orbitrap fusion instrument  (Thermo Fisher)


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    Name:
    Orbitrap Fusion Lumos Tribrid Mass Spectrometer
    Description:
    Excel at the most challenging of applications, including low level PTM analysis, multiplexed relative quantitation using isobaric tags, intact protein characterization, as well as MSn analysis of small molecules with the new Thermo Scientific Orbitrap Fusion Lumos Tribrid Mass Spectrometer. This system incorporates the brightest ion source, a segmented quadrupole mass filter with improved selectivity and ion transmission, Advanced Vacuum Technology for improved ion transmission to the Thermo Scientific Orbitrap mass analyzer, and ETD HD, a higher-capacity ETD fragmentation. Latest innovations include the Advanced Peak Determination (APD) algorithm for improved data-dependent experiments and two new hardware options: UVPD, a new fragmentation technique achieved with a 213 nm UV laser and 1M, which provides 1,000,000 FWHM ultra-high resolution for improved structural elucidation and quantitation of isobaric compounds.
    Catalog Number:
    IQLAAEGAAPFADBMBHQ
    Price:
    None
    Applications:
    Industrial & Applied Science|Industrial Mass Spectrometry
    Category:
    Instruments and Equipment, Mass Spectrometry Instruments & Equipment, Mass Spectrometry Systems & Components
    Score:
    85
    Buy from Supplier


    Structured Review

    Thermo Fisher orbitrap fusion instrument
    Excel at the most challenging of applications, including low level PTM analysis, multiplexed relative quantitation using isobaric tags, intact protein characterization, as well as MSn analysis of small molecules with the new Thermo Scientific Orbitrap Fusion Lumos Tribrid Mass Spectrometer. This system incorporates the brightest ion source, a segmented quadrupole mass filter with improved selectivity and ion transmission, Advanced Vacuum Technology for improved ion transmission to the Thermo Scientific Orbitrap mass analyzer, and ETD HD, a higher-capacity ETD fragmentation. Latest innovations include the Advanced Peak Determination (APD) algorithm for improved data-dependent experiments and two new hardware options: UVPD, a new fragmentation technique achieved with a 213 nm UV laser and 1M, which provides 1,000,000 FWHM ultra-high resolution for improved structural elucidation and quantitation of isobaric compounds.
    https://www.bioz.com/result/orbitrap fusion instrument/product/Thermo Fisher
    Average 92 stars, based on 11 article reviews
    Price from $9.99 to $1999.99
    orbitrap fusion instrument - by Bioz Stars, 2020-01
    92/100 stars

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    Related Articles

    Diagnostic Assay:

    Article Title: Serine is a new target residue for endogenous ADP-ribosylation on histones
    Article Snippet: Pure ETD and mixed HCD/ETD datasets were acquired on an Orbitrap Fusion instrument (Thermo Scientific). .. Our methods for targeted acquisition of ETD spectra of modified precursors fell into two essential types – offline and online.

    Article Title: Serine ADP-Ribosylation Depends on HPF1
    Article Snippet: For localization of ADPr sites pure ETD and mixed HCD/ETD datasets were acquired on an Orbitrap Fusion instrument (Thermo Scientific). .. Our method for targeted acquisition of ETD spectra of modified precursors used the product ion trigger feature in the decision tree of a TopSpeed acquisition method.

    Centrifugation:

    Article Title: Regulation of Human γδ T Cells by BTN3A1 Protein Stability and ATP-Binding Cassette Transporters
    Article Snippet: After centrifugation (10,000 g for 10 min), Streptavidin agarose resin (Thermo Fisher) was added to supernatants, with incubation for 2 h at 4°C. .. Resulting peptides were analyzed by LC-MS/MS analysis using an Orbitrap Fusion instrument (Thermo Fisher) utilizing a 60-min gradient.

    Incubation:

    Article Title: Regulation of Human γδ T Cells by BTN3A1 Protein Stability and ATP-Binding Cassette Transporters
    Article Snippet: After centrifugation (10,000 g for 10 min), Streptavidin agarose resin (Thermo Fisher) was added to supernatants, with incubation for 2 h at 4°C. .. Resulting peptides were analyzed by LC-MS/MS analysis using an Orbitrap Fusion instrument (Thermo Fisher) utilizing a 60-min gradient.

