orbitrap fusion instrument  (Thermo Fisher)


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    Structured Review

    Thermo Fisher orbitrap fusion instrument
    Tandem MS (EThcD) of an AGP middle-down glycopeptide on an <t>Orbitrap</t> Fusion instrument (precursor m/z : 1302.4178, [M+7H] 7+ ). ETD reaction time was 8.75 msec and HCD normalized collision energy was set at 20 for this scan. C* = Carbamidomethyl Cysteine.
    Orbitrap Fusion Instrument, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 97/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/orbitrap fusion instrument/product/Thermo Fisher
    Average 97 stars, based on 3 article reviews
    Price from $9.99 to $1999.99
    orbitrap fusion instrument - by Bioz Stars, 2020-04
    97/100 stars

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    1) Product Images from "Comparison of collisional and electron-based dissociation modes for middle-down analysis of multiply glycosylated peptides"

    Article Title: Comparison of collisional and electron-based dissociation modes for middle-down analysis of multiply glycosylated peptides

    Journal: Journal of the American Society for Mass Spectrometry

    doi: 10.1007/s13361-018-1909-y

    Tandem MS (EThcD) of an AGP middle-down glycopeptide on an Orbitrap Fusion instrument (precursor m/z : 1302.4178, [M+7H] 7+ ). ETD reaction time was 8.75 msec and HCD normalized collision energy was set at 20 for this scan. C* = Carbamidomethyl Cysteine.
    Figure Legend Snippet: Tandem MS (EThcD) of an AGP middle-down glycopeptide on an Orbitrap Fusion instrument (precursor m/z : 1302.4178, [M+7H] 7+ ). ETD reaction time was 8.75 msec and HCD normalized collision energy was set at 20 for this scan. C* = Carbamidomethyl Cysteine.

    Techniques Used: Mass Spectrometry

    Related Articles

    Centrifugation:

    Article Title: Mechanism of pharmacochaperoning in a mammalian KATP channel revealed by cryo-EM
    Article Snippet: Purified peptides were then dried by vacuum centrifugation, dissolved in 20 µl of 5% formic acid and analyzed by liquid chromatography/mass spectrometry. .. Data-dependent tandem mass spectrometry analysis was performed using an Orbitrap Fusion instrument fitted with an EasySpray source (Thermo Fisher Scientific).

    Article Title: Structure of the gene therapy vector, adeno-associated virus with its cell receptor, AAVR
    Article Snippet: Then biotinylated peptides were purified using an avidin column, dried by vacuum centrifugation, dissolved in 20 µl of 5% formic acid and analyzed by liquid chromatography/mass spectrometry. .. Data-dependent tandem mass spectrometry analysis was performed using an Orbitrap Fusion instrument fitted with an EasySpray source (Thermo Fisher Scientific).

    Injection:

    Article Title: Mechanism of pharmacochaperoning in a mammalian KATP channel revealed by cryo-EM
    Article Snippet: The digest was injected onto an Acclaim PepMap 100 μm x 2 cm NanoViper C18, 5 μm trap (Thermo Scientific), at 5 µl/min for 5 min in mobile phase A containing water, 0.1% formic acid, then switched on-line to a PepMap RSLC C18, 2 μm, 75 μm x 25 cm EasySpray column (Thermo Scientific). .. Data-dependent tandem mass spectrometry analysis was performed using an Orbitrap Fusion instrument fitted with an EasySpray source (Thermo Fisher Scientific).

    Article Title: Structure of the gene therapy vector, adeno-associated virus with its cell receptor, AAVR
    Article Snippet: Samples were injected onto an Acclaim PepMap 100 μm x 2 cm NanoViper C18, 5 μm trap (Thermo Fisher Scientific), at 5 µl/min for 10 min in mobile phase A containing water, 0.1% formic acid, then switched on-line to a PepMap RSLC C18, 2 μm, 75 μm x 25 cm EasySpray column (Thermo Fisher Scientific). .. Data-dependent tandem mass spectrometry analysis was performed using an Orbitrap Fusion instrument fitted with an EasySpray source (Thermo Fisher Scientific).

    Incubation:

    Article Title: Mechanism of pharmacochaperoning in a mammalian KATP channel revealed by cryo-EM
    Article Snippet: Following digestion, trifluoroacetic acid was added to a final 0.5%, the sample incubated at room temperature for 5 min, centrifuged at 16,000 x g for 15 min, and the supernatant removed. .. Data-dependent tandem mass spectrometry analysis was performed using an Orbitrap Fusion instrument fitted with an EasySpray source (Thermo Fisher Scientific).

    Mass Spectrometry:

    Article Title: Mechanism of pharmacochaperoning in a mammalian KATP channel revealed by cryo-EM
    Article Snippet: .. Data-dependent tandem mass spectrometry analysis was performed using an Orbitrap Fusion instrument fitted with an EasySpray source (Thermo Fisher Scientific). .. Survey scans (m/z = 400–1500) and data-dependent MS2 scans were performed in the Orbitrap mass analyzer at a resolution = 120,000, and 30,000, respectively, following higher energy collision dissociation (HCD) using a collision energy of 35 following quadrupole isolation at a 1.6 m/z isolation width.

    Article Title: Determination of Histidine pKa Values in the Propeptides of Furin and Proprotein Convertase 1/3 Using Histidine Hydrogen–Deuterium Exchange Mass Spectrometry
    Article Snippet: Mass analysis was performed using an Orbitrap Fusion instrument (Thermo Scientific). .. The instrument was set up to cycle between different ETD reaction times (5 ms/10 ms/20 ms) and MS3 analysis using collision-induced dissociation (CID) as indicated in the Results section.

    Article Title: Structure of the gene therapy vector, adeno-associated virus with its cell receptor, AAVR
    Article Snippet: .. Data-dependent tandem mass spectrometry analysis was performed using an Orbitrap Fusion instrument fitted with an EasySpray source (Thermo Fisher Scientific). .. Survey scans (m/z = 400–1500) and MS2 scans (m/z = 100–1800) were performed in the Orbitrap mass analyzer at a resolution = 120,000, and 30,000, respectively, following higher energy collision dissociation (HCD) using a collision energy of 35 following quadrupole isolation at a 1.6 m/z isolation width.

