Identification of Anomericity and Linkage of Arabinose and Ribose through Collision-Induced Dissociation

Abstract

Arabinose and ribose are two common pentoses that exist in both furanose and pyranose forms in plant and bacteria oligosaccharides. In this study, each pentose isomer, namely α-furanose, β-furanose, α-pyranose, and β-pyranose, was first separated through high-performance liquid chromatography followed by an investigation of collision-induced dissociation in an ion trap mass spectrometer. The major dissociation channels, dehydration and cross-ring dissociation, were analyzed by using high-level quantum chemistry calculations and transition state theory. The branching ratio of major dissociation channels was governed by two geometrical features: one being the cis or trans configuration of O1 and O2 atoms determining dehydration preferability and the other being the number of hydroxyl groups on the same side of the ring as the O1 atom determining the preferability of cross-ring dissociation. The relative branching ratios of the major channels were used to identify anomericity and the linkages of arabinose and ribose. Arabinose in the β-configuration and ribose in the α-configuration are predicted to have larger relative dehydration branching ratios than arabinose in the α-configuration and ribose in the β-configuration, respectively. Arabinose and ribose at the reducing end of oligosaccharides with 1 → 2 (pyranose and furanose), 1 → 3 (pyranose and furanose), 1 → 4 (pyranose only), and 1 → 5 (furanose only) linkages are predicted to undergo 0,2 X, 0,3 X, 0,2 A, and 0,2 A/ 0,3 A cross-ring dissociation, respectively. Application of the dissociation mechanism to the disaccharide linkage determination is demonstrated.

The collision-induced dissociation mechanism of sodiated Hex–HexNAc disaccharides

“…A brief description of the experimental method is reported here, and a complete description has been provided in our previous studies. 28–32 Disaccharides β-Glc-(1→3)-GlcNAc and β-Glc-(1→4)-GlcNAc were synthesized in our laboratory; β-Gal-(1→3)-GalNAc and β-Gal-(1→4)-GalNAc were purchased from Omicron Biochemicals, Inc. (South Bend, IN USA); trisaccharide β-Gal-(1→3)-β-GalNAc-(1→3)-Gal was purchased from Elicityl (Crolles, France). These compounds were used without further purification.…”

A simple tandem mass spectrometry method for structural identification of pentose oligosaccharides

“…A brief description of the experimental method is reported herein; the complete information is provided in our previous studies. 39,44,51,52 L-Arabinose (≥98%), D-ribose (≥99%), D-lyxose (≥99%), D-xylose (≥99%), D-ribulose (≥97%), and D-xylulose (≥98%) were purchased from Sigma-Aldrich (St Louis, MO, USA). A2 [1,5-…”

“…The experimental parameters for ESI were identical to those described in our previous article. 52 For the ESI-MS experiments, the analyte was dissolved in solution of 50 : 50 (v/v%) methanol : deionized water (with LiCl of 2 × 10 −4 M) to a concentration of 2 × 10 −4 M. The method for preparing 18 O-labeled analytes at the reducing end was the same as that described in our previous study. 43…”

“…A brief description of the experimental method is reported herein; the complete information is provided in our previous studies. 39,44,51,52 l -Arabinose (≥98%), d -ribose (≥99%), d -lyxose (≥99%), d -xylose (≥99%), d -ribulose (≥97%), and d -xylulose (≥98%) were purchased from Sigma-Aldrich (St Louis, MO, USA). A2 [1,5-α- l -arabinobiose α-Ara f -(1 → 5)-Ara f , >95%], A3X [α-Ara f -(1 → 3)-β-Xyl p -(1 → 4)-Xyl p , >95%], A2XX [α-Ara f -(1 → 2)-β-Xyl p -(1 → 4)-β-Xyl p -(1 → 4)-Xyl p , >90%], A4 [1,5-α- l -arabinotetraose, α-Ara f -(1 → 5)-α-Ara f -(1 → 5)-α-Ara f -(1 → 5)-Ara f , >95%], X4 [1,4-β-xylotetraose, β-Xyl p -(1 → 4)-β-Xyl p -(1 → 4)-βXyl p -(1 → 4)-Xyl p , >95%], A2,3XX {α-Ara f -(1 → 2)-[α-Ara f -(1 → 3)]-β-Xyl p -(1 → 4)-β-Xyl p -(1 → 4)-Xyl p , >95%}, and XA3XX {β-Xyl p -(1 → 4)-[α-Ara f -(1 → 3)]-β-Xyl p -(1 → 4)-β-Xyl p -(1 → 4)-Xyl p , >95%} were obtained from Megazyme (Chicago, IL, USA).…”

“…49,50 LODES/MS n uses intact oligosaccharides, reducing the sample loss in permethylation/reduction and simplifying the sample preparation process. The dissociation mechanisms of Xyl, 51 Ara, and Rib 52 have been studied recently, and extending LODES/MS n to pentose oligosaccharides is a natural progression. In this study, we first demonstrated that the monosaccharides Ara and Xyl can be differentiated using tandem mass spectrometry.…”