ltq orbitrapxl  (Thermo Fisher)


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    Structured Review

    Thermo Fisher ltq orbitrapxl
    Ltq Orbitrapxl, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 91/100, based on 18 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/ltq orbitrapxl/product/Thermo Fisher
    Average 91 stars, based on 18 article reviews
    Price from $9.99 to $1999.99
    ltq orbitrapxl - by Bioz Stars, 2020-07
    91/100 stars

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    Related Articles

    High Performance Liquid Chromatography:

    Article Title: Differential Reprogramming of Isogenic Colorectal Cancer Cells by Distinct Activating KRAS Mutations
    Article Snippet: .. LC– MS/MS and Data Processing A total of 5 μL of each sample was fractionated by nanoscale C18 high performance liquid chromatography (HPLC) on a Waters nanoACQUITY UPLC system coupled to an LTQ-OrbitrapXL (Thermo Fisher) fitted with a Proxeon nanoelectrospray source. .. Peptides were loaded onto a 5 cm × 180 μm trap column (BEH-C18 Symmetry; Waters Corporation) in 0.1% formic acid at a flow rate of 15 μL/min and then resolved using a 25 cm × 75 μm column using a 20 min linear gradient of 3 to 62.5% acetonitrile in 0.1% formic acid at a flow rate of 400 nL/min (column temperature of 65 °C).

    Liquid Chromatography with Mass Spectroscopy:

    Article Title: Regulation of PIK3C3/VPS34 complexes by MTOR in nutrient stress-induced autophagy
    Article Snippet: .. The resulting peptide sample was resuspended in 7 μL of 0.1% formic acid and 5 μL was analyzed by LC/ESI MS with a 2D Nano-HPLC (Eksigent) coupled to a LTQ-OrbiTrapXL (Thermo Scientific) mass spectrometer using an LC MS ion source configuration. .. In-line de-salting was accomplished using an IntegraFrit trap column (75 μm × 25 mm; New Objective, TRC-25) packed with reverse phase Magic C18AQ (5-μm, 200 Å resin; Michrom Bioresources, CN5/61270/00) followed by peptide separations on a PicoFrit column (75 μm × 200 mm; New Objective, PF75##-200) packed with reverse phase Magic C18AQ (5-μm, 100 Å resin; Michrom Bioresources, CN5/66170/00) directly mounted on the electrospray ion source.

    Chromatography:

    Article Title: Differential Impact of Caveolae and Caveolin-1 Scaffolds on The Membrane Raft Proteome *
    Article Snippet: .. In all experiments, digested peptides were also further fractionated by strong cation exchange chromatography into five fractions using 0, 20, 50, 100, and 500 mm of NH4 CH3 COO or 10 fractions using 0, 10, 20, 50, 75, 100, 150, 200, 350, and 500 mm of NH4 CH3 COO as described ( ) and analyzed as above on an LTQ-OrbitrapXL. .. Protein identification and quantification were done using Proteome Discover (v.1.2, ThermoFisher, Bremen, Germany) and Mascot (version 2.3, Matrix Science) to search against the International Protein Index (IPI) Mouse (version 3.69, 110,771 sequences—common serum contaminants and human keratins added and all reversed sequences were concatenated) database with the following criteria: electrospray ionization-ion trap fragmentation characteristics, tryptic specificity with up to one missed cleavages; ±10 parts-per-million and ±0.6 Da accuracy for MS and MS/MS measurements respectively; cysteine carbamidomethylation as a fixed modification; N-terminal protein acetylation, methionine oxidation, deamidation (NQ), duplex (2 H4 -Lys, 13 C6 -Arg) or triplex (13 C6 15 N2 -Lys and 13 C6 15 N4 -Arg) SILAC modifications as appropriate; peptide false discovery rate was set at 1%.

    other:

    Article Title: Quantitative Proteomic Analysis Reveals Metabolic Alterations, Calcium Dysregulation, and Increased Expression of Extracellular Matrix Proteins in Laminin α2 Chain–deficient Muscle *
    Article Snippet: Desalted and dried fractions were reconstituted into 0.1% formic acid and analyzed on an LTQ-OrbitrapXL (Thermo Fisher Scientific) interfaced with an in-house-constructed nano-LC column.

