The extracted metabolites (three biological and two technical replicates per treatment) were applied with C18, 2.7 μm (particle size) HPLC column, 15 cm × 100 μm ID (Supelco analytical, Sigma-Aldrich) and 96 min gradient ranging with 400 nL min-1 flow rate. The eluent was analyzed by LTQ-Orbitrap XL Hybrid Ion Trap-Orbitrap Mass Spectrometer (Thermo Fisher Scientific, Germany) with full scan range 130–1,800 m/z, enabled dynamic exclusion, exclusion duration 60 s, exclusion list size 500, repeat duration 30 s, repeat count 1, CID activation type and minimum required signal 50,000.
Ltq orbitrap xl hybrid ion trap orbitrap mass spectrometer
Manufactured by Thermo Fisher Scientific
Sourced in Germany, United States
The LTQ Orbitrap XL Hybrid Ion Trap-Orbitrap mass spectrometer is a high-performance analytical instrument that combines the features of an ion trap and an Orbitrap mass analyzer. It provides accurate mass measurement and high-resolution capabilities for the identification and characterization of a wide range of molecules in complex samples.
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Lab products found in correlation
Phantom v1610, by Ametek (2 mentions)
Syringe pump, by Harvard Apparatus (2 mentions)
Supelco analytical, by Merck Group (1 mentions)
Hplc grade solvents, by Thermo Fisher Scientific (1 mentions)
Avance 3 500 ft nmr spectrometer, by Bruker (1 mentions)
Lcq ion trap mass spectrometer, by Thermo Fisher Scientific (1 mentions)
P 2000 polarimeter, by Jasco (1 mentions)
Proteome discoverer v1, by Thermo Fisher Scientific (1 mentions)
Acquity uplc system, by Waters Corporation (1 mentions)
Sb 800 mhz spectrometer, by Bruker (1 mentions)
Reserpine, by Merck Group (1 mentions)
Ultimate 3000 rapid separation lc system, by Thermo Fisher Scientific (1 mentions)
Xcalibur, by Thermo Fisher Scientific (1 mentions)
Lcq fleet ion trap mass spectrometer, by Thermo Fisher Scientific (1 mentions)
Waters 486 tunable absorbance detector, by Waters Corporation (1 mentions)
Acclaim rslc 120 c18 column, by Thermo Fisher Scientific (1 mentions)
Uplc hss t3 column, by Waters Corporation (1 mentions)
Avance 400 mhz nmr spectrometer, by Bruker (1 mentions)
High performance liquid chromatography (hplc), by Waters Corporation (1 mentions)
Discovery hs c18 column, by Merck Group (1 mentions)
15 protocols using ltq orbitrap xl hybrid ion trap orbitrap mass spectrometer
1
Metabolite Profiling by HPLC-MS
2
Detailed Protocols for Sensitive Chemical Synthesis
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All chemicals were purchased from Sigma-Aldrich (St. Louis, MO). HPLC grade solvents were purchased from Fisher Scientific (Nepean, ON, Canada). Reactions were performed using glassware that was oven-dried. Air- and moisture-sensitive liquids and solutions were transferred via syringe or stainless steel cannula. Organic solutions were concentrated under reduced pressure (∼15 Torr) by rotary evaporation. Solvents were purified by passage under 12 psi through activated alumina columns. Detailed procedures for synthesis of substrate probes and reactions for Hammett analysis are provided in the ESI.† DESI-MS studies were performed on a high-resolution mass spectrometer (Thermo Scientific LTQ Orbitrap XL Hybrid Ion Trap-Orbitrap mass spectrometer) using a homebuilt DESI source. The details of DESI-MS experiments are described in the ESI.† The online ESI-MS experiment for real time monitoring of the Cu(i ) species was performed using the pressurized infusion method originally described by McIndoe and coworkers.20 See the ESI† for complete experimental details.
3
Spectroscopic Characterization of Organic Compounds
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Melting points (mp) were determined using a Büchi M560 apparatus (Büchi Labortechnik AG, Flawil, Switzerland) and are uncorrected. Optical rotations ([α]D) were measured using a P-2000 polarimeter (JASCO, Easton, MD, USA). Infrared (IR) spectra were reported in wave numbers (cm−1) using an IR Prestige-21/FTIR-8400S Fourier transform infrared spectrophotometer (Shimadzu Kyoto, Kyoto Prefecture, Japan). 1H and 13C-NMR spectra were recorded using a Bruker AVANCE III 500 FT-NMR spectrometer (Bruker, Rheinstetten, Germany) at room temperature, and the chemical shifts are reported in ppm using tetramethylsilane (TMS) as the internal standard. Mass spectra (MS) were obtained using a LCQ ion-trap mass spectrometer using the electrospray ionization (ESI) technique (Thermo-Finnigan, Mundelein, IL, USA). High-resolution electrospray ionization mass spectra (HRESI-MS) were recorded on a LTQ orbitrap XL hybrid ion trap-orbitrap mass spectrometer (Thermo Scientific, Waltham, MA, USA). Column chromatography was performed on 230−400 mesh silica gel.