    Article Title: Memory B Cells Activate Brain-Homing, Autoreactive CD4+ T Cells in Multiple Sclerosis
    Article Snippet: Fresh frozen brain tissue from cortical gray matter from brains (n = 6 controls, pooled and n = 6 MS, pooled) was dissociated and lysed using a PCT technology as previously described ( ). .. Resulting peptides were dissolved in 3% acetonitrile and 0.1% formic acid before injecting into an Easy-nLC 1000 linked to an Orbitrap Fusion instrument (Thermo Fisher Scientific) on a gradient of 120 min. As column material ReproSil-Pur, C18, 120 Å, AQ, 1.9 μm (Dr. Maisch GmbH) with column dimensions ID 0.075mm/ length 150mm was used.

    Article Title: Deciphering the Roles of N–Glycans on Collagen–Platelet Interactions
    Article Snippet: Paragraph title: Liquid-Chromatography Electrospray Ionization Tandem Mass Spectrometry ... TMT-labeled peptides were analyzed with an Orbitrap Fusion instrument (Thermo Scientific).

    Article Title: Temporal proteomic analysis of HIV infection reveals remodelling of the host phosphoproteome by lentiviral Vif variants
    Article Snippet: Paragraph title: Mass spectrometry ... Samples were analysed using a nanoLC-MS platform consisting of an Ultimate 3000 RSLC nano UHPLC coupled to an Orbitrap Fusion instrument (Thermo Scientific).

    Article Title: Assessment of susceptible chemical modification sites of trastuzumab and endogenous human immunoglobulins at physiological conditions
    Article Snippet: Paragraph title: Analysis and identification of proteolytic peptides in human IgG by liquid chromatography tandem mass spectrometry (LC–MS/MS) ... MS/MS experiments were performed on-line on an Orbitrap Fusion instrument (Thermo) performing a full scan acquisition (in the Orbitrap), followed by a MS/MS scan of the top five most intense ions of each full scan (in the Ion Trap) using helium as collision gas (low-energy CID).

    Article Title: Comparison of collisional and electron-based dissociation modes for middle-down analysis of multiply glycosylated peptides
    Article Snippet: A Waters NanoAcquity™ nano-flow chromatograph (Waters Corp., Milford, MA) mounted with a Waters Xbridge™ reversed-phase column (150 µm × 100 mm) packed with 1.7 µm BEH C18 resin and a Waters trap column (180 µm × 20 mm) packed with 5 µm Symmetry™ C18 stationary phase, was used for online LC-MS. Bottom-up transferrin glycopeptides were also analyzed using CAD on an Agilent 6550 Q-TOF mass spectrometer using online HILIC enrichment combined with reversed-phase separation, as described previously ( ). .. HCD and EThcD (Higher-energy Collisional Dissociation and Electron Transfer Dissociation supplemental collisional activation) ( – ) experiments were performed on ZIC-HILIC-enriched and unfractionated bottom-up and middle-down glycopeptide samples by LC-MS using an EASY-nLC chromatograph with an EASY-Spray C18 LC column on a Thermo Orbitrap Fusion™ instrument.

    Article Title: Mining the cellular inventory of pyridoxal phosphate-dependent enzymes with functionalized cofactor mimics
    Article Snippet: Paragraph title: Sample preparation and MS-based proteomic analysis ... LC-MS/MS analysis was performed with an Ultimate3000 Nano-HPLC system (Thermo Fisher Scientific) coupled to an Orbitrap Fusion instrument (Thermo Fisher Scientific).

    Modification:

    Article Title: Memory B Cells Activate Brain-Homing, Autoreactive CD4+ T Cells in Multiple Sclerosis
    Article Snippet: Resulting peptides were dissolved in 3% acetonitrile and 0.1% formic acid before injecting into an Easy-nLC 1000 linked to an Orbitrap Fusion instrument (Thermo Fisher Scientific) on a gradient of 120 min. As column material ReproSil-Pur, C18, 120 Å, AQ, 1.9 μm (Dr. Maisch GmbH) with column dimensions ID 0.075mm/ length 150mm was used. .. Carbamidomethyl at cysteine was set as a static modification, and oxidation of methionine, acetylation of lysine and protein N terminus were set as variable modification.

    Flow Cytometry:

    Article Title: Mechanism of pharmacochaperoning in a mammalian KATP channel revealed by cryo-EM
    Article Snippet: Peptides were then eluted using a 7.5–30% mobile phase B (acetonitrile, 0.1% formic acid) gradient over 90 min at a 300 nl/min flow rate. .. Data-dependent tandem mass spectrometry analysis was performed using an Orbitrap Fusion instrument fitted with an EasySpray source (Thermo Fisher Scientific).

    Article Title: Structure of the gene therapy vector, adeno-associated virus with its cell receptor, AAVR
    Article Snippet: Peptides were then eluted using a 7.5–30% mobile phase B (acetonitrile, 0.1% formic acid) gradient over 90 min at a 300 nl/min flow rate. .. Data-dependent tandem mass spectrometry analysis was performed using an Orbitrap Fusion instrument fitted with an EasySpray source (Thermo Fisher Scientific).

    Article Title: Deciphering the Roles of N–Glycans on Collagen–Platelet Interactions
    Article Snippet: The flow rate was 300 nL/min. .. TMT-labeled peptides were analyzed with an Orbitrap Fusion instrument (Thermo Scientific).

    Article Title: Assessment of susceptible chemical modification sites of trastuzumab and endogenous human immunoglobulins at physiological conditions
    Article Snippet: The chromatography was carried out using a gradient from 1 to 40% solvent B in 110 min at a flow rate of 0.3 mL/min and temperature of 65 °C. .. MS/MS experiments were performed on-line on an Orbitrap Fusion instrument (Thermo) performing a full scan acquisition (in the Orbitrap), followed by a MS/MS scan of the top five most intense ions of each full scan (in the Ion Trap) using helium as collision gas (low-energy CID).