    Mass Spectrometry:

    Article Title: The reaction of cinnamaldehyde and cinnam(o)yl derivatives with thiols
    Article Snippet: .. Low- and high-resolution ESI-MS spectra were obtained on an LTQ OrbitrapXL (Thermo Scientific) mass spectrometer. .. All compounds investigated are commercial (Aldrich) except the oxime 2a , its acetyl derivative 2b and the cinnamide 1d that were prepared according to literature.

    Article Title: A metabolomic view of how the human gut microbiota impacts the host metabolome using humanized and gnotobiotic mice
    Article Snippet: .. MS was performed on the LTQ orbitrapXL (Thermo Fisher) mass spectrometer operatedin positive electrospray mode (full scan/CID,m/z=206.2). .. Standards of tryptophan and indole-3-lactic acid were used in the analysis (Sigma-Aldrich).

    Article Title: Regulation of PIK3C3/VPS34 complexes by MTOR in nutrient stress-induced autophagy
    Article Snippet: .. The resulting peptide sample was resuspended in 7 μL of 0.1% formic acid and 5 μL was analyzed by LC/ESI MS with a 2D Nano-HPLC (Eksigent) coupled to a LTQ-OrbiTrapXL (Thermo Scientific) mass spectrometer using an LC MS ion source configuration. .. In-line de-salting was accomplished using an IntegraFrit trap column (75 μm × 25 mm; New Objective, TRC-25) packed with reverse phase Magic C18AQ (5-μm, 200 Å resin; Michrom Bioresources, CN5/61270/00) followed by peptide separations on a PicoFrit column (75 μm × 200 mm; New Objective, PF75##-200) packed with reverse phase Magic C18AQ (5-μm, 100 Å resin; Michrom Bioresources, CN5/66170/00) directly mounted on the electrospray ion source.

    Article Title: Quantitative Proteomic Analysis Reveals Metabolic Alterations, Calcium Dysregulation, and Increased Expression of Extracellular Matrix Proteins in Laminin α2 Chain–deficient Muscle *
    Article Snippet: .. The LTQ-OrbitrapXL was operated in a data-dependent mode with one MS1 Fourier transform MS scan of precursor ions followed by collision-induced dissociation and high-energy collision dissociation MS2 scans of the three most abundant doubly, triply, and quadruply protonated ions in each Fourier transform MS scan. ..

    Tandem Mass Spectroscopy:

    Article Title: Differential Reprogramming of Isogenic Colorectal Cancer Cells by Distinct Activating KRAS Mutations
    Article Snippet: .. LC– MS/MS and Data Processing A total of 5 μL of each sample was fractionated by nanoscale C18 high performance liquid chromatography (HPLC) on a Waters nanoACQUITY UPLC system coupled to an LTQ-OrbitrapXL (Thermo Fisher) fitted with a Proxeon nanoelectrospray source. .. Peptides were loaded onto a 5 cm × 180 μm trap column (BEH-C18 Symmetry; Waters Corporation) in 0.1% formic acid at a flow rate of 15 μL/min and then resolved using a 25 cm × 75 μm column using a 20 min linear gradient of 3 to 62.5% acetonitrile in 0.1% formic acid at a flow rate of 400 nL/min (column temperature of 65 °C).

