Thermo q exactive orbitrap mass spectrometer

Manufactured by Thermo Fisher Scientific

Sourced in United States, Germany

The Thermo Q-Exactive Orbitrap mass spectrometer is a high-resolution, accurate-mass (HRAM) instrument that combines the Orbitrap mass analyzer with a quadrupole mass filter. It is designed to provide high-performance mass spectrometry analysis for a variety of applications.

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Lab products found in correlation

26 protocols using thermo q exactive orbitrap mass spectrometer

MALDI-Orbitrap MS for Accurate Mass Measurement

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Accurate mass measurement was performed by matrix‐assisted laser ionization Orbitrap mass spectrometry (MALDI/Orbitrap MS) at the Department of Pharmacy, University of Copenhagen. Analysis was performed in positive ion mode with MALDI ionization on a Thermo QExactive Orbitrap mass spectrometer (Thermo Scientific, Bremen, Germany) equipped with an AP‐SMALDI 10 ion source (TransmitMIT, Giessen, Germany) and operated with mass resolving power 140 000 at m/z 200. 2,5‐Dihydroxybenzoic acid (CAS # 490‐79‐9) (Sigma‐Aldrich, Steinheim, Germany) was used as matrix and lock‐mass for internal mass calibration, providing a mass accuracy of 3 ppm or better. Samples were dissolved in a solution of 2,5‐dihydroxybenzoic acid in methanol (2 mg/mL) and 3 μL of the solution was loaded on a glass plate for analysis.

Breindahl T., Kimergård A., Andreasen M.F, & Pedersen D.S. (2016). Identification of a new psychoactive substance in seized material: the synthetic opioid N‐phenyl‐N‐[1‐(2‐phenethyl)piperidin‐4‐yl]prop‐2‐enamide (Acrylfentanyl). Drug Testing and Analysis, 9(3), 415-422.

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Non-targeted Metabolomics Profiling

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Samples were detected by performing non-targeted UPLC-MS/MS using an Ultimate 3000 UHPLC (Dionex) system combined with a Thermo Q-Exactive (Orbitrap) mass spectrometer (Thermo Fisher Scientific, San Jose, CA, USA). Data identifications were performed using a Trace Finder. First, based on the endogenous MS database, metabolites were identified by accurate masses. Subsequently, the metabolites were identified at the MS/MS level using in-house MS/MS library, which was built using chemical standards. The matching confidence of experimental MS/MS spectra with MS/MS in the library was evaluated using library score. Normally, the metabolites with library score >30 were considered as MS/MS confirmed (Tang et al., 2016 (link)). The MS/MS spectra of representative metabolites were shown in the Supplementary Figure. A 0.25-min retention time deviation was applied, and the mass shifts of the primary and secondary identifications were 10 and 15 ppm, respectively (Ning et al., 2018 (link)).

Tao T., He T., Mao H., Wu X, & Liu X. (2020). Non-Targeted Metabolomic Profiling of Coronary Heart Disease Patients With Taohong Siwu Decoction Treatment. Frontiers in Pharmacology, 11, 651.

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Analytical Methods for Phytochemical Characterization

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The HR-ESI-MS analysis was performed on the Thermo Q-Exactive Orbitrap Mass spectrometer (Thermo Fisher Scientific Corporation, Waltham, MA, USA) equipped with electrospray ionization source (ESI). The preparative HPLC was performed with Varian binary gradient LC system (Varian Inc. Corporate, Santa Clara, CA, USA) containing two solvent deliver modules (PrepStar 218), a photodiode array detector (ProStar 335) and a fraction collector (ProStar 704), using an the preparative Cosmosil ODS column (250 mm × 20.0 mm i.d., 5 μm, Cosmosil, Nakalai Tesque Co. Ltd., Kyoto, Japan). UV spectra were recorded on a Shimadzu UV-260 spectrometer (Shimadzu Corporation, Tokyo, Japan). IR spectra were determined on a Perkin-Elmer 683 infrared spectrometer (PerkinElmer, Inc., Waltham, MA, USA) in KBr pellets. Optical rotations were measured using a JASCO P-200 polarimeter (JASCO Corporation, Tokyo, Japan) with a 5-cm cell. The NMR spectra were taken with TMS as the internal standard on a Brucker Avance III 600 FT NMR spectrometer (Bruker Corporation, Billerica, MA, USA). Column chromatography was performed on silica gel (Yantai Chemical Industry Research Institute, Yantai, China) and Cosmosil 75 C₁₈-OPN (75 μm, Nakalai Tesque Co. Ltd., Kyoto, Japan).

