Isomeric Separation of Permethylated Glycans by Porous Graphitic Carbon (PGC)-LC-MS/MS at High- Temperatures

Transcription

1 Supplementary Information Isomeric Separation of Permethylated Glycans by Porous Graphitic Carbon (PGC)-LC-MS/MS at High- Temperatures Shiyue Zhou 1, Yifan Huang 1, Xue Dong 1, Wenjing Peng 1, Lucas Veillon 1, Daniel A. S. Kitagawa 2, Adelia J. A. Aquino 1,3,4 and Yehia Mechref 1 * 1 Department of Chemistry and Biochemistry, Texas Tech University, Lubbock Texas 79409, USA. 2 Institute of Defense, Chemical, Biological, Radiological and Nuclear (IDQBRN, Brazilian Army), Barra Guaratiba, Rio de Janeiro - RJ, , Brazil. 3 School of Pharmaceutical Sciences and Technology, Tianjin University, Tianjin, , P. R. China 4 Institute for Soil Research, University of Natural Resources and Life Sciences Vienna, Peter- Jordan-Strasse 82, A-1190 Vienna, Austria *Corresponding Author Department of Chemistry and Biochemistry Texas Tech University Lubbock, TX yehia.mechref@ttu.edu Tel: Fax:

2 Table of Contents Methods (pp. 3-4) Results and Discussion (p. 4) Table S-1. Relative abundance of glycan isomers in RNase B. (p. 5) Table S-2. Relative abundance of bi-antennary di-sialylated glycan isomers in bovine fetuin. (p. 6) Table S-3. N-glycan structures released from RNase B and used for Van t Hoff plot. (p. 7) Table S-4. N-glycan structures released from bovine fetuin and used for Van t Hoff plot. (p. 8) Table S-5. Relative abundance of N-glycan isomers in 231 and 231BR breast cancer cell lines. (pp. 9-13) Figure S-1. EIC of reduced and permethylated (A) Man 5, (B) Man 6 and (C) Man 9 N-glycan released from RNase B. The insets depicted total intensities changes at different temperatures when considering different charge states and adducts. (p. 14) Figure S-2. EIC of a reduced and permethylated sialylated complex N-glycans, (A) Hex 5 HexNAc 4 NeuAc 1, (B) Hex 6 HexNAc 5 NeuAc 3 and (C) Hex 6 HexNAc 5 NeuAc 4, released from fetuin. The insets depicted total intensities changes at different temperatures accounting for different charge states and adducts. Figure S-3. Full MS spectrums of (A) Man5, (B) Man6, (C) Man7 (D) Man8 and (E) Man9 glycans derived from RNase B. The formation of adducts is different at the different temperatures studied here. As the column temperature increases, formation of ammonium adduct is favored. Symbols as in Table S-1. Figure S-4. Van t Hoff plots of glycans released from (A) RNase B and (B) fetuin, which were separated on PGC-LC at ambient temperature (25 o C), 40 o C, 55 o C, and 75 o C. (p. 16) Figure S-5. MS/MS spectrum of core fucosylated complex N-glycan standard F1A2G1, the insert represents the EIC of the glycan standard F1A2G1. (p. 17) Figure S-6. (A) EIC of permethylated bi-antennary bi-sialylated glycans released from fetuin, the insert is the relative abundances of the four isomers from PGC-LC-MS quantitation. (B) EICs of glycan standard with (1) an ɑ2, 3 linked sialic acid and (2) an ɑ2, 6 linked sialic acid. (p. 18) Figure S-7. MS/MS spectra of mono-sialylated biantennary N-glycan standards with (A) ɑ2, 3 linked and (B) ɑ2, 6 linked sialic acid. (p. 19) Figure S-8. EICs of (A) tri-sialylated glycans and (B) Man 4 glycans released from the 231 cell line and the 231BR cell line. Distributions of isomeric glycans in the 231 and 231BR cell lines exhibited significant differences (P<0.05). (p. 20) References. (p. 21) 2