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  • 95
    Thermo Fisher ltq orbitrap mass spectrometer
    Human Parkin Ser 65 is a substrate of human PINK1 upon CCCP stimulation. ( a ) Confirmation by mass spectrometry that Ser 65 of human Parkin is phosphorylated by CCCP-induced activation of human wild-type PINK1-FLAG. Flp-In T-Rex HEK293 cells expressing FLAG-empty, wild-type PINK1-FLAG, and kinase-inactive PINK1-FLAG (D384A) were co-transfected with HA-Parkin, induced with doxycycline and stimulated with 10 μM of CCCP for 3 h. Whole-cell extracts were obtained following lysis with 1% Triton and approximately 30 mg of whole-cell extract were subjected to immunoprecipitation with anti-HA-agarose and run on 10% SDS-PAGE and stained with colloidal Coomassie blue. Coomassie-stained bands migrating with the expected molecular mass of HA-Parkin were excised from the gel, digested with trypsin, and subjected to high performance liquid chromatography with tandem mass spectrometry (LC-MS-MS) on an <t>LTQ-Orbitrap</t> mass spectrometer. Extracted ion chromatogram analysis of Ser 131 and Ser 65 phosphopeptide (3 + R.NDWTVQNCDLDQQ S IVHIVQRPWR.K+P). The total signal intensity of the phosphopeptide is plotted on the y -axis and retention time is plotted on the x -axis. The m / z value corresponding to the Ser 131 phosphopeptide was detected in all conditions whilst that of the Ser 65 phosphopeptide was only detected in samples from wild-type PINK1-FLAG-expressing cells following CCCP treatment. ( b ) Characterization of Parkin phospho-Ser 65 antibody. Flp-In T-Rex HEK293 cells expressing FLAG-empty, wild-type PINK1-FLAG, and kinase-inactive PINK1-FLAG were co-transfected with untagged wild-type (WT) or Ser 65 Ala (S65A) mutant Parkin, induced with doxycycline and stimulated with 10 μM of CCCP for 3 h. 0.25 mg of 1% Triton whole-cell lysate were subjected to immunoprecipitation with anti-Parkin antibody (S966C) covalently coupled to protein G Sepharose and then immunoblotted with anti-phospho-Ser 65 antibody in the presence of dephosphorylated peptide. Ten per cent of the immunoprecipitate (IP) was immunoblotted with total anti-Parkin antibody. Twenty five micrograms of whole cell lysate was immunoblotted with total PINK1 antibody.
    Ltq Orbitrap Mass Spectrometer, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 95/100, based on 3725 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/ltq orbitrap mass spectrometer/product/Thermo Fisher
    Average 95 stars, based on 3725 article reviews
    Price from $9.99 to $1999.99
    ltq orbitrap mass spectrometer - by Bioz Stars, 2020-07
    95/100 stars
      Buy from Supplier

    94
    Thermo Fisher ltq orbitrap velos mass spectrometer
    A schematic workflow illustrating the steps involved in the differential analysis of RA and OA synovial fluid proteome. Proteins from RA and OA synovial fluid were extracted and depleted to remove the 14 most abundant proteins using multiple affinity removal system, Human-14. The depleted protein from RA and OA were then digested with trypsin and labeled with iTRAQ reagents, 117 and 116 respectively. The labeled samples were pooled and subjected to fractionation using strong cation exchange chromatography. The fractions were then analyzed on a <t>LTQ-Orbitrap</t> <t>Velos</t> mass spectrometer. The MS/MS data obtained was searched against Human RefSeq 50 database using Sequest and Mascot search algorithms. Validation of the iTRAQ quantitation data was carried out using multiple reaction monitoring and Western blot.
    Ltq Orbitrap Velos Mass Spectrometer, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 94/100, based on 219 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/ltq orbitrap velos mass spectrometer/product/Thermo Fisher
    Average 94 stars, based on 219 article reviews
    Price from $9.99 to $1999.99
    ltq orbitrap velos mass spectrometer - by Bioz Stars, 2020-07
    94/100 stars
      Buy from Supplier