4
Quantitative Proteomics of Overexpressed Proteins
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Transient overexpression samples, OEL and NCL, were separated by 1-D SDS-PAGE and stained using Blue Silver dye. To assess the distribution and relative abundance of hCABS1, the resolving gels (complete lanes) were cut into 11 equal segments and sent for analysis to the Alberta Proteomics and Mass Spectrometry Facility (University of Alberta, Edmonton) for in-gel trypsin digestion and MS-seq analysis using a LTQ Orbitrap XL Hybrid Ion Trap-Orbitrap mass spectrometer (Thermo Fisher Scientific). Data were processed using Proteome Discoverer v.1.4 (Thermo Fisher Scientific) using the Sequest (Thermo Fisher Scientific) database search algorithm; only proteins with ≥2 tryptic peptides identified by MS-seq were included. Data on all the peptide fragments detected during our MS-seq studies are attached in the linked data repository folder, mass spectroscopy section, https://sites.ualberta.ca/~marcelo/Data_Repository.zip .
5
LC-MS Analysis of Bacterial Muropeptides
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The LC-MS setup consisted of a Waters Acquity UPLC system (Waters, Milford, MA, USA) and an LTQ Orbitrap XL hybrid ion Trap-Orbitrap mass spectrometer (Thermo Fisher Scientific, Waltham, MA, USA) equipped with an Ion Max electrospray source. Chromatographic separation of muropeptides and precursors was performed on an Acquity ultraperformance LC (UPLC) HSS T3 C18 column (1.8 μm, 100 Å, 2.1 by 100 mm). Mobile phase A consisted of 99.9% H2O and 0.1% formic acid, while mobile phase B consisted of 95% acetonitrile, 4.9% H2O, and 0.1% formic acid. All solvents used were of LC-MS grade or better. The flow rate was set to 0.5 ml min−1. The binary gradient program consisted of 1 min of 98% phase A, 12 min of from 98% A to 85% A, and 2 min of from 85% A to 0% A. The column was then flushed for 3 min with 100% phase B, after which the gradient was set to 98% and the column was equilibrated for 8 min. The column temperature was set to 30°C, and the injection volume used was 5 μl. The temperature of the autosampler tray was set to 8°C. Data were collected in the positive electrospray ionization (ESI) mode, with a scan range of m/z 500 to 2,500 in high-range mode. The resolution was set to 15,000 (at m/z 400).
6
Cytochrome c-Maltose Binding in Fused Droplets
7
Cytochrome c-Maltose Binding in Fused Droplets
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Thermo Scientific LTQ Orbitrap XL Hybrid Ion Trap-Orbitrap mass spectrometer was used for the cytochrome c–maltose binding studies in fused droplets. Two ESI-like spray sources are equipped with an X–Y–Z micro positioning linear and angular stage for accurate alignment of the two streams of droplets (See Fig. 1b ). This alignment is important for ensuring fusion of most of the incident droplets and to maintain a linear trajectory toward the mass spectrometer inlet. The best alignment was acquired with the angle between two crossed droplet streams at 78°, which showed the highest probability of droplet fusion and straight trajectories of the fused droplets to the inlet of the mass spectrometer. Two aqueous solutions of analytes (cytochrome c at a concentration of 100 μM and maltose at a concentration of 100 mM) were injected from the two ESI sources with a syringe pump (Harvard Apparatus, Holliston, MA) at a flow rate of 30 μl min−1 in positive ion mode. The heated capillary temperature was maintained at approximately 275 °C, and the ion-spray voltage was kept at +5 kV. For measurement of the size and velocities of the fused droplets over a distance x, we used a high-speed optical camera (Phantom v1610, Vision Research, Wayne, NJ).
8
Characterization of Photonic Nanostructures
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Proton (1H) and carbon (13C) NMR spectra were recorded on a Bruker WB 600 MHz or a Bruker SB 800 MHz spectrometer. Electrospray Ionization (ESI)/Mass Spectroscopy (MS) analysis was carried out using a Thermo Scientific LTQ Orbitrap XL Hybrid Ion Trap-Orbitrap Mass Spectrometer. A Hitachi U-2910 double beam spectrophotometer was used for UV-visible spectroscopy measurements. Two color interference lithography experiments were carried out using a Thorlabs M365LP1 mounted LED and a Cobolt Samba 532 05-01 CW diode pumped laser. Odhner holographics Stabilock II fringe stabilizer was used to correct for path length compensation and sample drift. Stimulated emission depletion (STED) microscopy measurements and point-by-point STED lithography experiments were carried out using an in-house built system utilizing a Picoquant LDH DC 640 laser for fluorescence excitation; Power Technologies 405 nm laser (LDCU8/9189) for spirothiopyran excitation; MPB-PRFL-P-30-775 laser for depletion; custom Abberior galvanometer scanner, electronics and acquisition software; Olympus UPLSAPO100XO Objective lens and a SPCM-AQRH-13-FC Excelitas single photon counting module detector. Optical power was measured using a Coherent LabMax-TO power meter with an LM-2 VIS Silicon optical sensor.
9
Synthesis and Mass Spectrometry of Benzaldehyde Imine
10
Mass Spectrometry Analysis of Proteins
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Proteins were either analyzed by a Tofspec SE (Micromass, Manchester, United Kingdom) and a LTQ Orbitrap XL Hybrid Ion Trap-Orbitrap Mass Spectrometer (Thermo Fisher Scientific, Bremen, Germany). Details are reported in the Supplementary Materials .
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