (Me 2 ) z2 V * C (Me) G (Me 2 ) - CH(Me)CH 3 V * T # C (Me) G (Me 2 ) - MeH S-23

24 V * TC (Me) G (Me 2 ) VTC (Me) G (Me 2 ) * loss of NMe 3 # loss of loss of side chain (-CH(Me)-CH 3 ) $ loss of side chain (-CH 2 -S-CH 2 -C-NMe 2 ) Relative Abundance a2 - NMe 2 (N*L) a2 (N*L) b N*LT # K * (N*L) b N*LT # K* # - Me (N*LT # ) N*LT # K m/z Supp. Figure S15: CID MS 2 fragmentation spectra of peptide N*LTK at m/z (1 + ) S-24

25 Supp. Table S9: N*LTK (synthetic peptide) Predicted fragment structure Amino acid sequence N*L Fragment type a2 - NMe 2 N*L a2 N*L b2 N*LT # b3 - Me N*LT # K* # S-25

26 N*LT # K* N*LT # K N*LTK * loss of NMe 3 # loss of loss of CMe S-26

27 Relative Abundance a2 - NMe 2 (N*L) a2 (N*L) b2 (N*L) b3 - Me (N*LT # ) m/z Supp. Figure S16: CID MS 3 fragmentation spectra of peptide N*LTK (Me) at m/z (1 + ) Supp. Table S10: N*LTK (Me) (synthetic peptide) N*LT # K* #(Me) N*LT # K* (Me) N*LT # K (Me) N*LTK (Me) Predicted fragment structure Amino acid sequence N*L Fragment type a2 - NMe 2 N*L a2 N*L b2 S-27

28 N*LT # b3 - Me N*LT # K* #(Me) N*LT # K* (Me) N*LT # K (Me) NMe 2 Me N Exact Mass: N Me Me Me N Me N*LTK (Me) NMe 3 * loss of NMe 3 # loss of Me S-28

29 Relative Abundance c2 - Me (S* #(3Me) A) z2 (NL) m/z Supp. Figure S17: CID MS 2 fragmentation spectra of peptide S* #(3Me) ANL at m/z (1 + ) Supp. Table S11: S* #(3Me) ANL (synthetic peptide) b3 y2 - Me (NL) (S* #(3Me) AN) y3 (ANL) S* #(3Me) ANL Predicted fragment structure Amino acid sequence Fragment type S* #(3Me) A c2 - Me NL z2 NL y2 S-29

30 S* #(3Me) AN b3 - Me ANL y3 S* #(3Me) ANL * loss of NMe 3 # loss of Me Relative Abundance b2 NMe 3 (Y*G) b3 NMe 3 (Y*GG) z3 (GFL) b4 NMe 3 (Y*GGF) Y*GGFL YGGFL m/z Supp. Figure S18: CID MS 2 fragmentation spectra of peptide YGGFL at m/z (1 + ) S-30

31 Supp. Table S12: YGGFL Predicted fragment structure Amino acid sequence Fragment type S-31

32 YGGFL * loss of NMe 3 Supp. Figure S19: CID MS 2 fragmentation spectra of peptide YGGFM $ at m/z (1 + ) Supp. Table S13: YGGFM $ Predicted fragment structure Amino acid sequence Fragment type S-32

33 Y*GG b3 GFM $ z3 - SMe Y*GGF b4 Y*GGFM $ YGGFM $ * - loss of NMe 3 $ - loss of SMe S-33

34 b2 - Me (S* #(3Me) F) S *#(2Me) FLLRN Relative Abundance a2 - Me (S* #(3Me) F) b2 - Me - Me (S* #(2Me) F) b3 - Me (S* #(3Me) FL) S *#(2Me) FLLR $ S *#(3Me) FLLR $ b Me (S* #(3Me) FLL) m/z Supp. Figure S20: CID MS 2 fragmentation spectra of peptide S* #(3Me) FLLRN at m/z (1 + ) Supp. Table S14: S*FLLRN Predicted fragment structure Amino acid sequence Fragment type S* #(3Me) F a2 - Me S* #(2Me) F b2 - Me - Me S* #(3Me) F b2 - Me S-34