    Image Search Results


    Human Parkin Ser 65 is a substrate of human PINK1 upon CCCP stimulation. ( a ) Confirmation by mass spectrometry that Ser 65 of human Parkin is phosphorylated by CCCP-induced activation of human wild-type PINK1-FLAG. Flp-In T-Rex HEK293 cells expressing FLAG-empty, wild-type PINK1-FLAG, and kinase-inactive PINK1-FLAG (D384A) were co-transfected with HA-Parkin, induced with doxycycline and stimulated with 10 μM of CCCP for 3 h. Whole-cell extracts were obtained following lysis with 1% Triton and approximately 30 mg of whole-cell extract were subjected to immunoprecipitation with anti-HA-agarose and run on 10% SDS-PAGE and stained with colloidal Coomassie blue. Coomassie-stained bands migrating with the expected molecular mass of HA-Parkin were excised from the gel, digested with trypsin, and subjected to high performance liquid chromatography with tandem mass spectrometry (LC-MS-MS) on an LTQ-Orbitrap mass spectrometer. Extracted ion chromatogram analysis of Ser 131 and Ser 65 phosphopeptide (3 + R.NDWTVQNCDLDQQ S IVHIVQRPWR.K+P). The total signal intensity of the phosphopeptide is plotted on the y -axis and retention time is plotted on the x -axis. The m / z value corresponding to the Ser 131 phosphopeptide was detected in all conditions whilst that of the Ser 65 phosphopeptide was only detected in samples from wild-type PINK1-FLAG-expressing cells following CCCP treatment. ( b ) Characterization of Parkin phospho-Ser 65 antibody. Flp-In T-Rex HEK293 cells expressing FLAG-empty, wild-type PINK1-FLAG, and kinase-inactive PINK1-FLAG were co-transfected with untagged wild-type (WT) or Ser 65 Ala (S65A) mutant Parkin, induced with doxycycline and stimulated with 10 μM of CCCP for 3 h. 0.25 mg of 1% Triton whole-cell lysate were subjected to immunoprecipitation with anti-Parkin antibody (S966C) covalently coupled to protein G Sepharose and then immunoblotted with anti-phospho-Ser 65 antibody in the presence of dephosphorylated peptide. Ten per cent of the immunoprecipitate (IP) was immunoblotted with total anti-Parkin antibody. Twenty five micrograms of whole cell lysate was immunoblotted with total PINK1 antibody.

    Journal: Open Biology

    Article Title: PINK1 is activated by mitochondrial membrane potential depolarization and stimulates Parkin E3 ligase activity by phosphorylating Serine 65

    doi: 10.1098/rsob.120080

    Figure Lengend Snippet: Human Parkin Ser 65 is a substrate of human PINK1 upon CCCP stimulation. ( a ) Confirmation by mass spectrometry that Ser 65 of human Parkin is phosphorylated by CCCP-induced activation of human wild-type PINK1-FLAG. Flp-In T-Rex HEK293 cells expressing FLAG-empty, wild-type PINK1-FLAG, and kinase-inactive PINK1-FLAG (D384A) were co-transfected with HA-Parkin, induced with doxycycline and stimulated with 10 μM of CCCP for 3 h. Whole-cell extracts were obtained following lysis with 1% Triton and approximately 30 mg of whole-cell extract were subjected to immunoprecipitation with anti-HA-agarose and run on 10% SDS-PAGE and stained with colloidal Coomassie blue. Coomassie-stained bands migrating with the expected molecular mass of HA-Parkin were excised from the gel, digested with trypsin, and subjected to high performance liquid chromatography with tandem mass spectrometry (LC-MS-MS) on an LTQ-Orbitrap mass spectrometer. Extracted ion chromatogram analysis of Ser 131 and Ser 65 phosphopeptide (3 + R.NDWTVQNCDLDQQ S IVHIVQRPWR.K+P). The total signal intensity of the phosphopeptide is plotted on the y -axis and retention time is plotted on the x -axis. The m / z value corresponding to the Ser 131 phosphopeptide was detected in all conditions whilst that of the Ser 65 phosphopeptide was only detected in samples from wild-type PINK1-FLAG-expressing cells following CCCP treatment. ( b ) Characterization of Parkin phospho-Ser 65 antibody. Flp-In T-Rex HEK293 cells expressing FLAG-empty, wild-type PINK1-FLAG, and kinase-inactive PINK1-FLAG were co-transfected with untagged wild-type (WT) or Ser 65 Ala (S65A) mutant Parkin, induced with doxycycline and stimulated with 10 μM of CCCP for 3 h. 0.25 mg of 1% Triton whole-cell lysate were subjected to immunoprecipitation with anti-Parkin antibody (S966C) covalently coupled to protein G Sepharose and then immunoblotted with anti-phospho-Ser 65 antibody in the presence of dephosphorylated peptide. Ten per cent of the immunoprecipitate (IP) was immunoblotted with total anti-Parkin antibody. Twenty five micrograms of whole cell lysate was immunoblotted with total PINK1 antibody.