    Mass Spectrometry:

    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).

    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: Serine ADP-Ribosylation Depends on HPF1
    Article Snippet: For localization of ADPr sites pure ETD and mixed HCD/ETD datasets were acquired on an Orbitrap Fusion instrument (Thermo Scientific). .. Our method for targeted acquisition of ETD spectra of modified precursors used the product ion trigger feature in the decision tree of a TopSpeed acquisition method.

    Article Title: A Mass Spectrometry-Based Approach for Mapping Protein Subcellular Localization Reveals the Spatial Proteome of Mouse Primary Neurons
    Article Snippet: Mass spectrometric analysis of LFQ and SILAC samples was performed with a Q Exactive HF (Thermo Fisher Scientific, Germany), as described previously ( ). .. For samples in the TMT workflow, MS was performed with an Orbitrap Lumos or an Orbitrap Fusion instrument (Thermo Fisher Scientific, San Jose, CA). .. Raw files were processed with MaxQuant version 1.5 ( , ) using the human or mouse reference protein datasets downloaded from UniProt (SwissProt canonical and isoforms database).

    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: Regulation of Human γδ T Cells by BTN3A1 Protein Stability and ATP-Binding Cassette Transporters
    Article Snippet: Paragraph title: Immunoblot and Quantitative Mass Spectroscopy of Surface-Biotinylated Proteins ... Resulting peptides were analyzed by LC-MS/MS analysis using an Orbitrap Fusion instrument (Thermo Fisher) utilizing a 60-min gradient.

    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: Multi-faceted quantitative proteomics analysis of histone H2B isoforms and their modifications
    Article Snippet: Paragraph title: Top-down H2B MS analysis ... Top-down H2B analysis of other cancer cell lines was performed on an Orbitrap Fusion instrument (Thermo Fisher Scientific, Waltham, MA, USA).

    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). .. For whole-protein ETD analysis, the sample was automatically desalted using a 1 × 10 mm protein Opti-Trap cartridge (Optimize Technologies, Oregon City, OR) and eluted using 50% acetonitrile/0.1% formic acid (v/v) directly into an electrospray ionization (HESI-II) probe (Thermo Scientific).

    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: On the other hand, the high positive charge makes PROFUR a promising candidate for electron transfer dissociation (ETD), a process that induces fragmentation along the peptide backbone in a sequence-independent manner. .. Hence, we initially employed the easy-ETD module of the OrbiTrap Fusion instrument to fragment PROFUR inside the mass spectrometer in a “top-down” manner. .. Injections of PROFUR into the OrbiTrap produce multiple charged states that range from +8 to +14 ( ).

    Modification:

    Article Title: Serine is a new target residue for endogenous ADP-ribosylation on histones
    Article Snippet: Pure ETD and mixed HCD/ETD datasets were acquired on an Orbitrap Fusion instrument (Thermo Scientific). .. Our methods for targeted acquisition of ETD spectra of modified precursors fell into two essential types – offline and online.

    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. .. 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.

    Flow Cytometry:

    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: Multi-faceted quantitative proteomics analysis of histone H2B isoforms and their modifications
    Article Snippet: Top-down H2B analysis of other cancer cell lines was performed on an Orbitrap Fusion instrument (Thermo Fisher Scientific, Waltham, MA, USA). .. Top-down H2B analysis of other cancer cell lines was performed on an Orbitrap Fusion instrument (Thermo Fisher Scientific, Waltham, MA, USA).

    Chromatography:

    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: 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). .. Phosphopeptides were purified with titanium dioxide microspheres and analyzed via LC-MS/MS on either an LTQ-Orbitrap or Orbitrap Fusion instrument (Thermo Scientific).

    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).

