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Microotof qiii

Manufactured by Bruker
Sourced in United States

The MicroOTOF-QIII is a high-performance quadrupole time-of-flight mass spectrometer (QTOF-MS) designed for accurate mass analysis and identification of molecular compounds. It features a compact, modular design and delivers precise mass measurements with high resolution and sensitivity.

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4 protocols using microotof qiii

1

Synthesis and Characterization of Collagen Peptides

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Model collagen fragments H-Gly-Hyp-Pro-Ala-Hyp-Pro-OH (1), H-(Pro)6-OH (2), H-(Pro)9-OH (3), H-(Hyp)6-OH (4) and H-(Hyp)9-OH (5) were synthesized on chlorotrityl resin according the Fmoc/tBu strategy.
Analytical RP-HPLC was performed on a LC Dionex UltiMate 3000 (ThermoFisher Scientific, Waltham, MA, USA), using a Kinetex Reversed Phase C18 column (100 × 4.6 mm). Gradients of 0.1% TFA in H2O (B) and 0.1% TFA in CH3CN (A) were used, at a flow rate 0.4 mL/min with UV detection at 220 and 254 nm. Preparative HPLC was done on a CombiFlash, EZPrep, Teledyne ISCO (Lincoln, NE, USA) using a Supelco Discovery BIO Wide Pore C18 column (25 cm × 21.2 mm, 10 mm; Sigma-Aldrich) flow rate 5 mL/min, detection wavelengths 220 and 254 nm, gradient ratio A (0.1% TFA in CH3CN) and B (0.1% TFA in H2O) 0:100 to 18:82 in 30 min, followed by an isocratic run for 5 min.
Mass Spectrometry analysis was performed on a Bruker microOTOF-QIII (Bruker Corporation, Billerica, MA, USA).
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2

Mapping m6G RNA Methylation Patterns

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From a 20 μL methylation reaction with 1 nmol target RNA, 1.2 nmol ribozyme, 100 μM m6G and 40 mM MgCl2 at pH 7.5 (120 mM KCl, 5 mM NaCl, 50 mM HEPES) for 21 h at 37°C, the methylated RNA product was isolated by PAGE, and subjected to HR-ESI-MS (Bruker microOTOF-Q III, direct injection), RNase T1 digestion (150 IPS of 5'-32P-RNA were digested with 0.5 U RNase T1 in 5 μL 50 mM Tris (pH 7.5) for 30 sec at 37 °C), and alkaline hydrolysis (250 IPS of 5'-32P-RNA in 5 μL 25 mM NaOH were incubated at 95°C for 5 min). Dimroth rearrangement was examined in a volume of 5 μL with 90 IPS of 5'-32P-RNA in 25 mM Na2CO3 buffer (pH 10) with 1 mM EDTA at 65 °C or 1 h. After quenching with high dye gel loading buffer, the samples were resolved on denaturing PAGE and visualized by autoradiography.
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3

Characterization of Organic Compounds

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NMR spectra were measured on a Bruker Avance II Plus (Bruker Corporation, Billerica, MA, USA) spectrometer (700 MHz for 1H-NMR and 176 MHz for 13C-NMR) in CDCl3 solution. 1H and 13C-NMR spectra were referenced according to the residual peak of the solvent based on literature data. Chemical shifts (d) were reported in ppm and coupling constants (J) were reported in Hz. 13C-NMR spectra were proton-decoupled. Flash chromatography was performed using a glass column packed with Baker silica gel (30–60 μm). For TLC, silica gel was used with a 254 nm indicator on Al foils (Sigma-Aldrich, St. Louis, MO, USA). All reagents and solvents were purchased and used as obtained from Sigma-Aldrich (Poznan, Poland). Melting points were obtained using a Büchi SMP-20 apparatus. Mass spectrometry analysis was performed on a Bruker microOTOF-QIII (Bruker Corporation, Billerica, MA, USA) equipped with electrospray ionization mode and a time-of-flight detector (TOF). IR spectra were measured on an FT-IR Alpha Bruker (ATR) instrument in cm−1.
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4

Mapping m6G RNA Methylation Patterns

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From a 20 μL methylation reaction with 1 nmol target RNA, 1.2 nmol ribozyme, 100 μM m6G and 40 mM MgCl2 at pH 7.5 (120 mM KCl, 5 mM NaCl, 50 mM HEPES) for 21 h at 37°C, the methylated RNA product was isolated by PAGE, and subjected to HR-ESI-MS (Bruker microOTOF-Q III, direct injection), RNase T1 digestion (150 IPS of 5'-32P-RNA were digested with 0.5 U RNase T1 in 5 μL 50 mM Tris (pH 7.5) for 30 sec at 37 °C), and alkaline hydrolysis (250 IPS of 5'-32P-RNA in 5 μL 25 mM NaOH were incubated at 95°C for 5 min). Dimroth rearrangement was examined in a volume of 5 μL with 90 IPS of 5'-32P-RNA in 25 mM Na2CO3 buffer (pH 10) with 1 mM EDTA at 65 °C or 1 h. After quenching with high dye gel loading buffer, the samples were resolved on denaturing PAGE and visualized by autoradiography.
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