    Article Title: Comparison of collisional and electron-based dissociation modes for middle-down analysis of multiply glycosylated peptides
    Article Snippet: Bottom-up glycopeptide samples were either directly infused for analysis using an Advion NanoMate™ alone or analyzed using online LC-MS at nanoliter flow-rates on a Bruker solariX™ 12T hybrid Qh-FTICR (Fourier-transform ion cyclotron resonance) mass spectrometer mounted with an Advion NanoMate nanoESI source (Advion Inc., Ithaca, NY). .. HCD and EThcD (Higher-energy Collisional Dissociation and Electron Transfer Dissociation supplemental collisional activation) ( – ) experiments were performed on ZIC-HILIC-enriched and unfractionated bottom-up and middle-down glycopeptide samples by LC-MS using an EASY-nLC chromatograph with an EASY-Spray C18 LC column on a Thermo Orbitrap Fusion™ instrument.

    Chromatography:

    Article Title: Mechanism of pharmacochaperoning in a mammalian KATP channel revealed by cryo-EM
    Article Snippet: Purified peptides were then dried by vacuum centrifugation, dissolved in 20 µl of 5% formic acid and analyzed by liquid chromatography/mass spectrometry. .. Data-dependent tandem mass spectrometry analysis was performed using an Orbitrap Fusion instrument fitted with an EasySpray source (Thermo Fisher Scientific).

    Article Title: Structure of the gene therapy vector, adeno-associated virus with its cell receptor, AAVR
    Article Snippet: Then biotinylated peptides were purified using an avidin column, dried by vacuum centrifugation, dissolved in 20 µl of 5% formic acid and analyzed by liquid chromatography/mass spectrometry. .. Data-dependent tandem mass spectrometry analysis was performed using an Orbitrap Fusion instrument fitted with an EasySpray source (Thermo Fisher Scientific).

    Article Title: iProteinDB: An Integrative Database of Drosophila Post-translational Modifications
    Article Snippet: Proteins from embryos lysed in 8 M urea were digested with trypsin and separated into 12 fractions by strong cation exchange chromatography. .. Phosphopeptides were purified with titanium dioxide microspheres and analyzed via LC-MS/MS on either an LTQ-Orbitrap or Orbitrap Fusion instrument (Thermo Scientific).

    Article Title: Assessment of susceptible chemical modification sites of trastuzumab and endogenous human immunoglobulins at physiological conditions
    Article Snippet: The chromatography was carried out using a gradient from 1 to 40% solvent B in 110 min at a flow rate of 0.3 mL/min and temperature of 65 °C. .. MS/MS experiments were performed on-line on an Orbitrap Fusion instrument (Thermo) performing a full scan acquisition (in the Orbitrap), followed by a MS/MS scan of the top five most intense ions of each full scan (in the Ion Trap) using helium as collision gas (low-energy CID).

    Ligation:

    Article Title: Mining the cellular inventory of pyridoxal phosphate-dependent enzymes with functionalized cofactor mimics
    Article Snippet: PL3 -labeled samples were instead conjugated to EZ-Link™ Phosphine-PEG3 -Biotin (Sigma Aldrich) via Staudinger ligation (0.2 mM per 1 ml sample, 2 mg protein, 4 h at 37°C, then 20 h at 25°C). .. LC-MS/MS analysis was performed with an Ultimate3000 Nano-HPLC system (Thermo Fisher Scientific) coupled to an Orbitrap Fusion instrument (Thermo Fisher Scientific).

    Generated:

    Article Title: Comparison of collisional and electron-based dissociation modes for middle-down analysis of multiply glycosylated peptides
    Article Snippet: HCD and EThcD (Higher-energy Collisional Dissociation and Electron Transfer Dissociation supplemental collisional activation) ( – ) experiments were performed on ZIC-HILIC-enriched and unfractionated bottom-up and middle-down glycopeptide samples by LC-MS using an EASY-nLC chromatograph with an EASY-Spray C18 LC column on a Thermo Orbitrap Fusion™ instrument. .. The instrument was set to perform HCD-triggered EThcD, which allowed EThcD to be performed only on precursor ions that generated saccharide oxonium ions.

    other:

    Article Title: Myxobacterial Response to Methyljasmonate Exposure Indicates Contribution to Plant Recruitment of Micropredators
    Article Snippet: LC-MS/MS analysis of the extracted samples was performed on an Orbitrap Fusion instrument (Thermo Scientific, San Jose, CA, United States) controlled with Xcalibur version 2.0.7 and coupled to a Dionex Ultimate 3000 nanoUHPLC system.

    Tandem Mass Spectroscopy:

    Article Title: Mechanism of pharmacochaperoning in a mammalian KATP channel revealed by cryo-EM
    Article Snippet: Data-dependent tandem mass spectrometry analysis was performed using an Orbitrap Fusion instrument fitted with an EasySpray source (Thermo Fisher Scientific). .. The instrument was also configured to collect MS/MS scans for only the heavy labeled peptide pair.

    Article Title: Deciphering the Roles of N–Glycans on Collagen–Platelet Interactions
    Article Snippet: TMT-labeled peptides were analyzed with an Orbitrap Fusion instrument (Thermo Scientific). .. The gradient profile consisting of a stepwise gradient began with 4–7% B for 7 min, 7–40% B for 90 min, 40–90% B for 5 min, and 90% B for 10 min, followed by equilibration (4% B) for 10 min. MS conditions were as follows: spray voltage was set to 2.2 kV, and Orbitrap MS1 spectra (AGC 4 × 105 ) were collected from 350 to 1800 m/z at an Orbitrap resolution of 120 K followed by data-dependent higher-energy collisional dissociation tandem mass spectrometry (HCD MS/MS; resolution 60 K, collisional energy 35%, activation time 0.1 ms) of the 20 most abundant ions using an isolation width of 2.0 Da.

    Article Title: Assessment of susceptible chemical modification sites of trastuzumab and endogenous human immunoglobulins at physiological conditions
    Article Snippet: .. MS/MS experiments were performed on-line on an Orbitrap Fusion instrument (Thermo) performing a full scan acquisition (in the Orbitrap), followed by a MS/MS scan of the top five most intense ions of each full scan (in the Ion Trap) using helium as collision gas (low-energy CID). ..