Yan X., Zhou Y.X., Tang X.X., Liu X.X., Yi Z.W., Fang M.J., Wu Z., Jiang F.Q, & Qiu Y.K. (2016). Macrolactins from Marine-Derived Bacillus subtilis B5 Bacteria as Inhibitors of Inducible Nitric Oxide and Cytokines Expression. Marine Drugs, 14(11), 195.

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Chromatographic Separation and Mass Spectrometry

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Chromatographic separation was accomplished with a Dionex Ultimate 3000RS UHPLC instrument, equipped with a Thermo Accucore C₁₈ (100 mm × 2.1 mm i. d., 2.6 μm) analytical column for the separation of compounds. Water (A) and methanol (B) containing 0.1% formic acid were employed as mobile phases, respectively. The total run time was 70 min for the elution profile. Mass spectrum analysis was carried out using a Thermo Q-Exactive Orbitrap mass spectrometer (Thermo Scientific, Waltham, MA, USA) equipped with an electrospray ionisation probe interface in positive and negative-ion mode. All detailed analytical conditions have been published [62 (link)].

Zengin G., Mahomoodally M.F., Aktumsek A., Jekő J., Cziáky Z., Rodrigues M.J., Custodio L., Polat R., Cakilcioglu U., Ayna A., Gallo M., Montesano D, & Picot-Allain C. (2021). Chemical Profiling and Biological Evaluation of Nepeta baytopii Extracts and Essential Oil: An Endemic Plant from Turkey. Plants, 10(6), 1176.

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LC-MS/MS Analysis of Tissue Extracts

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With 10 μL injection amount, extract of each tissue/hemolymph was subjected to LC-MS/MS analysis using Thermo Q Exactive Orbitrap mass spectrometer (Thermo Scientific) interfaced with Dionex UltiMate 3000 LC system. Molecules were separated by C18 column at 30 °C using a flow rate of 0.450 mL/min with mobile phase A as 0.1% FA water and mobile phase B (MPB) being 0.1% FA ACN. The binary gradient was set as follows: 0-2 min, 0% MPB; 2-5 min, 0-0.5% MPB; 5-10 min, 0.5-5% MPB; 10-13min, 5-98% MPB; 13-16 min, 98% MPB; 16-24 min, 0% MPB for column conditioning. A top 5 data-dependent acquisition (DDA) method was used with an inclusion list of 46 compounds of interest. Full MS scan (m/z 70-1000) was acquired with a resolution of 70 K, AGC target of 1e6 and maximum injection time of 100 msec. For MS/MS scans, the following parameters were used: dynamic exclusion 6.0 s, isolation window 0.5 m/z, normalized collision energy 30, resolution 17.5 K, AGC target 1e5, maximum injection time 100 msec, and underfill ratio 10%. To acquire MS/MS spectra of low abundance compounds, a parallel-reaction monitoring (PRM) method was employed to achieve best sensitivity.
Raw data from DDA experiments were processed by Compound Discoverer 2.0 software with a workflow shown in Figure S1 for MS/MS spectral comparison and small molecule identification.

Cao Q., Ouyang C., Zhong X, & Li L. (2018). Profiling of Small Molecule Metabolites and Neurotransmitters in Crustacean Hemolymph and Neuronal Tissues Using Reversed-Phase LC-MS/MS. Electrophoresis, 39(9-10), 1241-1248.

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Ultrapure LC-MS/MS Metabolomics Analysis

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The UltiMate 3000 Ultra High-performance Liquid Chromatograph (Thermo Fisher, USA) and Thermo Q-Exactive Orbitrap Mass Spectrometer were used for ultrapure LC-MS/MS analysis (Thermo Fisher). Chromatographic separations were performed on Waters ACQUITY UPLC HSS T3 (100 mm × 2.1 mm × 1.8 μm). Thereafter, all the raw data were fed into Progenesis QI (Waters, Milford, MA, USA) and SIMCA-P14.0 (Umetrics AB, Umea, Vasterbotten, Sweden), software for further analysis [15 (link)]. The partial least-squares discriminant analysis (PLS-DA) and orthogonal partial least-squares discriminant analysis (OPLS-DA) supervised pattern recognition methods were applied to identify the overall metabolic differences among the three groups and the variable importance in the projection (VIP) was used to identify characteristic metabolites in the three groups. Distinct metabolites were analyzed based on VIP > 1.0 and P < 0.05. Further information is provided in the Supplemental Materials and Methods.