35 S* #(3Me) FL b3 - Me S* #(3Me) FLL b4 - Me S* #(2Me) FLLR $ S* #(3Me) FLLR $ S* #(2Me) FLLRN S* #(3Me) FLLRN S-35

36 * - loss of NMe 3 $ - C(NMe)NMe - loss of CMe Relative Abundance z3 (H 2(Me) PF (Me) ) a4 NMe 3 (D*RVY) c5 NMe 3 (D*RVYI) y5 (YIH 2(Me) PF) a6 NMe 3 (D*RVYIH 2(Me) ) a7 NMe 3 (D*RVYIH 2(Me) P) c7 NMe 3 (D*RVYIH 2(Me) P) b2 NMe (D*R) a5 NMe a3 NMe 3 3 (D*RVYI) (D*RV) m/z Supp. Figure S21: CID MS 2 fragmentation spectra of peptide D*RVYIHPF at m/z (1 + ) Relative Abundance a7 NMe 3 c5 NMe (D*RVYIH 2(Me) P) 3 Z3 a6 NMe a4 NMe (D*RVYI) 3 3 (H 2(Me) PF (Me) ) (D*RVYIH 2(Me) ) (D*RVY) y (YIH 2(Me) PF (Me) ) b2 NMe (D*R) a3 NMe 3 c7 NMe (D*RV) a5 NMe (D*RVYIH 2(Me) P) (D*RVYI) D*RVYIH 2(Me) PF (Me) m/z Supp. Figure S22: HCD MS 2 fragmentation spectra of peptide D*RVYIH 2(Me) PF (Me) at m/z (1 + ) S-36

37 Supp. Table S15: D*RVYIH 2(Me) PF (Me) Predicted fragment structure Amino acid sequence D*R Fragment type b2 D*RV a3 HPF z3 D*RVY a4 D*RVYI a5 S-37

38 D*RVYI c5 YIH 2(Me) PF (Me) y5 D*RVYIH 2(Me) a6 D*RVYIH 2(Me) P a7 D*RVYIH 2(Me) P c7 S-38

39 D*RVYIH 2(Me) PF (Me ) * - loss of NMe 3 Relative Abundance c5 NMe 3 (D*RVYI) Z3 (H 3(Me) PF (Me) ) y (YIH 3(Me) PF (Me) ) a4 NMe 3 (D*RVY) a6 NMe 3 (D*RVYIH 3(Me) ) a7 NMe 3 (D*RVYIH 3(Me) P) D*RVYIH 3(Me) PF (Me) c7 NMe 3 (D*RVYIH 3(Me) P) b2 NMe 3 (D*R) a3 NMe a5 NMe (D*RV) 3 (D*RVYI) m/z Supp. Figure S23: CID MS 2 fragmentation spectra of peptide D*RVYIH 3(Me) PF (Me) at m/z (1 + ) Relative Abundance a3 NMe 3 (D*RV) b2 NMe 3 (D*R) Z3 (H 3(Me) PF (Me) ) a4 NMe 3 (D*RVY) y5 (YIH 3(Me) PF (Me) ) c5 NMe 3 (D*RVYI) a6 NMe 3 (D*RVYIH 3(Me) ) a7 NMe 3 (D*RVYIH 3(Me) P) c7 NMe a5 NMe (D*RVYI) (D*RVYIH 3(Me) P) D*RVYIH 3(Me) PF (Me) m/z Supp. Figure S24: HCD MS 2 fragmentation spectra of peptide D*RVYIH 3(Me) PF (Me) at m/z (1 + ) S-39

40 Supp. Table S16: D*RVYIH 3(Me) PF (Me) Predicted fragment structure Amino acid sequence D*R Fragme nt type b2 D*RV a3 H 3(Me) PF (Me) z3 D*RVY a4 D*RVYI a5 S-40

41 D*RVYI c5 YIH 3(Me) PF (Me) y5 D*RVYIH 3(Me) a6 D*RVYIH 3(Me) P a7 D*RVYIH 3(Me) P c7 S-41

42 Me MeN N Me NMe NMe 2 Me N Exact Mass: N Me Me N Me N Me Me NMe Me N Me N N Me Me Me D*RVYIH 3(Me) P F (Me) * - loss of NMe b2 NMe 3 (F*V) Relative Abundance b1 NMe 3 (F*) c1 NMe 3 (F*) b3 NMe 3 (F*VQ) (F*VQW) (F*VQWL) m/z Supp. Figure S25: CID MS 2 fragmentation spectra of peptide F*VQWLM $ NT (Me) at m/z (1 + ) Supp. Table S17: F*VQWLM $ NT (Me) b4 NMe 3 b5 NMe 3 y6 SMe, - Me (QWLM # NT) F*VQWLM $ NT - Me Predicted fragment structure Amino acid sequence Fragment type F* b1 F* c1 S-42

43 F*V b2 F*VQ b3 F*VQW b4 F*VQWL b5 QWLM $ NT y6 - SMe - Me S-43

44 F*VQWLM $ NT - Me F*VQWLM $ NT (Me) * - loss of NMe 3 $ - loss SMe Supp. Figure S26: Identification of terminal sialic acid linkage isomers on human transferrin by MS n analysis. CID MS 5 spectrum of permethylated di-antennary di-sialylated N-linked glycopeptide N*K (Me) from the pronase digest of transferrin showing the presence of both α 2,3 and α 2,6 linked sialic acid (lithium adducts). S-44

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