    Article Title: Comparison of collisional and electron-based dissociation modes for middle-down analysis of multiply glycosylated peptides
    Article Snippet: HCD and EThcD (Higher-energy Collisional Dissociation and Electron Transfer Dissociation supplemental collisional activation) ( – ) experiments were performed on ZIC-HILIC-enriched and unfractionated bottom-up and middle-down glycopeptide samples by LC-MS using an EASY-nLC chromatograph with an EASY-Spray C18 LC column on a Thermo Orbitrap Fusion™ instrument. .. For LC-MS/MS data acquisition using the solariX, precursor ions of interest were isolated using a front-end quadrupole mass filter and accumulated in the collision cell for 100 to 1000 ms prior to MS/MS analyses.

    Affinity Purification:

    Article Title: Mechanism of pharmacochaperoning in a mammalian KATP channel revealed by cryo-EM
    Article Snippet: Crosslinked peptides were then affinity purified using reagents and hardware provided in a Cleavable ICAT Reagent Kit for Protein Labeling (monoplex version) using the manufacturer’s recommended protocol (Sciex), except the digest was applied directly to the avidin affinity cartridge without the prior cation exchange purification, the digest was diluted in 1.0 ml the manufacturer’s avidin cartridge loading buffer, and the pH of the solution was adjusted to seven by addition of 1.0 M Tris, pH 8.0 buffer prior to injection onto the avidin cartridge. .. Data-dependent tandem mass spectrometry analysis was performed using an Orbitrap Fusion instrument fitted with an EasySpray source (Thermo Fisher Scientific).

    Article Title: Structure of the gene therapy vector, adeno-associated virus with its cell receptor, AAVR
    Article Snippet: Affinity purification was performed using reagents and hardware provided in a Cleavable ICAT Reagent Kit for Protein Labeling (monoplex version) using the manufacturer’s recommended protocol (Sciex). .. Data-dependent tandem mass spectrometry analysis was performed using an Orbitrap Fusion instrument fitted with an EasySpray source (Thermo Fisher Scientific).

    Recombinant:

    Article Title: Assessment of susceptible chemical modification sites of trastuzumab and endogenous human immunoglobulins at physiological conditions
    Article Snippet: Data parameters for MS and MS/MS detection were adjusted according to general experience available from peptide analysis of recombinant antibodies. .. MS/MS experiments were performed on-line on an Orbitrap Fusion instrument (Thermo) performing a full scan acquisition (in the Orbitrap), followed by a MS/MS scan of the top five most intense ions of each full scan (in the Ion Trap) using helium as collision gas (low-energy CID).

    Isolation:

    Article Title: Mechanism of pharmacochaperoning in a mammalian KATP channel revealed by cryo-EM
    Article Snippet: Data-dependent tandem mass spectrometry analysis was performed using an Orbitrap Fusion instrument fitted with an EasySpray source (Thermo Fisher Scientific). .. Survey scans (m/z = 400–1500) and data-dependent MS2 scans were performed in the Orbitrap mass analyzer at a resolution = 120,000, and 30,000, respectively, following higher energy collision dissociation (HCD) using a collision energy of 35 following quadrupole isolation at a 1.6 m/z isolation width.

    Article Title: Structure of the gene therapy vector, adeno-associated virus with its cell receptor, AAVR
    Article Snippet: Data-dependent tandem mass spectrometry analysis was performed using an Orbitrap Fusion instrument fitted with an EasySpray source (Thermo Fisher Scientific). .. Survey scans (m/z = 400–1500) and MS2 scans (m/z = 100–1800) were performed in the Orbitrap mass analyzer at a resolution = 120,000, and 30,000, respectively, following higher energy collision dissociation (HCD) using a collision energy of 35 following quadrupole isolation at a 1.6 m/z isolation width.

    Article Title: Deciphering the Roles of N–Glycans on Collagen–Platelet Interactions
    Article Snippet: TMT-labeled peptides were analyzed with an Orbitrap Fusion instrument (Thermo Scientific). .. The gradient profile consisting of a stepwise gradient began with 4–7% B for 7 min, 7–40% B for 90 min, 40–90% B for 5 min, and 90% B for 10 min, followed by equilibration (4% B) for 10 min. MS conditions were as follows: spray voltage was set to 2.2 kV, and Orbitrap MS1 spectra (AGC 4 × 105 ) were collected from 350 to 1800 m/z at an Orbitrap resolution of 120 K followed by data-dependent higher-energy collisional dissociation tandem mass spectrometry (HCD MS/MS; resolution 60 K, collisional energy 35%, activation time 0.1 ms) of the 20 most abundant ions using an isolation width of 2.0 Da.

    Article Title: Comparison of collisional and electron-based dissociation modes for middle-down analysis of multiply glycosylated peptides
    Article Snippet: HCD and EThcD (Higher-energy Collisional Dissociation and Electron Transfer Dissociation supplemental collisional activation) ( – ) experiments were performed on ZIC-HILIC-enriched and unfractionated bottom-up and middle-down glycopeptide samples by LC-MS using an EASY-nLC chromatograph with an EASY-Spray C18 LC column on a Thermo Orbitrap Fusion™ instrument. .. For LC-MS/MS data acquisition using the solariX, precursor ions of interest were isolated using a front-end quadrupole mass filter and accumulated in the collision cell for 100 to 1000 ms prior to MS/MS analyses.

    Avidin-Biotin Assay:

    Article Title: Mechanism of pharmacochaperoning in a mammalian KATP channel revealed by cryo-EM
    Article Snippet: Crosslinked peptides were then affinity purified using reagents and hardware provided in a Cleavable ICAT Reagent Kit for Protein Labeling (monoplex version) using the manufacturer’s recommended protocol (Sciex), except the digest was applied directly to the avidin affinity cartridge without the prior cation exchange purification, the digest was diluted in 1.0 ml the manufacturer’s avidin cartridge loading buffer, and the pH of the solution was adjusted to seven by addition of 1.0 M Tris, pH 8.0 buffer prior to injection onto the avidin cartridge. .. Data-dependent tandem mass spectrometry analysis was performed using an Orbitrap Fusion instrument fitted with an EasySpray source (Thermo Fisher Scientific).

