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6 protocols using ms pump plus

1

LC-MS Analysis of Small Molecules

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Sample separation was carried out using a Surveyor autosampler and an MSPumpPlus (Thermo Fisher Scientific, Runcorn, UK) LC system on a reverse phase Thermo Fisher Scientific Hypersil Gold LC column (1.0 × 100 mm, 5 μm) operated with a Hypersil guard cartridge, suitable for general separations. Mass spectrometry detection was performed using an LCQ ion trap (Thermo Fisher Scientific, Hemel Hempstead, UK) operated using an ESI source in positive mode. Instrument control and data analysis were carried out using Xcalibur 2.0.7 software with data processed using both the Quan Browser Xcalibur tool and Microsoft Excel.
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2

HPLC-PDA-ESI-MS/MS Analysis of Metabolites

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HPLC-PDA-ESI-MS/MS analysis was carried out on a Finnigan LCQ-Duo ion trap mass spectrometer (Thermo Quest, San Jose, CA, USA) with an ESI source coupled to a Finnigan Surveyor HPLC system (Accela autosampler, MS pump plus, and PDA detector plus) (Thermo, San Jose, CA, USA) with an EC 150/3 Nucleodur 100-3 C18ec column (Macherey-Nagel, Düren, Germany). A gradient of water and acetonitrile (ACN) (with 0.1% formic acid for ESI+ mode and without formic acid for ESI mode) was applied from 2% to 100% ACN in 60 min at 30 °C at a flow rate of 0.5 mL/min. The injection volume was 20 µL. All samples were measured in the positive and negative ion mode. The MS was operated at +10 V capillary voltage for ESI+ and −10 V for ESI, 240 °C source temperature, and high purity nitrogen as a sheath and auxiliary gas at a flow rate of 80 and 40 (arbitrary units), respectively. The ions were detected in a mass range of 50–2000 m/z. A collision energy of 35 eV was used in MS/MS fragmentation. Data acquisitions and analyses were executed by XcaliburTM 2.0.7 software (Thermo Scientific, Karlsruhe, Germany). Tentative metabolite assignments were achieved by comparison of mass and UV spectral data of the detected compounds in both negative and positive ionization modes with reported data alongside online public databases where references are added Table 2.
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3

Analysis of C. elegans N-Glycans by LC/MS

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The characterization of N-glycans released from C. elegans and labeled with 2-AB was carried out by LC/MS analysis on an LTQ XL linear ion trap mass spectrometer equipped with an ESI source (Thermo-Electron, San Jose, CA, USA). The mass spectrometry coupled liquid chromatography was performed using a Surveyor autosampler plus and MS pump plus (Thermo Scientific). The column used was a 1.0 mm x 15 cm, 5 µm TSK gel Amide-80 column (Tosoh Bioscience LLC, PA, USA). Solvent A was 20 mM ammonium acetate (pH 6.9) and solvent B was 100% acetonitrile. The flow rate was 40 µl/min. Initial conditions were 20% solvent A/80% solvent B. After 5 minutes solvent B was decreased from 80% to 25% over 100 minutes followed by re-equilibration for 10 minutes at initial conditions.
Mass spectrometer conditions were a spray voltage of 5.0 kV and the capillary temperature was 170°C. The sheath gas flow was set to 20.00 units. For the generation of the MSn spectra, normalized collision energies were set to 35%. The method used was triple play operated by Xcalibur software, with second scan being Zoom MS and third scan was Dependent MS/MS of most intense ion from scan event 2. The isolation width was set to 2 amu. All experiments were performed in the positive ion mode.
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4

Chiral Compound Analysis Using Finnigan

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A Finnigan Surveyor Plus system (Thermo Fisher Scientific, Waltham MA, USA) consisting of a Finnigan Surveyor Autosampler Plus, an MS Pump Plus, a PDA Plus detector, a Thermo LTQ ESI MS system (Thermo Fisher Scientific), and a CD-2095 Plus Chiral Detector (JASCO) was used.
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5

Quantitative Lipid Profiling by Mass Spectrometry

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Analysis of phospholipids containing a choline headgroup (PC, lyso-PC, SPH) and of PE was performed as described before [21, 27] , using a Thermo TSQ Quantum Discovery MAX triple quadrupole mass spectrometer (Thermo, Dreieich, Germany) equipped with a heated electrospray ionization (H-ESI) interface. In brief, 25µL sample (6µmol/L phospholipid in butanol:methanol:water (75:23:2,v/v)) containing dieicosanoyl-PC and dimyristoyl-PC as internal standards were introduced via loop injection using a Finnigan Surveyor Autosampler Plus and MS Pump Plus (Thermo, Dreieich, Germany), and a mobile phase comprising butanol:methanol:water:25% NH 4 OH (75:23:1.7:0.3;v/v). PC species were quantified from precursor ions of the respective diagnostic fragment ions. These were phosphocholine for endogenous PC, lyso-PC and SPH (mass / charge (m/z)=184), D 9 -phosphocholine (m/z=193) for PC synthesized de novo by direct [methyl-D 9 ]choline incorporation, and D 3 -phosphocholine (m/z=187) and D 6 -phosphocholine (m/ z=190) for PC synthesized by sequential PE N-methylation to yield PC. Here, sequential transfer of one or two deuterated methyl groups (CD 3 -) from D 3 -S-adenosylmethionine originating from [D 9 -methyl]-choline catabolism leads to mass shifts of PC species of M+3 and M+6. PE species were analyzed from the neutral loss fragment phosphoethanolamine (m/z=+141) of the individual masses.
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6

LC-MS/MS Analysis of Compounds

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A TSQ Quantum Access Max (TSQ Quantum, Thermo Scientific, CA, USA), supplied with a Finnigan Surveyor MS Pump Plus and a Finnigan Surveyor Autosampler Plus was used to perform the analysis. The mass spectrometer was equipped with a Thermo Scientific Hypurity Aquastar C18 (50 × 2.1 mm) column with a particle size of 5 μm. The spray voltage was set to 3500 V. Sheath and auxiliary gas pressure were set on 35 and 10 bar, respectively. Capillary temperature was set on 350°C. Autosampler temperature was set to 10°C.
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