In-source fragmentation of nucleosides in electrospray ionization towards more sensitive and accurate nucleoside analysis

Abstract

Nucleosides were first found to suffer in-source fragmentation (ISF) in electrospray ionization of mass spectrometry, which led to reduced sensitivity and ambiguous identification. In this work, combination of theoretical calculation...

Qualitative and Quantitative Analytical Techniques of Nucleic Acid Modification Based on Mass Spectrometry for Biomarker Discovery

“…The structural analysis of fragments is also performed by comparing between naturally modified nucleosides and stable isotope-labeled nucleosides [ 141 ]. Chen et al discovered that in-source fragmentation usually occurs in glycosidic bonds, and they found a correlation between glycosidic bond length and cleavage ratio through theoretical calculations, and proposed a qualitative method based on the mass spectrometry of parent ions and in-source cleavage fragments [ 95 ]. (c) Compare chromatographic retention times.…”

“…Yu et al and Yuan et al developed a series of reaction routes through labeling the aldehyde group with hydrazino- s -triazine-based reagents (Me 2 N, Et 2 N, and i-Pr 2 N) [ 88 , 89 ] directly, labeling the carboxyl group under catalysis, and converting the hydroxyl group to the reactive aldehyde group through oxidation before labeling (5hmC to 5fC, and 5hmU to 5fU), which increased the sensitivity of 5fC, 5caC, 5hmC, 5fU, and 5hmU by up to 850 folds ( Figure 3 ) [ 90 , 91 , 92 ]. Other reported hydrazine-based labeling reagents include Girard’s reagents (GirP, GirT, GirD and 4-APC) [ 93 , 94 ] and rhodamine B hydrazine [ 95 ]. In addition, cationic xylyl-bromide (CAX-B) [ 96 ], N -dimethyl-amino naphthalene-1-sulfonyl chloride (Dns-Cl, Dens-Cl) [ 97 ], hydroxyl amine-based reagents [ 98 ], and N -cyclohexyl- N ′- β -(4-methylmorpholinium) ethylcarbodiimide p -toluenesulfonate (CMCT) [ 99 ] play important roles in labeling and improving the sensitivity of nucleic acid modifications.…”

“…Multistage MS (MS/MS/MS) was introduced during modification identification to supplement MS/MS, especially for isomers which share precursor ions and fragment ions, such as m 3 U and m 5 U, or m 1 A and m 6 A [ 103 , 104 ]. The process of nucleoside electrospray ionization (ESI) was estimated, and the sensitivity was found to be limited by the formation of dimers, ion adducts, and in-source fragmentation, which could be prevented through the optimization of pipeline material, gas flow, heating temperature, collision energy, LC elution buffer, and appropriate derivatization reagent [ 95 , 105 ].…”