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24 protocols using maxis 4g q tof mass spectrometer

1

Comprehensive Spectroscopic Characterization

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Optical rotations were measured on a Perkin-Elmer model 343 polarimeter. UV spectra were recorded on a Hitachi U2910 UV spectrophotometer. ECD measurements were performed on a JASCO J-810 spectropolarimeter. IR spectra were recorded on a Nicolet 6700 FT-IR spectrometer. 1H and 13C, DEPT, HSQC, HMBC, NOESY, and COSY NMR spectra were recorded on a Bruker Avance DRX-400, DRX-700, or a DRX-800 MHz NMR spectrometer. ESIMS, HRESIMS, and MS2 spectra were measured on a Bruker Maxis 4G Q-TOF mass spectrometer. All mass spectrometric data were obtained in the positive-ion mode using an ESI ion source, with scan ranges (m/z) from 100 to 1000. For MS2 measurements, a dilute sample (around 1 µM in MeOH) was introduced via a syringe pump at a flow rate of 3 µL/min. Column chromatography was conducted using silica gel (65 × 250 or 230 × 400 mesh, Sorbent Technologies). Analytical thin-layer chromatography (TLC) was performed on precoated silica gel 60 F254 plates (Sorbent Technologies). Sephadex LH-20 was purchased from Amersham Biosciences. For visualization of TLC plates, sulfuric acid reagent was used. Fluorescence was tested using a Spectroline (model ENF-260C) UV light source at 386 nm wavelength. All procedures were carried at room temperature using solvents purchased from commercial sources and employed without further purification.
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2

Synthetic Methodology for Organic Compounds

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Commercially available starting materials, reagents, and solvents were used as received. Unless otherwise indicated, all reactions were conducted in oven-dried glassware. In general, anhydrous reactions were performed under nitrogen. Reactions were monitored by thin-layer chromatography (TLC) carried out on pre-coated glass plates of silica gel (0.25 mm) 60 F254 from EMD Chemicals Inc. Visualization was accomplished with ultraviolet light (UV 254 nm), or by shaking the TLC plate in a sealed jar containing silica gel and iodine. Flash column chromatography was performed using 230–400 mesh silica gel purchased from Silicycle. All work-up and purification procedures were carried out with reagent grade solvents in the air. Yields refer to isolate yield unless otherwise stated. Melting points were determined on a MEL-TEMP 3.0 apparatus. 1H NMR and 13C NMR spectra were recorded on Varian 400 MHz instrument. Chemical shifts are reported in parts per million (ppm) and are calibrated using residual undeuterated solvent as an internal reference (CDCl3: δ 7.26 ppm; CD3OD: δ 3.31 ppm; DMSO: δ 2.50 ppm). Data are reported as follows: chemical shift, multiplicity, coupling constants (Hz), and integration. High resolution positive ion mass (HRMS) analyses were conducted on a Bruker MaXis 4G Q-TOF mass spectrometer with electrospray ionization source.
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3

Spectroscopic Analysis of Organic Compounds

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Optical rotations were measured on a Perkin–Elmer 241 Polarimeter. UV spectra were recorded on an Aminco/OLIS UV-Vis Spectrophotometer. ECD spectra were recorded on an AVIV Model 420 Circular Dichroism Spectrometer. IR spectra were measured with a Bruker Equinox 55/S FT–IR Spectrophotometer. Both 1D and 2D NMR spectra were obtained using a Bruker Avance 600 MHz spectrometer with 1H{13C/15N} cryoprobe and a 500 MHz spectrometer with 13C/15N{1H} cryoprobe; chemical shifts were referenced to the residual solvent peaks (CD3OD: δH = 3.31, δC = 49.15). HRMS and MS/MS data were acquired with a Bruker MaXis 4G QTOF mass spectrometer. RP HPLC was performed using a Shimadzu Prominence HPLC system and a Phenomenex Luna C18 column (250 × 10 mm, 5 µm).
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4

Characterization of Novel Organic Compounds

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All the starting materials, and solvents were purchased commercially and used as received, unless otherwise stated. Reactions were monitored by thin-layer chromatography (TLC) using silica gel 60 F254 (EMD Chemicals Inc, Billerica, MA) Flash column chromatography was conducted using 230–400 mesh silica gel (SiliCycle Inc, Quebec, Canada). Melting points were determined using MEL-TEMP 3.0 apparatus without correction. 1H NMR and 13C NMR spectra were recorded at 400 MHz on a Varian spectrometer with CDCl3 as solvent and tetramethylsilane (TMS) as the internal standard. All chemical shift values are reported in parts per million (ppm) and were calibrated using a residual undeuterated solvent as an internal reference (CDCl3: δ 7.26 ppm). Coupling constants (J) are reported in units of Hertz (Hz). The following abbreviations are used to describe multiplicities – s (singlet), d (doublet), t (triplet), q (quartet), m (multiplet), br. (broad). High resolution mass spectra (HRMS, m/z) was acquired by a Bruker MaXis 4G Q-TOF mass spectrometer with electrospray ionization source.
All animal experiments were conducted under Washington University’s Institutional Animal Care and Use Committee IACUC)-approved protocols in accordance with the US National Research Council’s Guide for the Care and Use of Laboratory Animals.
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5