3 Supplementary Methods Section Glycan Release and Purification Glycoproteins or blood serum samples were first suspended in 20 mm ammonium bicarbonate buffer (ph 7.5) and subjected to thermal denaturation, at 90 o C, for 20 minutes. Enzymatic release of glycans was next conducted by overnight incubation in a 37 o C water bath with the addition of 100 units of PNGase F. After digestion, the protein in the sample mixture was precipitated by the addition of ice-cold 90% ethanol, to purify glycans. For cell line samples, cells were lysed by freeze/thaw cycling in 20 mm phosphate buffered saline and then sonicated in ice water for 1 h. 1 After sonication, 2.5% of sodium deoxycholate (SDC) was added to enhance the solubility of hydrophobic proteins. Then glycans were released from the cell line proteome by PNGase F digestion at 37 o C for 18 h. After PNGase F digestion, 1% of formic acid was added to remove the SDC. After centrifuging at maximum speed for 10 min, supernatant was collected and dried. Dried glycan samples were then resuspended in 90% ethanol at -20 o C for 10 min to precipitate proteins. Then sample solutions were centrifuged at maximum speed for 10 min and supernatants were collected. After drying, glycan samples were dissolved in 50 µl of water and dialyzed using dialysis membranes, with a Da molecular weight cutoff, to remove salts. Reduction and Permethylation Purified glycan fractions were reduced by adding a 10-µL aliquot of 10µg/µL borane-ammonia complex solution and incubating in a 60 o C water bath for one hour, as described in previous works. 1,2 Reduced glycans were subjected to permethylation using a solid-phase permethylation method. 3-5 Briefly, dried glycans were resuspended in 30 µl DMSO, 1.2 µl water, and 20 µl iodomethane; the solution was then applied to spin columns packed with sodium hydroxide 3

4 beads. After a 25 minute incubation period, another 20 µl of iodomethane was added to the spin columns. Permethylated glycans were eluted from the spin columns by brief centrifugation, followed by the addition of 100 µl of acetonitrile and a final centrifugation step. The eluted product was dried using a centrifugal vacuum concentrator and resuspended in a 20% aqueous acetonitrile solution, containing 0.1% formic acid, at which point it was ready for LC-MS analysis. Supplementary Results and Discussion Section Van t Hoff plots represent the relationship between column temperature and retention times of permethylated glycans on PGC column. The relationship between retention factor and temperature T (in Kelvin) is described by the Van t Hoff equation: lnk= H RT + S R +lnφ where k is retention factor, H is enthalpy, S is entropy, Φ is the phase ratio of the mobile phase and stationary phase, R is the gas constant, and T is thermodynamic temperature. The retention factor, k, was determined by retention time (t R ) and dead time (t 0 ) of the LC system. 6 k= t t 1 4

5 Table S-1. Relative abundance of glycan isomers in RNase B, data acquired on PGC-LC-MS vs NMR data from the literature. 7 Symbols:, N-acetylglucosamine (GlcNAc);, Galactose (Gal);, Fucose (Fuc);, Mannose (Man);, N-acetylneuraminic acid (NeuAc/Sialic Acid) Name PGC-LC-MS relative abundance (%) NMR relative abundance 7 (%) 55.1± ± ± ± ± ± ± ± ± ±

6 Table S-2. Relative abundance of bi-antennary di-sialylated glycan isomers in bovine fetuin, LC- MS data vs NMR data. 8 Name PGC-LC-MS relative abundance (%) NMR relative abundance 8 (%) 3.52± ± ± ±

7 Table S-3. Van t Hoff plot (Figure S3A) generated from data collected during the separation of N-glycan structures, which were released from RNase B and separated on PGC-LC at ambient temperature (25 o C), 40 o C, 55 o C, and 75 o C. Name Structures t R 25 o C (min) t R 40 o C (min) t R 55 o C (min) t R 75 o C (min) Linearity R 2 = R 2 = R 2 = R 2 = R 2 = R 2 = R 2 = R 2 = R 2 =

8 Table S-4. Van t Hoff plot (Figure S3B) generated from data collected during the separation of N-glycan structures, which were released from bovine fetuin and separated on PGC- LC at ambient temperature (25 o C), 40 o C, 55 o C, and 75 o C. In cases where there were multiple peaks, due to isomeric structures that could not be assigned, the retention time of the highest peak was utilized for the construction of the plot. Symbols: as in Table S-1. Name Structures t R 25 o C (min) t R 40 o C (min) t R 55 o C (min) t R 75 o C (min) Linearity R 2 = R 2 = R 2 = R 2 = R 2 = R 2 = R 2 =

9 Table S-5. Relative abundance and putative structures of N-glycan isomers in 231 and 231BR breast cancer cell lines determined by PGC-LC-MS/MS. Symbols: as in Table S-1. Glycan Isomer a 231 b 231_SEM c 231BR b 231BR_SEM c p-value d ND ND ND ND ND ND ND ND ND ND ND ND ND ND E-04 2E-04 2E-06 2E-06 7E-04 3E-03 3E-03 9E-09 8E-05 1E-06 9E-04 2E-04 1E-03 2E-05 2E-05 1E-04 1E-04 3E-01 3E-01 4E-04 4E-04 4E-05 2E-03 7E-10 3E-07 9

10 Glycan Isomer a 231 b 231_SEM c 231BR b 231BR_SEM c p-value d 3 ND ND E E E E-02 1 ND ND E-06 2 ND ND E E E E E E-06 1 ND ND E-08 2 ND ND E E E E E E E-04 1 ND ND E-04 2 ND ND E E E E E E E-03 10