    Protease Inhibitor:

    Article Title: Regulation of Human γδ T Cells by BTN3A1 Protein Stability and ATP-Binding Cassette Transporters
    Article Snippet: After quenching, cells were harvested by scraping and processed for immunoprecipitation, by lysis in 1% Tx-100 TBS pH 8 buffer with protease inhibitor (Complete EDTA free, Roche) and end-over-end rotation for 30 min at 4°C. .. Resulting peptides were analyzed by LC-MS/MS analysis using an Orbitrap Fusion instrument (Thermo Fisher) utilizing a 60-min gradient.

    Transmission Assay:

    Article Title: Multi-faceted quantitative proteomics analysis of histone H2B isoforms and their modifications
    Article Snippet: The LTQ-Orbitrap XL was set to have an automatic gain control (AGC) value of 5 × 105 for the FT full-MS scans and the FT MS/MS scans, the HCD gas and the ‘FT zero offset’ were turned off, and the detection delay was set to ‘low.’ Next, the LTQ ion optics were tuned on the myoglobin 848.64 m/z ion to improve ion transmission for large ions. .. Top-down H2B analysis of other cancer cell lines was performed on an Orbitrap Fusion instrument (Thermo Fisher Scientific, Waltham, MA, USA).

    Injection:

    Article Title: Serine ADP-Ribosylation Depends on HPF1
    Article Snippet: For localization of ADPr sites pure ETD and mixed HCD/ETD datasets were acquired on an Orbitrap Fusion instrument (Thermo Scientific). .. Our method for targeted acquisition of ETD spectra of modified precursors used the product ion trigger feature in the decision tree of a TopSpeed acquisition method.

    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: Serine ADP-Ribosylation Depends on HPF1
    Article Snippet: For localization of ADPr sites pure ETD and mixed HCD/ETD datasets were acquired on an Orbitrap Fusion instrument (Thermo Scientific). .. As they eluted, multiply-charged precursors were rapidly fragmented in HCD mode (low injection time: 30 ms; resolution 15,000; AGC target: 50,000) to screen a maximum number of precursors for diagnostic Adenine ions (typically among the strongest fragment ion signals, 136.062 Da).

    Tandem Mass Spectroscopy:

    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). .. The collision energy was adjusted according to stability and mass of the parent ion.

    Article Title: Multi-faceted quantitative proteomics analysis of histone H2B isoforms and their modifications
    Article Snippet: The LTQ-Orbitrap XL was set to have an automatic gain control (AGC) value of 5 × 105 for the FT full-MS scans and the FT MS/MS scans, the HCD gas and the ‘FT zero offset’ were turned off, and the detection delay was set to ‘low.’ Next, the LTQ ion optics were tuned on the myoglobin 848.64 m/z ion to improve ion transmission for large ions. .. Top-down H2B analysis of other cancer cell lines was performed on an Orbitrap Fusion instrument (Thermo Fisher Scientific, Waltham, MA, USA).

    Avidin-Biotin Assay:

    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: 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: 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). .. Peptides were filtered to a 1% FDR.

    Immunoprecipitation:

    Article Title: Regulation of Human γδ T Cells by BTN3A1 Protein Stability and ATP-Binding Cassette Transporters
    Article Snippet: After quenching, cells were harvested by scraping and processed for immunoprecipitation, by lysis in 1% Tx-100 TBS pH 8 buffer with protease inhibitor (Complete EDTA free, Roche) and end-over-end rotation for 30 min at 4°C. .. Resulting peptides were analyzed by LC-MS/MS analysis using an Orbitrap Fusion instrument (Thermo Fisher) utilizing a 60-min gradient.

    Liquid Chromatography:

    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: Regulation of Human γδ T Cells by BTN3A1 Protein Stability and ATP-Binding Cassette Transporters
    Article Snippet: Agarose beads were washed (20×) in lysis buffer, 20× in 0.5% SDS in PBS, 20× in 6 M urea/triethylammonium bicarbonate (TEAB) pH 8.5, 5× in TEAB pH 8.5 before digestion overnight with 0.5 µg trypsin in a final volume of 50 µl TEAB ( ). .. Resulting peptides were analyzed by LC-MS/MS analysis using an Orbitrap Fusion instrument (Thermo Fisher) utilizing a 60-min gradient. .. Raw data were searched using MASCOT from within Proteome Discoverer (Thermo Fisher) v2.0 against the Uniprot human reference proteome.