Spectroscopic Characterization of Compounds

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UV spectra were recorded on an Aminco/OLIS UV-Vis Spectrophotometer (Bogart, GA, USA). IR spectra were measured with a Bruker Equinox 55/S FT–IR Spectrophotometer (Santa Barbara, CA, USA). Both 1D and 2D NMR spectra were obtained using a Bruker Avance 500 MHz spectrometer (Billerica, MA, USA) with 1H{13C/15N} cryoprobe and a 500 MHz spectrometer with 13C/15N{1H} cryoprobe; chemical shifts were referenced to the residual solvent peaks (CD3OD: δH = 3.31, δC = 49.15; DMSO-d6: δH = 2.50, δC = 39.51). HRMS data were acquired with a Bruker MaXis 4G QTOF mass spectrometer (Billerica, MA, USA). RP HPLC was performed using a Shimadzu Prominence HPLC system and a Phenomenex Luna C18 column (250 × 10 mm, 5 µm) (Torrance, CA, USA).
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6

Comprehensive Analytical Characterization Protocol

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Optical rotations were measured with a Perkin-Elmer 241 polarimeter. UV spectra were recorded with an Aminco/OLIS UV-Vis spectrophotometer. IR spectra were measured with a Bruker Equinox 55/S FT-IR spectrophotometer. 1D and 2D NMR data were recorded using a Bruker Avance 600 MHz spectrometer with a 1H{13C/15N} cryoprobe and a 500 MHz spectrometer with a 13C/15N{1H} cryoprobe, AVANCE-500, or DRX-400 spectrometers. Chemical shift values were referenced to the residual solvent peaks (CDCl3: δH7.26, δC 77.18; methanol-d4: δH 3.31, δC 49.15) HRMS data were acquired with a Bruker Maxis 4G QTOF mass spectrometer. Reverse phase (RP) HPLC was performed using a Shimadzu Prominence HPLC System and a Phenomenex Luna C-18 semi-prep column (250 × 10 mm, 5 μm), Phenomenex Luna phenyl-hexyl semi-prep column (250 × 10 mm, 5 μm) or a Phenomenex Luna phenyl-hexyl analytical column (250 × 4.6 mm, 5 μm).
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7

Characterization of dCREG Protein by Mass Spectrometry

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N-terminal sequence analysis of bands blotted onto PVDF membranes (Bio-Rad) as described previously [21] (link) was performed by Edman degradation on an Applied Biosystems Procise 492 protein sequencer (Protein Micro-Analysis Facility, Medical University of Innsbruck, Austria). dCREG treated with cathepsin L was also characterized by LC-electrospray ionization-MS, either as intact protein or after digestion with trypsin or chymotrypsin subsequent to separation by SDS-PAGE [22] (link). The samples were fractionated by nano-LC (150 × 0.32 mm BioBasic-18, Thermo Scientific, Waltham, MA) using a gradient of 1–80% acetonitrile. On-line data acquisition was conducted in positive-ion mode on a maXis-4GQ-TOF mass spectrometer (Bruker, Billerica, MA). MS2 scans of dominant precursor peaks were manually analyzed with Data Analysis software version 4.0 (Bruker).
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8

Kinetic Characterization of mVP24/Kelch Interaction

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All protein samples were prepared in PBS buffer (pH 7.4) at 60 µM concentrations. NEM labeling experiments were performed as described before [21 (link)]. Briefly, 100 µl of mVP24/Kelch was mixed with NEM (60 µM, 100 µl) and incubated at 25 °C with aliquots removed at different time points. As a control, the footprinting of mVP24 alone was performed under identical conditions. At certain selected time point (0, 30, 60, 120, 360, 900, 1800, 3600 and 14400s), 4-µL fractions were removed and added to a series of microcentrifuge tubes containing 4 µL of DTT (20 mM) to quench the labeling reaction. Following quenching, 2 µl of each sample was diluted with water and injected into a maXis 4G Q-TOF mass spectrometer (Bruker, Billerica, MA) coupled to an Agilent 1200 HPLC (Agilent, Sana Clara, CA) for mass measurement of the intact protein. Protein samples were loaded on a ZORBAX Eclipse XDB C8 column (2.1 mm × 15 mm, Agilent) for desalting (3min) and then eluted to the mass spectrometer by using 50% (v/v) acetonitrile with 0.1% formic acid (FA) at a flow rate of 10 µl/min.
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9

Alkylation and Mass Spectrometry of RBD-215

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Purified RBD-215 proteins were S-alkylated with iodoacetamide and digested in solution with endoproteinases LysC (Roche) and GluC (Promega). Digested samples were analyzed using a maXis 4G QTOF mass spectrometer (Bruker) as described (Klausberger et al., 2021 (link)).
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10

Spectroscopic Characterization of Organic Compounds

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Optical rotations were measured at room temperature on an Anton Paar polarimeter (Anton Paar, Graz, Austria). UV spectra were recorded on a Hitachi U2910 ultraviolet spectrophotometer. ECD measurements were performed using a JASCO J-810 spectropolarimeter. IR spectra were recorded on a Nicolet 6700 FT-IR spectrometer. 1H and 13C, DEPT 90, DEPT 135, HSQC, HMBC, NOESY, and COSY NMR spectra were recorded at room temperature on a Bruker Avance II 400, Bruker Avance III HD 700, or a Bruker Avance III HD 800 MHz NMR spectrometer. ESIMS or HRESIMS data were collected on a Bruker Maxis 4G Q-TOF mass spectrometer in the positive-ion mode. Column chromatography was conducted using silica gel (65 × 250 or 230 × 400 mesh, Sorbent Technologies, Atlanta, GA, USA). Analytical TLC was performed on precoated silica gel 60 F254 plates (Sorbent Technologies, Atlanta, GA, USA). Sephadex LH-20 was purchased from Amersham Biosciences, Uppsala, Sweden. For visualization of TLC plates, H2SO4 was used as a spray reagent. All procedures were carried out using solvents purchased from commercial sources and employed without further purification. (+)-Digoxin, paclitaxel, and other reagents for chemical synthesis were purchased from Sigma-Aldrich (St. Louis, MO, USA) (purity ≥ 98%).
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