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20 protocols using maxis q tof

1

Comprehensive Structural Elucidation Protocol

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UV and IR spectra were measured on an UV-2401PC spectrometer (Shimadzu, Beijing, China) and IR Affinity-1 spectrometer (Shimadzu, Beijing, China), respectively. Optical rotations were performed on a Perkine Elmer 341 polarimeter, and CD spectra were measured with a chirascan circular dichroism spectrometer (Applied Photophysics, Surrey, UK). HR-ESIMS were determined with a Bruker maXis Q-TOF in positive/negative ion mode. The NMR spectra including (1D and 2D NMR) were recorded on a Bruker AC 500 MHz spectrometer using TMS as standard. All chemical shifts were assigned with δ-values. X-ray diffraction intensity data were collected on Agilent Xcalibur Nova single-crystal diffractometer using Cu Kα radiation. Column chromatography (CC) was performed on silica gel (200–300 mesh, 300–400 mesh), and Sephadex LH-20 (Amersham Biosciences, Sweden), respectively. TLC were carried out on silica gel GF254 (10–40 µm) plates (Qingdao Marine Chemical Factory, China). All solvents used were of analytical grade (Tianjin Fuyu Chemical and Industry Factory). Semipreparative HPLC (Agilent Technologies, 1260 infinity series) was performed using an ODS column (YMC-pack ODS-A, 10 × 250 mm, 5 µm, 1.5 mL/min).
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2

Structural Elucidation of Compounds

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The structures were elucidated based on ESI-MS, 1D, and 2D NMR. NMR spectra were recorded on a Bruker Avance III-600 NMR spectrometer (Bruker, Billerica, MA, USA) with TMS as an internal standard. Mass spectrometry analysis was performed using an XTerraMS (Waters, Milford, MA, USA) equipped with an electrospray ionization (ESI) source. HR-ESI-MS data were acquired in m/z by using a BioTOFTM-Q mass spectrometer (Bruker, Billerica, MA, USA) and a Dionex Ultimate 3000 coupled to a Bruker Maxis Q-TOF.
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3

Protein-Clathrochelate Interaction Analysis

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A weighted amount of the HSA (delipidated, Sigma, St. Louis, MI, USA) was dissolved in 20 mM ammonium bicarbonate aqueous buffer to obtain a solution with concentration equal to 200 µM. A weighted amount of a given cage iron(II) complex was dissolved in methanol just prior to the corresponding MS experiment to obtain a 2 mM solution. The reaction mixture containing 20 μM of the above protein and 60 μM of the clathrochelate in 20 mM aqueous ammonium bicarbonate was incubated at room temperature for 15 min.
Electrospray ionization mass spectra were measured on a Maxis QToF (Bruker Daltonics, Germany) using the Q-Tof control (Version 3.2.31.0) and the DataAnalysis (Version 4.1.359.0) software packages. The samples were injected under native conditions into the mass-spectrometer using the following parameters: infusion rate 350 μL/min, capillary voltage 4 kV, end plate offset −500 V, dry temperature 210 °C, dry gas 6 L/min, nebulizer 0.8 bar, transfer time 120 μs, acquisition rate 1 Hz and rolling average 2. The instrument was tuned to the high-mass range. Signals of HSA were detected in the range of m/z 3000–5000. The mass spectra were acquired over 5 min and averaged. Then, each of these experimental spectra was smoothed using the Savitzky–Golay algorithm with 0.2 smoothing width in five cycles.
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4

Untargeted Metabolomics of Azithromycin in Human Milk

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The presence of azithromycin suspects was investigated using human breast milk data (MassIVE dataset identifier MSV000081432 [10.25345/C58K7570Q])29 (link). Human milk samples were extracted using 80:20 methanol and water. Untargeted metabolomics was performed using an UltiMate 3000 liquid chromatography system (Thermo Scientific) coupled to a Maxis Q-TOF (Bruker Daltonics) mass spectrometer with a Kinetex C18 column (Phenomenex). Samples were run using a linear gradient of mobile phase A (water 0.1% formic acid (v/v)) and phase B (acetonitrile 0.1% formic acid (v/v)). A representative linear gradient consisted of 0–0.5 min isocratic at 5% B, 0.5–8.5 min 100% B, 8.5–11 min isocratic at 100% B, 11–11.5 min 5% B, and 11.5–12 min 5% B. Data were collected in positive ion mode using data-dependent acquisition. All solvents used were LC-MS grade.
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5

Lyso-PAF-C16 Analysis by LC-MS/MS

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Mass spectrometry was performed using a Bruker® Daltonics Maxis qTOF mass spectrometer equipped with an electrospray ionization source. A water–acetonitrile gradient (from 98 : 2 to 2 : 98 water : acetonitrile, 0.1% formic acid) was used as the mobile phase. The flow rate was 0.5 ml min−1 and the mass spectrometer was operated in data-dependent positive ion mode, automatically switching between full scan MS and MS/MS acquisitions after every 10 MS/MS fragmentations. Automatic exclusion was used with parameters set such that an ion would be ignored if seen for three scans, but then refragmented if its intensity was 2.5× the previous scan. A Lyso-PAF-C16 standard was purchased from Sigma-Aldrich, diluted to 3 µM in ethanol and subjected to LC-MS/MS analysis according to the same parameters as outlined above.
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6