    Article Title: Structure of the gene therapy vector, adeno-associated virus with its cell receptor, AAVR
    Article Snippet: Then biotinylated peptides were purified using an avidin column, dried by vacuum centrifugation, dissolved in 20 µl of 5% formic acid and analyzed by liquid chromatography/mass spectrometry. .. Data-dependent tandem mass spectrometry analysis was performed using an Orbitrap Fusion instrument fitted with an EasySpray source (Thermo Fisher Scientific).

    Article Title: Mining the cellular inventory of pyridoxal phosphate-dependent enzymes with functionalized cofactor mimics
    Article Snippet: Upon avidin-bead enrichment, samples were reduced with 5 mM TCEP (1 h at 37°C), alkylated using 10 mM IAA (30 min at 25°C) and quenched with 10 mM DTT (30 min at 25°C) on-bead. .. LC-MS/MS analysis was performed with an Ultimate3000 Nano-HPLC system (Thermo Fisher Scientific) coupled to an Orbitrap Fusion instrument (Thermo Fisher Scientific).

    Labeling:

    Article Title: Mechanism of pharmacochaperoning in a mammalian KATP channel revealed by cryo-EM
    Article Snippet: Crosslinked peptides were then affinity purified using reagents and hardware provided in a Cleavable ICAT Reagent Kit for Protein Labeling (monoplex version) using the manufacturer’s recommended protocol (Sciex), except the digest was applied directly to the avidin affinity cartridge without the prior cation exchange purification, the digest was diluted in 1.0 ml the manufacturer’s avidin cartridge loading buffer, and the pH of the solution was adjusted to seven by addition of 1.0 M Tris, pH 8.0 buffer prior to injection onto the avidin cartridge. .. Data-dependent tandem mass spectrometry analysis was performed using an Orbitrap Fusion instrument fitted with an EasySpray source (Thermo Fisher Scientific).

    Article Title: Structure of the gene therapy vector, adeno-associated virus with its cell receptor, AAVR
    Article Snippet: Affinity purification was performed using reagents and hardware provided in a Cleavable ICAT Reagent Kit for Protein Labeling (monoplex version) using the manufacturer’s recommended protocol (Sciex). .. Data-dependent tandem mass spectrometry analysis was performed using an Orbitrap Fusion instrument fitted with an EasySpray source (Thermo Fisher Scientific).

    Article Title: Mining the cellular inventory of pyridoxal phosphate-dependent enzymes with functionalized cofactor mimics
    Article Snippet: PL3 -labeled samples were instead conjugated to EZ-Link™ Phosphine-PEG3 -Biotin (Sigma Aldrich) via Staudinger ligation (0.2 mM per 1 ml sample, 2 mg protein, 4 h at 37°C, then 20 h at 25°C). .. LC-MS/MS analysis was performed with an Ultimate3000 Nano-HPLC system (Thermo Fisher Scientific) coupled to an Orbitrap Fusion instrument (Thermo Fisher Scientific).

    Purification:

    Article Title: Mechanism of pharmacochaperoning in a mammalian KATP channel revealed by cryo-EM
    Article Snippet: Purified peptides were then dried by vacuum centrifugation, dissolved in 20 µl of 5% formic acid and analyzed by liquid chromatography/mass spectrometry. .. Data-dependent tandem mass spectrometry analysis was performed using an Orbitrap Fusion instrument fitted with an EasySpray source (Thermo Fisher Scientific).

    Article Title: Structure of the gene therapy vector, adeno-associated virus with its cell receptor, AAVR
    Article Snippet: Then biotinylated peptides were purified using an avidin column, dried by vacuum centrifugation, dissolved in 20 µl of 5% formic acid and analyzed by liquid chromatography/mass spectrometry. .. Data-dependent tandem mass spectrometry analysis was performed using an Orbitrap Fusion instrument fitted with an EasySpray source (Thermo Fisher Scientific).

    Article Title: iProteinDB: An Integrative Database of Drosophila Post-translational Modifications
    Article Snippet: .. Phosphopeptides were purified with titanium dioxide microspheres and analyzed via LC-MS/MS on either an LTQ-Orbitrap or Orbitrap Fusion instrument (Thermo Scientific). ..

    Liquid Chromatography:

    Article Title: Deciphering the Roles of N–Glycans on Collagen–Platelet Interactions
    Article Snippet: Paragraph title: Liquid-Chromatography Electrospray Ionization Tandem Mass Spectrometry ... TMT-labeled peptides were analyzed with an Orbitrap Fusion instrument (Thermo Scientific).

    Article Title: Assessment of susceptible chemical modification sites of trastuzumab and endogenous human immunoglobulins at physiological conditions
    Article Snippet: Paragraph title: Analysis and identification of proteolytic peptides in human IgG by liquid chromatography tandem mass spectrometry (LC–MS/MS) ... MS/MS experiments were performed on-line on an Orbitrap Fusion instrument (Thermo) performing a full scan acquisition (in the Orbitrap), followed by a MS/MS scan of the top five most intense ions of each full scan (in the Ion Trap) using helium as collision gas (low-energy CID).

    Software:

    Article Title: Memory B Cells Activate Brain-Homing, Autoreactive CD4+ T Cells in Multiple Sclerosis
    Article Snippet: Resulting peptides were dissolved in 3% acetonitrile and 0.1% formic acid before injecting into an Easy-nLC 1000 linked to an Orbitrap Fusion instrument (Thermo Fisher Scientific) on a gradient of 120 min. As column material ReproSil-Pur, C18, 120 Å, AQ, 1.9 μm (Dr. Maisch GmbH) with column dimensions ID 0.075mm/ length 150mm was used. .. For protein identification, “raw” files were converted into “mgf” files and analyzed on MASCOT software with a human UniProtKB/Swiss-Prot protein database (date: March 22, 2016 with 40912 entries).