    Article Title: Memory B Cells Activate Brain-Homing, Autoreactive CD4+ T Cells in Multiple Sclerosis
    Article Snippet: Paragraph title: Proteomics by LC-MS/MS ... 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.

    Software:

    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).

    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 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: 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.

    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: Reference peptides (iRT) were added (iRT, Biognosys, Schlieren, Switzerland) to each sample. .. 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.

    Sample Prep:

    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).

    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.

    Concentration Assay:

    Article Title: Multi-faceted quantitative proteomics analysis of histone H2B isoforms and their modifications
    Article Snippet: Top-down H2B analysis of other cancer cell lines was performed on an Orbitrap Fusion instrument (Thermo Fisher Scientific, Waltham, MA, USA). .. Top-down H2B analysis of other cancer cell lines was performed on an Orbitrap Fusion instrument (Thermo Fisher Scientific, Waltham, MA, USA).

    Lysis:

    Article Title: Regulation of Human γδ T Cells by BTN3A1 Protein Stability and ATP-Binding Cassette Transporters
    Article Snippet: Agarose beads were washed (20×) in lysis buffer, 20× in 0.5% SDS in PBS, 20× in 6 M urea/triethylammonium bicarbonate (TEAB) pH 8.5, 5× in TEAB pH 8.5 before digestion overnight with 0.5 µg trypsin in a final volume of 50 µl TEAB ( ). .. Resulting peptides were analyzed by LC-MS/MS analysis using an Orbitrap Fusion instrument (Thermo Fisher) utilizing a 60-min gradient.

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  • 93
    Thermo Fisher orbitrap fusion lumos tribrid mass spectrometer lc ms
    Orbitrap Fusion Lumos Tribrid Mass Spectrometer Lc Ms, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 93/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/orbitrap fusion lumos tribrid mass spectrometer lc ms/product/Thermo Fisher
    Average 93 stars, based on 3 article reviews
    Price from $9.99 to $1999.99
    orbitrap fusion lumos tribrid mass spectrometer lc ms - by Bioz Stars, 2020-01
    93/100 stars
      Buy from Supplier

    92
    Thermo Fisher orbitrap fusion lumos instrument
    Evaluation of phosphorylation-optimized MS 2 - and MS 3 -based TMT methods. a Colored peaks illustrate MS n peak selection. MS 2 analysis either took place in the <t>orbitrap</t> (OT) or ion trap (IT). Ion selection for MS 3 analysis was based on synchronous precursor selection (SPS) or neutral loss (NL)-triggered peak isolation. In the multiple charge state (MC) method, the MS 3 isolation width was decreased for higher charge states. IT, OT and OT MC used multi-stage activation (MSA) with neutral loss mass 97.9673 Da. b Heatmap of correlation slopes of the 5% highest and lowest log2 ratios for all replicates. U2OS cells were treated 2 h with 5 µ M doxorubicin (DOX) or DMSO (C). The resulting TMT sample was measured on an Orbitrap Fusion <t>Lumos</t> three times as technical replicates with each quantification method. c Bar plot showing the total number of quantified phosphopeptide DOX vs. C ratios per method for all replicates. d Violin plot showing log 10 signal-to-noise ratio distributions of the TMT reporter ions with the median marked as a dash
    Orbitrap Fusion Lumos Instrument, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 92/100, based on 8 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/orbitrap fusion lumos instrument/product/Thermo Fisher
    Average 92 stars, based on 8 article reviews
    Price from $9.99 to $1999.99
    orbitrap fusion lumos instrument - by Bioz Stars, 2020-01
    92/100 stars
      Buy from Supplier

