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A. Development of an optimized bioinert LC-MS/MS workflow for modified nucleoside analysis. Comparison of the reference (left) and optimized (right) workflows, highlighting the replacement of the conventional LC column and mobile phase with a Synergy Hydro-RP bioinert column and optimized mobile-phase composition. Common analytical steps include autosampling, chromatographic separation, ionization, and MS/MS detection. B. Comparison of nucleoside retention times obtained using the reference method (5 mM ammonium acetate, <t>Synergi</t> <t>Fusion-RP</t> column) and the new method (0.5% acetic acid, Synergi Hydro-RP column). The dashed line represents the line of identity (y = x). C. Comparison of fold-change values obtained using the new method relative to the reference method for canonical nucleosides. Fold-change values were calculated relative to the reference method, which was set to 1. Data are presented as mean ± SD. D. Comparison of fold-change values obtained using the new method relative to the reference method for uridine and selected uridine-derived modifications. Fold-change values were calculated relative to the reference method, which was set to 1. Bars represent mean values, and error bars indicate SD. E. Effect of transferring the method to a bioinert LC system on nucleoside detection sensitivity. Data are presented as the ratio of peak areas obtained with the bioinert LC system (LC XSi) to those obtained with the conventional LC-40 system.
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A. Development of an optimized bioinert LC-MS/MS workflow for modified nucleoside analysis. Comparison of the reference (left) and optimized (right) workflows, highlighting the replacement of the conventional LC column and mobile phase with a Synergy Hydro-RP bioinert column and optimized mobile-phase composition. Common analytical steps include autosampling, chromatographic separation, ionization, and MS/MS detection. B. Comparison of nucleoside retention times obtained using the reference method (5 mM ammonium acetate, <t>Synergi</t> <t>Fusion-RP</t> column) and the new method (0.5% acetic acid, Synergi Hydro-RP column). The dashed line represents the line of identity (y = x). C. Comparison of fold-change values obtained using the new method relative to the reference method for canonical nucleosides. Fold-change values were calculated relative to the reference method, which was set to 1. Data are presented as mean ± SD. D. Comparison of fold-change values obtained using the new method relative to the reference method for uridine and selected uridine-derived modifications. Fold-change values were calculated relative to the reference method, which was set to 1. Bars represent mean values, and error bars indicate SD. E. Effect of transferring the method to a bioinert LC system on nucleoside detection sensitivity. Data are presented as the ratio of peak areas obtained with the bioinert LC system (LC XSi) to those obtained with the conventional LC-40 system.
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A. Development of an optimized bioinert LC-MS/MS workflow for modified nucleoside analysis. Comparison of the reference (left) and optimized (right) workflows, highlighting the replacement of the conventional LC column and mobile phase with a Synergy Hydro-RP bioinert column and optimized mobile-phase composition. Common analytical steps include autosampling, chromatographic separation, ionization, and MS/MS detection. B. Comparison of nucleoside retention times obtained using the reference method (5 mM ammonium acetate, Synergi Fusion-RP column) and the new method (0.5% acetic acid, Synergi Hydro-RP column). The dashed line represents the line of identity (y = x). C. Comparison of fold-change values obtained using the new method relative to the reference method for canonical nucleosides. Fold-change values were calculated relative to the reference method, which was set to 1. Data are presented as mean ± SD. D. Comparison of fold-change values obtained using the new method relative to the reference method for uridine and selected uridine-derived modifications. Fold-change values were calculated relative to the reference method, which was set to 1. Bars represent mean values, and error bars indicate SD. E. Effect of transferring the method to a bioinert LC system on nucleoside detection sensitivity. Data are presented as the ratio of peak areas obtained with the bioinert LC system (LC XSi) to those obtained with the conventional LC-40 system.

Journal: bioRxiv

Article Title: SPEAR: Spatial Epitranscriptomic Analysis by Mass Spectrometry Reveals Localized RNA Modification Remodeling During Glioma Progression

doi: 10.64898/2026.10.13.758238

Figure Lengend Snippet: A. Development of an optimized bioinert LC-MS/MS workflow for modified nucleoside analysis. Comparison of the reference (left) and optimized (right) workflows, highlighting the replacement of the conventional LC column and mobile phase with a Synergy Hydro-RP bioinert column and optimized mobile-phase composition. Common analytical steps include autosampling, chromatographic separation, ionization, and MS/MS detection. B. Comparison of nucleoside retention times obtained using the reference method (5 mM ammonium acetate, Synergi Fusion-RP column) and the new method (0.5% acetic acid, Synergi Hydro-RP column). The dashed line represents the line of identity (y = x). C. Comparison of fold-change values obtained using the new method relative to the reference method for canonical nucleosides. Fold-change values were calculated relative to the reference method, which was set to 1. Data are presented as mean ± SD. D. Comparison of fold-change values obtained using the new method relative to the reference method for uridine and selected uridine-derived modifications. Fold-change values were calculated relative to the reference method, which was set to 1. Bars represent mean values, and error bars indicate SD. E. Effect of transferring the method to a bioinert LC system on nucleoside detection sensitivity. Data are presented as the ratio of peak areas obtained with the bioinert LC system (LC XSi) to those obtained with the conventional LC-40 system.

Article Snippet: The reference method was performed on a Nexera LC-40 system equipped with a Synergi Fusion-RP column (250×2mm, 4μm, 80A, 00G-4424-B0, Phenomenex).

Techniques: Liquid Chromatography with Mass Spectroscopy, Modification, Analysis, Comparison, Tandem Mass Spectroscopy, Derivative Assay, Transferring, Sensitivity