    Article Title: Assessment of susceptible chemical modification sites of trastuzumab and endogenous human immunoglobulins at physiological conditions
    Article Snippet: MS/MS experiments were performed on-line on an Orbitrap Fusion instrument (Thermo) performing a full scan acquisition (in the Orbitrap), followed by a MS/MS scan of the top five most intense ions of each full scan (in the Ion Trap) using helium as collision gas (low-energy CID). .. MS/MS-data were analyzed manually using PEAKS software for mass detection and data interpretation.

    Article Title: Mining the cellular inventory of pyridoxal phosphate-dependent enzymes with functionalized cofactor mimics
    Article Snippet: LC-MS/MS analysis was performed with an Ultimate3000 Nano-HPLC system (Thermo Fisher Scientific) coupled to an Orbitrap Fusion instrument (Thermo Fisher Scientific). .. Data were acquired using Xcalibur software version 3.0sp2 (Thermo Fisher Scientific).

    Hydrophilic Interaction Liquid Chromatography:

    Article Title: Brain Citrullination Patterns and T Cell Reactivity of Cerebrospinal Fluid-Derived CD4+ T Cells in Multiple Sclerosis
    Article Snippet: .. Data-Dependent Acquisition (DDA) of the HILIC Fractionated Samples The HILIC fractionated samples, 44 in total, were run on Easy-nLC 1000 linked to an Orbitrap Fusion instrument (Thermo Fisher, Waltham, Massachusetts, USA) on a gradient of 80 min. .. Column material was ReproSil-Pur, C18, 120 Å, AQ, 1.9 μm (Dr. Maisch GmbH, Ammerbuch Germany) and column dimensions ID 0.075 mm/length 150 mm.

    Article Title: Comparison of collisional and electron-based dissociation modes for middle-down analysis of multiply glycosylated peptides
    Article Snippet: A Waters NanoAcquity™ nano-flow chromatograph (Waters Corp., Milford, MA) mounted with a Waters Xbridge™ reversed-phase column (150 µm × 100 mm) packed with 1.7 µm BEH C18 resin and a Waters trap column (180 µm × 20 mm) packed with 5 µm Symmetry™ C18 stationary phase, was used for online LC-MS. Bottom-up transferrin glycopeptides were also analyzed using CAD on an Agilent 6550 Q-TOF mass spectrometer using online HILIC enrichment combined with reversed-phase separation, as described previously ( ). .. HCD and EThcD (Higher-energy Collisional Dissociation and Electron Transfer Dissociation supplemental collisional activation) ( – ) experiments were performed on ZIC-HILIC-enriched and unfractionated bottom-up and middle-down glycopeptide samples by LC-MS using an EASY-nLC chromatograph with an EASY-Spray C18 LC column on a Thermo Orbitrap Fusion™ instrument.

    Sample Prep:

    Article Title: Memory B Cells Activate Brain-Homing, Autoreactive CD4+ T Cells in Multiple Sclerosis
    Article Snippet: In order to obtain peptides for mass spectrometric analysis, dry pellets of magnetically sorted untouched CD19+ B cells (HD and MS (REM), each n = 4; samples sizes of 2-6x106 cells) were lysed with an adapted filter aided sample preparation (FASP) protocol as previously described ( ). .. Resulting peptides were dissolved in 3% acetonitrile and 0.1% formic acid before injecting into an Easy-nLC 1000 linked to an Orbitrap Fusion instrument (Thermo Fisher Scientific) on a gradient of 120 min. As column material ReproSil-Pur, C18, 120 Å, AQ, 1.9 μm (Dr. Maisch GmbH) with column dimensions ID 0.075mm/ length 150mm was used.

    Article Title: Mining the cellular inventory of pyridoxal phosphate-dependent enzymes with functionalized cofactor mimics
    Article Snippet: Paragraph title: Sample preparation and MS-based proteomic analysis ... LC-MS/MS analysis was performed with an Ultimate3000 Nano-HPLC system (Thermo Fisher Scientific) coupled to an Orbitrap Fusion instrument (Thermo Fisher Scientific).

    Activation Assay:

    Article Title: Deciphering the Roles of N–Glycans on Collagen–Platelet Interactions
    Article Snippet: TMT-labeled peptides were analyzed with an Orbitrap Fusion instrument (Thermo Scientific). .. The gradient profile consisting of a stepwise gradient began with 4–7% B for 7 min, 7–40% B for 90 min, 40–90% B for 5 min, and 90% B for 10 min, followed by equilibration (4% B) for 10 min. MS conditions were as follows: spray voltage was set to 2.2 kV, and Orbitrap MS1 spectra (AGC 4 × 105 ) were collected from 350 to 1800 m/z at an Orbitrap resolution of 120 K followed by data-dependent higher-energy collisional dissociation tandem mass spectrometry (HCD MS/MS; resolution 60 K, collisional energy 35%, activation time 0.1 ms) of the 20 most abundant ions using an isolation width of 2.0 Da.

    Article Title: Comparison of collisional and electron-based dissociation modes for middle-down analysis of multiply glycosylated peptides
    Article Snippet: .. HCD and EThcD (Higher-energy Collisional Dissociation and Electron Transfer Dissociation supplemental collisional activation) ( – ) experiments were performed on ZIC-HILIC-enriched and unfractionated bottom-up and middle-down glycopeptide samples by LC-MS using an EASY-nLC chromatograph with an EASY-Spray C18 LC column on a Thermo Orbitrap Fusion™ instrument. .. The instrument was set to perform HCD-triggered EThcD, which allowed EThcD to be performed only on precursor ions that generated saccharide oxonium ions.

    Liquid Chromatography with Mass Spectroscopy:

    Article Title: Deciphering the Roles of N–Glycans on Collagen–Platelet Interactions
    Article Snippet: Liquid-chromatography mass spectrometry (LC-MS) experiments were performed using a Q-Exactive mass spectrometer (Thermo Fisher Scientific) equipped with a Dionex Ultimate 3000 RSLC nano system with a 75 μ m × 15 cm Acclaim PepMap100 separating column protected with a 2 cm guard column (Thermo Scientific). .. TMT-labeled peptides were analyzed with an Orbitrap Fusion instrument (Thermo Scientific).