Liu Y., Li H., Wang X., Huang J., Zhao D., Tan Y., Zhang Z., Zhang Z., Zhu L., Wu B., Chen Z, & Peng W. (2023). Anti-Alzheimers molecular mechanism of icariin: insights from gut microbiota, metabolomics, and network pharmacology. Journal of Translational Medicine, 21, 277.

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Enterococcus faecalis Proteome Analysis

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The proteome analysis of the E. faecalis protein extracts by mass spectrometry and their corresponding data processing were carried out in a Thermo Scientific EASY-nLC 1000 nano-liquid chromatograph system/Thermo Q-Exactive Orbitrap mass spectrometer (Thermo Scientific, San Jose, CA, USA) at the CICT facilities of the University of Jaén in collaboration with the staff. For this, samples were digested in a solution following the protocol of the FASP protein digestion kit (Expedeon, Heidelberg, Germany) followed by a desalination according to the Pierce C18 Spin Columns protocol of Thermo Fisher Scientific. The results were compared with a specific database for Enterococcus faecalis in Uniprot.org with Proteome Discoverer 1.4 (Thermo Fisher Scientific, San Jose, CA, USA) and the search engine Sequest HT.

Sánchez B., Cobo A., Hidalgo M., Martínez-Rodríguez A.M., Prieto I., Gálvez A, & Martínez-Cañamero M. (2020). Prevalence of an Intestinal ST40 Enterococcus faecalis over Other E. faecalis Strains in the Gut Environment of Mice Fed Different High Fat Diets. International Journal of Molecular Sciences, 21(12), 4330.

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Serum Metabolomic Profiling by LC-MS

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Details of the mass spectrometry-based analyses for metabolomics are described in the supplementary methods. Briefly, 50 μL of serum were precipitated for reversed-phase or hydrophilic interaction chromatography. Samples were analysed using an Ultimate 3000 UHPLC system coupled to a Thermo Q-Exactive (Orbitrap) mass spectrometer (Thermo Fisher Scientific, San Jose, CA, USA). Peak deconvolution was performed using the TraceFinder software v3.1 (Thermo Fisher Scientific). Metabolites were identified by matching accurate mass and retention time to an in-house chemical reference database of 600 metabolites, with confirmation determined by comparing tandem mass spectrometry (MS/MS) fragmentation patterns and product ion abundance to those of chemical standards. All metabolites included in statistical analyses were confirmed by MS/MS or by a targeted assay.

Reinke S.N., Gallart-Ayala H., Gómez C., Checa A., Fauland A., Naz S., Kamleh M.A., Djukanović R., Hinks T.S, & Wheelock C.E. (2017). Metabolomics analysis identifies different metabotypes of asthma severity. The European Respiratory Journal, 49(3), 1601740.

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Protein Identification via Mass Spectrometry

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Example 4

All insecticidal proteins were fractionated and enriched as described. For identification candidate protein bands were excised, digested with trypsin and analyzed by nano-liquid chromatography/electrospray tandem mass spectrometry (nano-LC/ESI-MS/MS) on a Thermo Q Exactive™ Orbitrap™ mass spectrometer (Thermo Fisher Scientific) interfaced with an Eksigent® NanoLC-1D™ Plus nanoLC™ system (AB Sciex). Ten product ion spectra were collected in an information dependent acquisition mode after a MS1 survey scan.

Protein identification was done by database searches using Mascot (Matrix Science). The searches were done against the in-house database Bacteria-Plus, which combines all bacterial protein sequences and keratin sequences derived from the NCBI non-redundant database (nr) as well as in-house protein sequences.

US11780891B2. Insecticidal proteins and methods for their use (2023-10-10). PIONEER HI-BRED INTERNATIONAL, INC. [US]. Inventors: Steven D Gruver [US], Heather Kozy [US], Jessica O'Rear [US], Barbara Rosen [US], Ute Schellenberger [US], Jun-Zhi Wei [US], Weiping Xie [US], Xiaohong Zhong [US], Genhai Zhu [US].

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Protein Identification by Tandem Mass Spectrometry

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Example 4

US10820596B2. Insecticidal proteins and methods for their use (2020-11-03). PIONEER HI-BRED INTERNATIONAL, INC. [US]. Inventors: Steven D Gruver [US], Heather Kozy [US], Jessica O'Rear [US], Barbara Rosen [US], Ute Schellenberger [US], Jun-Zhi Wei [US], Weiping Xie [US], Xiaohong Zhong [US], Genhai Zhu [US].

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