11 Glycan Isomer a 231 b 231_SEM c 231BR b 231BR_SEM c p-value d E E E ND ND 6E ND ND 4E ND ND 4E ND ND 3E ND ND 2E ND ND 2E E E E E E ND ND 2E ND ND 2E ND ND 6E ND ND 5E ND ND 4E ND ND 5E ND ND 1E-09 1 ND ND E-11 2 ND ND E E E E E-01 11

12 Glycan Isomer a 231 b 231_SEM c 231BR b 231BR_SEM c p-value d E E E E E E E E ND ND 7E E ND ND 1E ND ND 2E E E E E E E E ND ND 1E ND ND 3E ND ND 9E ND ND 9E ND ND 9E-08 1 ND ND E-05 2 ND ND E-05 3 ND ND E-05 12

13 a the number of isomers detected for a structure, sorted by their retention time, from smallest to largest. b the relative abundance of glycan isomers associated with 231 and 231BR cell lines. c the standard error of the mean for each quantitation. d the P-value resulted from student T-tests between 231 and 231BR cell line. ND Not Detected. 13

14 (A) (B) Zhou et al. Figure S-1 (C) Figure S-1. EIC of reduced and permethylated (A) Man 5, (B) Man 6 and (C) Man 9 N-glycan released from RNase B. The insets depicted total intensities changes at different temperatures when considering different charge states and adducts. 14

15 (A) (B) Zhou et al. Figure S-2 (C) Figure S-2. EIC of a reduced and permethylated sialylated complex N-glycans, (A) Hex 5 HexNAc 4 NeuAc 1, (B) Hex 6 HexNAc 5 NeuAc 3 and (C) Hex 6 HexNAc 5 NeuAc 4, released from fetuin. The insets depicted total intensities changes at different temperatures accounting for different charge states and adducts. 15

16 Zhou et al. Figure S-3 Figure S-3. Full MS spectrums of (A) Man5, (B) Man6, (C) Man7 (D) Man8 and (E) Man9 glycans derived from RNase B. The formation of adducts is different at the different temperatures studied here. As the column temperature increases, the formation of ammonium adduct is favored. Symbols as in Table S-1. 16

17 Zhou et al. Figure S-4 (A) lnk /T (K -1 ) (B) lnk /T (K -1 ) Figure S-4. Van t Hoff plots of glycans released from (A) RNase B and (B) fetuin, which were separated on PGC-LC at ambient temperature (25 o C), 40 o C, 55 o C, and 75 o C. 17

18 Zhou et al. Figure S-5 Figure S-5. MS/MS spectrum of core fucosylated complex N-glycan standard F1A2G1, the insert represents the EIC of the glycan standard F1A2G1. 18

19 Zhou et al. Figure S-6 Figure S-6. (A) EIC of permethylated bi-antennary bi-sialylated glycans released from fetuin, the insert is the relative abundances of the four isomers from PGC-LC-MS quantitation. (B) EICs of glycan standard with (1) an ɑ2, 3 linked sialic acid and (2) an ɑ2, 6 linked sialic acid. 19

20 Zhou et al. Figure S-7 Figure S-7. MS/MS spectra of mono-sialylated biantennary N-glycan standards with (A) ɑ2, 3 linked and (B) ɑ2, 6 linked sialic acid. 20

21 Zhou et al. Figure S-8 (A) (B) Figure S-8. EICs of (A) tri-sialylated glycans and (B) Man 4 glycans released from the 231 cell line and the 231BR cell line. Distributions of isomeric glycans in the 231 and 231BR cell lines exhibited significant differences (P<0.05). 21

22 References (1) Zhou, S.; Hu, Y.; DeSantos-Garcia, J. L.; Mechref, Y. J Am Soc Mass Spectrom 2015, 26, (2) Dong, X.; Zhou, S.; Mechref, Y. Electrophoresis 2016, 37, (3) Kang, P.; Mechref, Y.; Klouckova, I.; Novotny, M. V. Rapid Commun Mass Spectrom 2005, 19, (4) Kang, P.; Mechref, Y.; Novotny, M. V. Rapid Commun. Mass Spectrom 2008, 22, (5) Mechref, Y.; Kang, P.; Novotny, M. V. Methods Mol Biol 2009, 534, (6) Soukup, J.; Jandera, P. biologija 2011, 57, (7) Fu, D.; Chen, L.; O'Neill, R. A. Carbohydrate research 1994, 261, (8) Green, E. D.; Adelt, G.; Baenziger, J. U.; Wilson, S.; Van Halbeek, H. J. Biol. Chem. 1988, 263,