    Article Title: Comparison of collisional and electron-based dissociation modes for middle-down analysis of multiply glycosylated peptides
    Article Snippet: .. HCD and EThcD (Higher-energy Collisional Dissociation and Electron Transfer Dissociation supplemental collisional activation) ( – ) experiments were performed on ZIC-HILIC-enriched and unfractionated bottom-up and middle-down glycopeptide samples by LC-MS using an EASY-nLC chromatograph with an EASY-Spray C18 LC column on a Thermo Orbitrap Fusion™ instrument. .. The instrument was set to perform HCD-triggered EThcD, which allowed EThcD to be performed only on precursor ions that generated saccharide oxonium ions.

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  • 99
    Thermo Fisher orbitrap fusion tribrid mass spectrometer
    Proteomic analysis of tryptic peptides from (a) expressed archetype and splice variants of human OGDH E1 and (b) OGDH E1 separated from rat brain and heart mitochondria. Results are shown as PSM for the indicated peptide or the mean of peptides a and b expressed as percentages of the total E1 protein PSM and are means ± S.E.M. for three or four observations. Values of total E1 protein PSM were archetype 3571 ± 552 ( n = 4), LS1 3719 ± 552 ( n = 3), Insert 3782 ± 1961 ( n = 3), LS1/Insert 3407 ± 156 ( n = 3), rat brain OGDH E1 620 ± 126 ( n = 4) and rat heart OGDH E1 1086 ± 126 ( n = 4). All observations were obtained using an <t>Orbitrap</t> Fusion <t>Tribrid</t> mass spectrometer. The number of PSM is a measure of the amount of a peptide.
    Orbitrap Fusion Tribrid Mass Spectrometer, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 1054 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/orbitrap fusion tribrid mass spectrometer/product/Thermo Fisher
    Average 99 stars, based on 1054 article reviews
    Price from $9.99 to $1999.99
    orbitrap fusion tribrid mass spectrometer - by Bioz Stars, 2020-04
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    99
    Thermo Fisher orbitrap fusion lumos mass spectrometer
    Gas phase segmentation (GPS) improves ADPr peptide detection. (A) A screenshot of the ADP-ribose product ion triggered EThcD and HCD data acquisition method on the <t>Orbitrap</t> Fusion <t>Lumos.</t> (B) Area under the curve (AUC) of the four ADPr fragment ions (136.06, 250.09, 348.07, and 428.04 m / z ) dissociated from an ARTD8/PARP14-MARylated STAT1 peptide using HCD. (C) Pilot Af1521 enrichment study to determine the optimal collision energy for ADP-ribose product ion screening and ADPr peptide identification. Only high confidence (HCD and EThcD combined peptides) were used in this plot (more details in Figure 3 ). (D) A schematic showing the principle of GPS using multiple injections. (E) The extracted ion chromatograms of the ADPr fragment peak (348.07 m / z ) in each full scan and GPS injection. (F,G) Precursor ion m / z and retention time of triggered EThcD spectra in full scan and combined GPS scans.
    Orbitrap Fusion Lumos Mass Spectrometer, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 61 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/orbitrap fusion lumos mass spectrometer/product/Thermo Fisher
    Average 99 stars, based on 61 article reviews
    Price from $9.99 to $1999.99
    orbitrap fusion lumos mass spectrometer - by Bioz Stars, 2020-04
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      Buy from Supplier

    Image Search Results


    Proteomic analysis of tryptic peptides from (a) expressed archetype and splice variants of human OGDH E1 and (b) OGDH E1 separated from rat brain and heart mitochondria. Results are shown as PSM for the indicated peptide or the mean of peptides a and b expressed as percentages of the total E1 protein PSM and are means ± S.E.M. for three or four observations. Values of total E1 protein PSM were archetype 3571 ± 552 ( n = 4), LS1 3719 ± 552 ( n = 3), Insert 3782 ± 1961 ( n = 3), LS1/Insert 3407 ± 156 ( n = 3), rat brain OGDH E1 620 ± 126 ( n = 4) and rat heart OGDH E1 1086 ± 126 ( n = 4). All observations were obtained using an Orbitrap Fusion Tribrid mass spectrometer. The number of PSM is a measure of the amount of a peptide.

    Journal: The Biochemical journal

    Article Title: Calcium-insensitive splice variants of mammalian E1 subunit of 2-oxoglutarate dehydrogenase complex with tissue-specific patterns of expression

    doi: 10.1042/BCJ20160135

    Figure Lengend Snippet: Proteomic analysis of tryptic peptides from (a) expressed archetype and splice variants of human OGDH E1 and (b) OGDH E1 separated from rat brain and heart mitochondria. Results are shown as PSM for the indicated peptide or the mean of peptides a and b expressed as percentages of the total E1 protein PSM and are means ± S.E.M. for three or four observations. Values of total E1 protein PSM were archetype 3571 ± 552 ( n = 4), LS1 3719 ± 552 ( n = 3), Insert 3782 ± 1961 ( n = 3), LS1/Insert 3407 ± 156 ( n = 3), rat brain OGDH E1 620 ± 126 ( n = 4) and rat heart OGDH E1 1086 ± 126 ( n = 4). All observations were obtained using an Orbitrap Fusion Tribrid mass spectrometer. The number of PSM is a measure of the amount of a peptide.

    Article Snippet: The number of peptide spectral matches (PSM) can be used as a measure of the amount of a particular peptide [ – ]. shows the values of PSM for the various relevant peptides with mass/charge ratios in the range 300–2000 which were detected in studies using the Orbitrap Fusion Tribrid mass spectrometer on samples of expressed human archetype and the three splice variants.

    Techniques: Mass Spectrometry

    Metabolic Labeling and Workflow. ( A ) Glucose, acetate, fatty acids, and amino acids produce acetyl-CoA for use in acetylating cytoplasmic and nuclear proteins. The thicker arrows indicate that glucose contributes more to the production of acetyl-coA that subsequently acetylates proteins, compared to acetate. ( B ) The workflow consisted of growing HeLa cells in heavy-labeled media, collecting samples at eight time points, lysing the cells, digesting the proteins, enriching for acetylated peptides, and analyzing the peptides by mass spectrometry. The Orbitrap image is adapted from Thermo Fisher Scientific 56 . The cartoon cell matter and lab equipment were slightly modified from Servier Medical Art 57 .