    98
    Thermo Fisher lc ms analysis
    Evaluation of phosphorylation-optimized MS 2 - and MS 3 -based TMT methods. a Colored peaks illustrate MS n peak selection. MS 2 analysis either took place in the <t>orbitrap</t> (OT) or ion trap (IT). Ion selection for MS 3 analysis was based on synchronous precursor selection (SPS) or neutral loss (NL)-triggered peak isolation. In the multiple charge state (MC) method, the MS 3 isolation width was decreased for higher charge states. IT, OT and OT MC used multi-stage activation (MSA) with neutral loss mass 97.9673 Da. b Heatmap of correlation slopes of the 5% highest and lowest log2 ratios for all replicates. U2OS cells were treated 2 h with 5 µ M doxorubicin (DOX) or DMSO (C). The resulting TMT sample was measured on an Orbitrap Fusion <t>Lumos</t> three times as technical replicates with each quantification method. c Bar plot showing the total number of quantified phosphopeptide DOX vs. C ratios per method for all replicates. d Violin plot showing log 10 signal-to-noise ratio distributions of the TMT reporter ions with the median marked as a dash
    Lc Ms Analysis, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 98/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/lc ms analysis/product/Thermo Fisher
    Average 98 stars, based on 2 article reviews
    Price from $9.99 to $1999.99
    lc ms analysis - by Bioz Stars, 2020-01
    98/100 stars
      Buy from Supplier

    Image Search Results


    Evaluation of phosphorylation-optimized MS 2 - and MS 3 -based TMT methods. a Colored peaks illustrate MS n peak selection. MS 2 analysis either took place in the orbitrap (OT) or ion trap (IT). Ion selection for MS 3 analysis was based on synchronous precursor selection (SPS) or neutral loss (NL)-triggered peak isolation. In the multiple charge state (MC) method, the MS 3 isolation width was decreased for higher charge states. IT, OT and OT MC used multi-stage activation (MSA) with neutral loss mass 97.9673 Da. b Heatmap of correlation slopes of the 5% highest and lowest log2 ratios for all replicates. U2OS cells were treated 2 h with 5 µ M doxorubicin (DOX) or DMSO (C). The resulting TMT sample was measured on an Orbitrap Fusion Lumos three times as technical replicates with each quantification method. c Bar plot showing the total number of quantified phosphopeptide DOX vs. C ratios per method for all replicates. d Violin plot showing log 10 signal-to-noise ratio distributions of the TMT reporter ions with the median marked as a dash

    Journal: Nature Communications

    Article Title: Benchmarking common quantification strategies for large-scale phosphoproteomics

    doi: 10.1038/s41467-018-03309-6

    Figure Lengend Snippet: Evaluation of phosphorylation-optimized MS 2 - and MS 3 -based TMT methods. a Colored peaks illustrate MS n peak selection. MS 2 analysis either took place in the orbitrap (OT) or ion trap (IT). Ion selection for MS 3 analysis was based on synchronous precursor selection (SPS) or neutral loss (NL)-triggered peak isolation. In the multiple charge state (MC) method, the MS 3 isolation width was decreased for higher charge states. IT, OT and OT MC used multi-stage activation (MSA) with neutral loss mass 97.9673 Da. b Heatmap of correlation slopes of the 5% highest and lowest log2 ratios for all replicates. U2OS cells were treated 2 h with 5 µ M doxorubicin (DOX) or DMSO (C). The resulting TMT sample was measured on an Orbitrap Fusion Lumos three times as technical replicates with each quantification method. c Bar plot showing the total number of quantified phosphopeptide DOX vs. C ratios per method for all replicates. d Violin plot showing log 10 signal-to-noise ratio distributions of the TMT reporter ions with the median marked as a dash

    Article Snippet: All samples were analyzed on an Easy-nLC 1000 coupled to a Q-Exactive HF instrument (Thermo Fisher Scientific; TMT MS2 of Fig. ), an Orbitrap Fusion Lumos instrument (Thermo Fisher Scientific; Figs. , , TMT MS3 of 3, , Supplementary Fig. ), or a Q-Exactive HF-X instrument (Thermo Fisher Scientific; Fig. ), all equipped with a nanoelectrospray source.