High-Resolution Mass Spectrometry of Proteins

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All mass spectra for intact proteins were acquired on a Bruker MaXis Q-TOF (Bremen, Germany) in the positive-ion mode, as was reported previously.18 (link)For proteolytic peptides, digests were analyzed on a Q Exactive Plus hybrid quadrupole orbitrap mass spectrometer coupled with a Nanospray Flex ion source (Thermo Fisher, Santa Clara, CA). A C18 column was custom fabricated with an integrated emitter (75 μm × 150 mm, 1.8 μm, 100 Å). The gradient was from 2.0% solvent B (80% acetonitrile, 0.1% formic acid) to 20% solvent B over 55 min, then to 50% solvent B over 25 min, and finally to 90% solvent B for 10 min followed by a 15 min re-equilibration step. The 15 most abundant molecular ions were automatically chosen for fragmentation (DDA) by using the mass spectra scanned from m/z 380−2200 at a resolving power (RP) of 70 K (at m/z 200) throughout the chromatography. Precursor ions were isolated in the quadrupole with an isolation window of 2.0 m/z and fragmented with higher-energy collisional dissociation (HCD) with a normalized collision energy (NCE) of 32%. The automatic gain control (AGC) targets were 5 × 105 for MS and 5 × 104 for MS/MS acquisitions. Maximum injection times (maxIT) were 200 ms for MS and 100 ms for MS/MS.
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7

LC-MS/MS Analysis of Metabolite Extracts

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Prior to LC-MS/MS analysis, samples were diluted 10-fold. Mass spectrometry was performed using a Bruker Daltronics Maxis qTOF mass spectrometer equipped with a standard electrospray ionization source. The mass spectrometer was tuned by infusion of Tuning Mix ES-TOF (Agilent Technologies) at a 3 L/min flow rate. For accurate mass measurements, a wick saturated with hexakis(1H,1H,3H-tetrafluoropropoxy)phophazene ions (Synquest Laboratories; m/z 922.0098) located within the source was used for lock mass internal calibration. Samples were introduced by a Thermo Scientific UltraMate 3000 Dionex ultraperformance liquid chromatograph (UPLC) using a 20-µL injection volume. Ethyl acetate-methanol extracts were separated using a Phenomenex Kinetex 2.6 m C18 (30×2.10 mm) UPLC column. A linear water-acetonitrile gradient (from 98:2 to 2:98 water/acetonitrile) containing 0.1% formic acid was utilized. The flow rate was 0.5 mL/min. The mass spectrometer was operated in data-dependent positive-ion mode, automatically switching between full-scan MS and MS/MS acquisitions. Full-scan MS spectra (m/z 50 to 2,000) were acquired, and the top 10 most intense ions in a particular scan were fragmented using collision-induced dissociation at 35 eV for +1 ions and 25 eV for +2 ions in the collision cell.
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8

Mass Spectrometry-Based Protein Identification

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Samples were analysed by the Centre of Excellence in Mass Spectrometry at the University of York. Following in-gel digestion, peptides were analysed over 20 min acquisitions with elution from a 10 cm Waters T3 nano C18 column onto a Bruker maXis qTOF operated in DDA mode. The resulting peptide spectra were searched against provided sequences and the appropriate species-specific entries in the SwissProt protein database using Mascot.
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9

Spectroscopic Analysis of Chemical Compounds

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UV spectra were acquired
on a Thermo Fisher Scientific Genesys 10S. Infrared (IR) spectra were
taken on film in a KBr window on a Perkin Elmer 500 series FTIR Panagon
1000. 1D and 2D NMR spectra were recorded on a Bruker AVANCE III spectrometer
at 500/125 MHz (1H/13C NMR, respectively) equipped
with a 1.7 mm TCI MicroCryoProbe (Bruker Biospin, Fällanden,
Switzerland). All shifts are given in δ (ppm) using the signal
of tetramethylsilane as reference. All coupling constants (J) are given in Hz. ESI-TOF spectra and HRESIMS experiments
were acquired using a Bruker maXis QTOF (Bruker Daltonik GmbH, Bremen,
Germany) mass spectrometer coupled to an Agilent 1200 LC (Agilent
Technologies, Waldbronn, Germany). Flash chromatography was performed
on a semiautomatic chromatographic system (CombiFlashTeledyne ISCO
Rf400x) with a precast reverse-phase column. Semipreparative HPLC
separation was performed on a Gilson GX-281 322H2 (Gilson Technologies,
USA) coupled to a DAD detector and an automatic fraction collector
with a semipreparative reversed-phase column (Zorbax SB-C18, 250 ×
9.4 mm, 5 μm).
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10

Proteomic Analysis of Rat Proteins

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Protein spots were excised from the polyacrylamide gels and then analyzed as described in [17 (link),31 (link),32 (link)]. Briefly, after purification with STAGE-TIPs, peptide separation was achieved using a nano-LC device (Proxeon, Odense, Denmark) coupled to a maXis Q-TOF (quadrupole-time of flight) mass spectrometer with ultra-high resolution (Bruker Daltonics, Bremen, Germany). Appropriate software was used (HyStar 3.2 and MicroTOF control Version 3.0., ProteinScape 3.0 and DataAnalysis 4.0 (Bruker Daltonics, Billerica, MA, USA)) for data analysis. Only significant hits (MASCOT score ≥80 for proteins; ≥30 for peptides) were accepted. Proteins were identified by correlating tandem mass spectra with the UniProt/Swiss-Prot database (taxonomy = Rattus norvegicus). The MASCOT online search engine (http://www.matrixscience.com) was used. All nLC-MS/MS analyses were performed in duplicates (two samples per spot).
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