    Journal: Scientific Reports

    Article Title: Proteome-wide acetylation dynamics in human cells

    doi: 10.1038/s41598-017-09918-3

    Figure Lengend Snippet: Metabolic Labeling and Workflow. ( A ) Glucose, acetate, fatty acids, and amino acids produce acetyl-CoA for use in acetylating cytoplasmic and nuclear proteins. The thicker arrows indicate that glucose contributes more to the production of acetyl-coA that subsequently acetylates proteins, compared to acetate. ( B ) The workflow consisted of growing HeLa cells in heavy-labeled media, collecting samples at eight time points, lysing the cells, digesting the proteins, enriching for acetylated peptides, and analyzing the peptides by mass spectrometry. The Orbitrap image is adapted from Thermo Fisher Scientific 56 . The cartoon cell matter and lab equipment were slightly modified from Servier Medical Art 57 .

    Article Snippet: Acetylated peptides were then enriched using anti-acetyl-lysine antibodies and run on nano liquid chromatography coupled online with tandem mass spectrometry (nanoLC-MS/MS) on an Orbitrap Fusion mass spectrometer (Thermo Fisher Scientific), which allows for detection of isotope incorporation into acetylated proteins.

    Techniques: Labeling, Mass Spectrometry, Modification

    Experiment workflow. A) Control and AD human postmortem frontal cortex brain tissues (n=5 each group) were homogenized in 8M urea lysis buffer. For both global and ubiquitylome analysis, brain protein extracts from each sample was first denatured, alkylated and proteolytically digested followed by peptide desalting as described in methods. For global proteome analysis, peptides were analyzed by LC-MS/MS on Orbitrap Fusion Tribrid mass spectrometer. For brain ubiquitylome analysis, peptides were subjected to di-Gly affinity enrichment as described in methods followed by LC-MS/MS analysis in replicate on an Orbitrap Fusion Tribrid mass spectrometer. Protein abundance was calculated by peptide ion-intensity measurements across LC-MS runs using the label free quantification (LFQ) algorithm in MaxQuant.

    Journal: Proteomics

    Article Title: Quantitative Analysis of the Brain Ubiquitylome in Alzheimer’s Disease

    doi: 10.1002/pmic.201800108

    Figure Lengend Snippet: Experiment workflow. A) Control and AD human postmortem frontal cortex brain tissues (n=5 each group) were homogenized in 8M urea lysis buffer. For both global and ubiquitylome analysis, brain protein extracts from each sample was first denatured, alkylated and proteolytically digested followed by peptide desalting as described in methods. For global proteome analysis, peptides were analyzed by LC-MS/MS on Orbitrap Fusion Tribrid mass spectrometer. For brain ubiquitylome analysis, peptides were subjected to di-Gly affinity enrichment as described in methods followed by LC-MS/MS analysis in replicate on an Orbitrap Fusion Tribrid mass spectrometer. Protein abundance was calculated by peptide ion-intensity measurements across LC-MS runs using the label free quantification (LFQ) algorithm in MaxQuant.

    Article Snippet: Peptides were analyzed on an Orbitrap Fusion Tribrid Mass Spectrometer (ThermoFisher Scientific).

    Techniques: Lysis, Liquid Chromatography with Mass Spectroscopy, Mass Spectrometry

    Gas phase segmentation (GPS) improves ADPr peptide detection. (A) A screenshot of the ADP-ribose product ion triggered EThcD and HCD data acquisition method on the Orbitrap Fusion Lumos. (B) Area under the curve (AUC) of the four ADPr fragment ions (136.06, 250.09, 348.07, and 428.04 m / z ) dissociated from an ARTD8/PARP14-MARylated STAT1 peptide using HCD. (C) Pilot Af1521 enrichment study to determine the optimal collision energy for ADP-ribose product ion screening and ADPr peptide identification. Only high confidence (HCD and EThcD combined peptides) were used in this plot (more details in Figure 3 ). (D) A schematic showing the principle of GPS using multiple injections. (E) The extracted ion chromatograms of the ADPr fragment peak (348.07 m / z ) in each full scan and GPS injection. (F,G) Precursor ion m / z and retention time of triggered EThcD spectra in full scan and combined GPS scans.

    Journal: Journal of Proteome Research

    Article Title: A Study into the ADP-Ribosylome of IFN-γ-Stimulated THP-1 Human Macrophage-like Cells Identifies ARTD8/PARP14 and ARTD9/PARP9 ADP-Ribosylation

    doi: 10.1021/acs.jproteome.8b00895

    Figure Lengend Snippet: Gas phase segmentation (GPS) improves ADPr peptide detection. (A) A screenshot of the ADP-ribose product ion triggered EThcD and HCD data acquisition method on the Orbitrap Fusion Lumos. (B) Area under the curve (AUC) of the four ADPr fragment ions (136.06, 250.09, 348.07, and 428.04 m / z ) dissociated from an ARTD8/PARP14-MARylated STAT1 peptide using HCD. (C) Pilot Af1521 enrichment study to determine the optimal collision energy for ADP-ribose product ion screening and ADPr peptide identification. Only high confidence (HCD and EThcD combined peptides) were used in this plot (more details in Figure 3 ). (D) A schematic showing the principle of GPS using multiple injections. (E) The extracted ion chromatograms of the ADPr fragment peak (348.07 m / z ) in each full scan and GPS injection. (F,G) Precursor ion m / z and retention time of triggered EThcD spectra in full scan and combined GPS scans.

    Article Snippet: LC–MS/MS Analysis All peptide samples were analyzed on an Orbitrap Fusion Lumos mass spectrometer fronted with an EASY-Spray Source, coupled to an Easy-nLC1000 HPLC pump (Thermo Fisher Scientific).

    Techniques: Injection