    Techniques: Mass Spectrometry, Selection, Isolation, Activation Assay

    Evaluation of quantification methods with focus on accuracy and precision. a Yeast phosphopeptides were diluted in fixed ratios 1:4:10 and added to a background of 1:1:1 HeLa phosphopeptides. Same total protein starting amounts were used for each method and SILAC ratios were mixed before digestion. All samples were measured on an Orbitrap Fusion Lumos three times as technical replicates with each quantification method. For SILAC and TMT, MS samples were diluted to contain a total peptide amount equal to one LFQ injection based on protein starting amount. For TMT, all mixing replicates were measured within the same TMT10-plex run. b Box plot showing yeast 4:1 and 10:1 phosphopeptide ratios for the different quantification methods and all replicates. Boxes mark the first and third quartile, with the median highlighted as dash, and whiskers marking the minimum/maximum value within 1.5 interquartile range. Outliers are not shown. Both LFQ and SILAC were tested with and without the MaxQuant feature match-between-runs (MBR), and SILAC additionally with both MBR and requantify (REQ) activated. As SILAC-MBR only results were essentially identical to SILAC only, they are not shown here. c Mean squared errors were calculated as a sum of positive bias and variance for each method and all replicates. d Receiver operating characteristic (ROC) curves were calculated by using the d-score from SAM testing as an indicator for significant regulation at 4:1 and 10:1 dilution. SAM testing for significantly regulated phosphopeptides was performed at default settings (s0 estimation automatic). ROC plots are presented as zoomed-in excerpts from the total plots, shown on the lower right each

    Journal: Nature Communications

    Article Title: Benchmarking common quantification strategies for large-scale phosphoproteomics

    doi: 10.1038/s41467-018-03309-6

    Figure Lengend Snippet: Evaluation of quantification methods with focus on accuracy and precision. a Yeast phosphopeptides were diluted in fixed ratios 1:4:10 and added to a background of 1:1:1 HeLa phosphopeptides. Same total protein starting amounts were used for each method and SILAC ratios were mixed before digestion. All samples were measured on an Orbitrap Fusion Lumos three times as technical replicates with each quantification method. For SILAC and TMT, MS samples were diluted to contain a total peptide amount equal to one LFQ injection based on protein starting amount. For TMT, all mixing replicates were measured within the same TMT10-plex run. b Box plot showing yeast 4:1 and 10:1 phosphopeptide ratios for the different quantification methods and all replicates. Boxes mark the first and third quartile, with the median highlighted as dash, and whiskers marking the minimum/maximum value within 1.5 interquartile range. Outliers are not shown. Both LFQ and SILAC were tested with and without the MaxQuant feature match-between-runs (MBR), and SILAC additionally with both MBR and requantify (REQ) activated. As SILAC-MBR only results were essentially identical to SILAC only, they are not shown here. c Mean squared errors were calculated as a sum of positive bias and variance for each method and all replicates. d Receiver operating characteristic (ROC) curves were calculated by using the d-score from SAM testing as an indicator for significant regulation at 4:1 and 10:1 dilution. SAM testing for significantly regulated phosphopeptides was performed at default settings (s0 estimation automatic). ROC plots are presented as zoomed-in excerpts from the total plots, shown on the lower right each

    Article Snippet: All samples were analyzed on an Easy-nLC 1000 coupled to a Q-Exactive HF instrument (Thermo Fisher Scientific; TMT MS2 of Fig. ), an Orbitrap Fusion Lumos instrument (Thermo Fisher Scientific; Figs. , , TMT MS3 of 3, , Supplementary Fig. ), or a Q-Exactive HF-X instrument (Thermo Fisher Scientific; Fig. ), all equipped with a nanoelectrospray source.