    Article Snippet: Isolated phosphopeptides were analysed by LC-MS-MS on a proxeon Easy-nLC nano liquid chromatography system coupled to a Thermo LTQ-orbitrap mass spectrometer.

    Techniques: Mass Spectrometry, Activation Assay, Expressing, Transfection, Lysis, Immunoprecipitation, SDS Page, Staining, High Performance Liquid Chromatography, Liquid Chromatography with Mass Spectroscopy, Mutagenesis

    Schematic diagram of proteomic analysis of the mouse organ of Corti (OC) sample. ( 1 ) The OCs were reconstituted in 100 μL lysis buffer (100 mM ammonium bicarbonate, pH 8.4); ( 2 ) The lysates were reduced by 5 mM DL-Dithiothreitol (DTT) and digested by trypsin overnight; ( 3 ) The digests were desalted and dried in a vacuum centrifuge immediately after digestion; ( 4 ) Dried peptides were subjected to the in-house assembled reverse phase metal-free multiple-column nanoLC system coupled with ( 5 ) LTQ-Orbitrap XL mass spectrometer for MS analysis.

    Journal: International Journal of Molecular Sciences

    Article Title: Proteomic Analysis of the Organ of Corti Using Nanoscale Liquid Chromatography Coupled with Tandem Mass Spectrometry

    doi: 10.3390/ijms13078171

    Figure Lengend Snippet: Schematic diagram of proteomic analysis of the mouse organ of Corti (OC) sample. ( 1 ) The OCs were reconstituted in 100 μL lysis buffer (100 mM ammonium bicarbonate, pH 8.4); ( 2 ) The lysates were reduced by 5 mM DL-Dithiothreitol (DTT) and digested by trypsin overnight; ( 3 ) The digests were desalted and dried in a vacuum centrifuge immediately after digestion; ( 4 ) Dried peptides were subjected to the in-house assembled reverse phase metal-free multiple-column nanoLC system coupled with ( 5 ) LTQ-Orbitrap XL mass spectrometer for MS analysis.

    Article Snippet: The nanoLC system was interfaced with a LTQ-Orbitrap XL mass spectrometer equipped with a nanoelectrospray ion source (Thermo Scientific, Waltham, MA, USA).

    Techniques: Lysis, Mass Spectrometry

    Quantification of calcium-dependent regulation of phosphorylation sites of Toxoplasma invasion motor complex components. A ) Work flow to identify individual phosphorylation sites and quantitatively assess their responsiveness to calcium signals using a SILAC-based proteomics approach. A 1∶1 mixture of Triton X-100 lysates from “Heavy” (H; Arg4/Lys8)-labeled ethanol-stimulated tachyzoites or

    Journal: PLoS Pathogens

    Article Title: Quantitative in vivo Analyses Reveal Calcium-dependent Phosphorylation Sites and Identifies a Novel Component of the Toxoplasma Invasion Motor Complex

    doi: 10.1371/journal.ppat.1002222

    Figure Lengend Snippet: Quantification of calcium-dependent regulation of phosphorylation sites of Toxoplasma invasion motor complex components. A ) Work flow to identify individual phosphorylation sites and quantitatively assess their responsiveness to calcium signals using a SILAC-based proteomics approach. A 1∶1 mixture of Triton X-100 lysates from “Heavy” (H; Arg4/Lys8)-labeled ethanol-stimulated tachyzoites or "Light" (L; Arg0/Lys0)-labeled non-stimulated parasites was generated, and a TiO 2 -enriched phosphopeptide sample of H/L-labeled Toxoplasma invasion motor complexes was prepared and analysed by LC-MS/MS on an LTQ-Orbitrap instrument. Mascot and MaxQuant search engines facilitated subsequent manual identification, phosphosite localization and quantification of proteins or peptides as detailed in materials and mathods. B ) Sypro Ruby-stained SDS-PAGE separation of the relative amounts of light (lane 1) or heavy (lane 2) Triton X-100 whole protein extracts are shown. Intact tachyzoite invasion motor complexes comprising the five major components MyoA, GAP50, GAP45 and MLC1 were precipitated from a 1∶1 H/L mixture by GAP45-specific immuno-affinity chromatography (lane 3).

    Article Snippet: The nano HPLC was coupled on-line to an LTQ-Orbitrap mass spectrometer equipped with a nanoelectrospray ion source (Thermo Fisher Scientific) for automated MS/MS.

    Techniques: Flow Cytometry, Labeling, Generated, Liquid Chromatography with Mass Spectroscopy, Mass Spectrometry, Staining, SDS Page, Affinity Chromatography

    A schematic workflow illustrating the steps involved in the differential analysis of RA and OA synovial fluid proteome. Proteins from RA and OA synovial fluid were extracted and depleted to remove the 14 most abundant proteins using multiple affinity removal system, Human-14. The depleted protein from RA and OA were then digested with trypsin and labeled with iTRAQ reagents, 117 and 116 respectively. The labeled samples were pooled and subjected to fractionation using strong cation exchange chromatography. The fractions were then analyzed on a LTQ-Orbitrap Velos mass spectrometer. The MS/MS data obtained was searched against Human RefSeq 50 database using Sequest and Mascot search algorithms. Validation of the iTRAQ quantitation data was carried out using multiple reaction monitoring and Western blot.

    Journal: Clinical proteomics

    Article Title: Differential proteomic analysis of synovial fluid from rheumatoid arthritis and osteoarthritis patients

    doi: 10.1186/1559-0275-11-1

    Figure Lengend Snippet: A schematic workflow illustrating the steps involved in the differential analysis of RA and OA synovial fluid proteome. Proteins from RA and OA synovial fluid were extracted and depleted to remove the 14 most abundant proteins using multiple affinity removal system, Human-14. The depleted protein from RA and OA were then digested with trypsin and labeled with iTRAQ reagents, 117 and 116 respectively. The labeled samples were pooled and subjected to fractionation using strong cation exchange chromatography. The fractions were then analyzed on a LTQ-Orbitrap Velos mass spectrometer. The MS/MS data obtained was searched against Human RefSeq 50 database using Sequest and Mascot search algorithms. Validation of the iTRAQ quantitation data was carried out using multiple reaction monitoring and Western blot.

    Article Snippet: LC-MS/MS analysis Tandem mass spectrometric analysis of the iTRAQ labeled peptides were carried out using LTQ-Orbitrap Velos mass spectrometer (Thermo Scientific, Bremen, Germany) interfaced with Easy nanoLC II (previously Proxeon, Thermo Scientific, Bremen, Germany).

    Techniques: Labeling, Fractionation, Chromatography, Mass Spectrometry, Quantitation Assay, Western Blot