    Techniques: Mass Spectrometry, Injection

    Evaluation of quantification methods in a biological setting. a Non- or SILAC-labeled U2OS cells were treated with 5 µ M doxorubicin (DOX), 2.5 µ M 4-nitroquinoline 1-oxide (4NQO) or DMSO (C) for 2 h before lysis. Three biological replicates were measured for all quantification methods. For MS measurement, each quantification method was given a total of 2 days instrument time (including LC overhead). SILAC samples were fractionated into ten fractions per sample on an Ultimate 3000 high-flow system, and TMT into 24 fractions total on an Ultimate 3000 micro-flow system. Samples were then measured using a 15- or 50-cm (only LFQ) column on a Q Exactive HF or Orbitrap Fusion Lumos (only TMT MS 3 OT MC). For SILAC and TMT, MS samples were injected without dilution, so that each labeling channel resembles one LFQ injection. b Bar plot showing total numbers of identified and quantified phosphopeptides for all replicates of each quantification method, respectively. Calculations of ratios were performed within biological replicates and filtered for measurement in a minimum of one, two or three replicates, and > 75% confident phosphorylation site localization. For further analysis, ratios quantified in all three replicates only and with a localization probability of at least 75% (black arrows) were used. c SAM-based identification of significantly regulated phosphorylation sites was performed with two sample paired t- test and standard settings (s0 estimation automatic, delta estimation based on FDR = 0.20). Significantly regulated phosphorylation sites (sig) are highlighted in red, non-significant sites in gray. Applied s0 and delta values, as well as the total number of tested phosphorylation sites ( n ) are shown. For LFQ and SILAC nearest neighbor imputation (IMP), phosphorylation sites quantified in at least one replicate and with a localization probability of at least 75% were used. d , e The bar plots show the number of significantly regulated phosphorylation sites for each quantification method d in total, and e as a fraction relative to the total number of tested sites. f , g The Venn diagrams show the overlap of SAM-regulated phosphorylation sites identified f in total, and g for commonly identified sites

    Journal: Nature Communications

    Article Title: Benchmarking common quantification strategies for large-scale phosphoproteomics

    doi: 10.1038/s41467-018-03309-6

    Figure Lengend Snippet: Evaluation of quantification methods in a biological setting. a Non- or SILAC-labeled U2OS cells were treated with 5 µ M doxorubicin (DOX), 2.5 µ M 4-nitroquinoline 1-oxide (4NQO) or DMSO (C) for 2 h before lysis. Three biological replicates were measured for all quantification methods. For MS measurement, each quantification method was given a total of 2 days instrument time (including LC overhead). SILAC samples were fractionated into ten fractions per sample on an Ultimate 3000 high-flow system, and TMT into 24 fractions total on an Ultimate 3000 micro-flow system. Samples were then measured using a 15- or 50-cm (only LFQ) column on a Q Exactive HF or Orbitrap Fusion Lumos (only TMT MS 3 OT MC). For SILAC and TMT, MS samples were injected without dilution, so that each labeling channel resembles one LFQ injection. b Bar plot showing total numbers of identified and quantified phosphopeptides for all replicates of each quantification method, respectively. Calculations of ratios were performed within biological replicates and filtered for measurement in a minimum of one, two or three replicates, and > 75% confident phosphorylation site localization. For further analysis, ratios quantified in all three replicates only and with a localization probability of at least 75% (black arrows) were used. c SAM-based identification of significantly regulated phosphorylation sites was performed with two sample paired t- test and standard settings (s0 estimation automatic, delta estimation based on FDR = 0.20). Significantly regulated phosphorylation sites (sig) are highlighted in red, non-significant sites in gray. Applied s0 and delta values, as well as the total number of tested phosphorylation sites ( n ) are shown. For LFQ and SILAC nearest neighbor imputation (IMP), phosphorylation sites quantified in at least one replicate and with a localization probability of at least 75% were used. d , e The bar plots show the number of significantly regulated phosphorylation sites for each quantification method d in total, and e as a fraction relative to the total number of tested sites. f , g The Venn diagrams show the overlap of SAM-regulated phosphorylation sites identified f in total, and g for commonly identified sites

    Article Snippet: All samples were analyzed on an Easy-nLC 1000 coupled to a Q-Exactive HF instrument (Thermo Fisher Scientific; TMT MS2 of Fig. ), an Orbitrap Fusion Lumos instrument (Thermo Fisher Scientific; Figs. , , TMT MS3 of 3, , Supplementary Fig. ), or a Q-Exactive HF-X instrument (Thermo Fisher Scientific; Fig. ), all equipped with a nanoelectrospray source.

    Techniques: Labeling, Lysis, Mass Spectrometry, Liquid Chromatography, Flow Cytometry, Injection