ultimate3000 rslc nano hplc system  (Thermo Fisher)


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    Structured Review

    Thermo Fisher ultimate3000 rslc nano hplc system
    Ultimate3000 Rslc Nano Hplc System, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 90/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/ultimate3000 rslc nano hplc system/product/Thermo Fisher
    Average 90 stars, based on 2 article reviews
    Price from $9.99 to $1999.99
    ultimate3000 rslc nano hplc system - by Bioz Stars, 2020-02
    90/100 stars

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    Centrifugation:

    Article Title: Characterization of the Canine MHC Class I DLA-88*50101 Peptide Binding Motif as a Prerequisite for Canine T Cell Immunotherapy
    Article Snippet: The sample was finally concentrated to a volume of 40 μl by vacuum centrifugation (Bachofer Vacuum Concentrator) and desalted using C18 ZipTip®pipette tips (Millipore). .. An UltiMate 3000 RSLCnano nano-HPLC system coupled online to an LTQ Orbitrap XL mass spectrometer (both Thermo Scientific) was applied.

    Filtration:

    Article Title: Characterization of the Canine MHC Class I DLA-88*50101 Peptide Binding Motif as a Prerequisite for Canine T Cell Immunotherapy
    Article Snippet: For peptide filtration, the eluate was transferred into a thoroughly washed 0.5 ml 3 kDa Amicon filter (Merck Millipore Ltd.) and centrifuged at 13000 rpm (Heraeus Biofuge 13) for 15 min at 4°C. .. An UltiMate 3000 RSLCnano nano-HPLC system coupled online to an LTQ Orbitrap XL mass spectrometer (both Thermo Scientific) was applied.

    Article Title: Controlled Measurement and Comparative Analysis of Cellular Components in E. coli Reveals Broad Regulatory Changes in Response to Glucose Starvation
    Article Snippet: Tryptic peptides were filtered through Amicon Ultra 30 kD spin filtration columns and bound, washed, and eluted from HyperSep C18 SpinTips (Thermo Scientific). .. For LC-MS/MS analysis, peptides were subjected to separation by C18 reverse phase chromatography on a Dionex Ultimate 3000 RSLCnano UHPLC system (Thermo Scientific).

    SDS-Gel:

    Article Title: Cytoplasmic retention and degradation of a mitotic inducer enable plant infection by a pathogenic fungus
    Article Snippet: After separation of the protein samples by SDS-PAGE and Coomassie Brilliant Blue R250 (Serva, 17525, Heidelberg, Germany) staining and distaining of the SDS-Gel was performed and each lane was cut into 10 pieces. .. The eluates of the five upper and the five lower gel pieces were combined, suspended in sample buffer (98% H2O, 2% acetonitrile and 0.1% formic acid) and analyzed by LC-MS. Peptides generated with trypsin on-bead digestion were subjected to LC-MS analysis: 1.5 µL of each peptide sample were separated with nano-flow LC using an RSLCnano Ultimate 3000 system (Thermo Fisher Scientific).

    Incubation:

    Article Title: Marine Bacteria, A Source for Alginolytic Enzyme to Disrupt Pseudomonas aeruginosa Biofilms
    Article Snippet: Dried gel cubes were saturated with 20 µg/mL of trypsin protease (Pierce Thermo Scientific) for 2 h, then 20 µL of 50 mM ammonium bicarbonate was added and the samples were incubated overnight at 37 °C. .. The samples were transferred to a 300 µL HPLC vial and subject to analysis by LC-MS/MS on a VelosPRO orbitrap mass spectrometer (Thermo Fisher Scientific) equipped with an UltiMate 3000 Nano-LC system (Thermo Fisher Scientific).

    Article Title: Cytoplasmic retention and degradation of a mitotic inducer enable plant infection by a pathogenic fungus
    Article Snippet: Proteomic sample preparation and LC-MS analysis of peptides Crude extracts were obtained and incubated with GFP-trap beads as explained above. .. The eluates of the five upper and the five lower gel pieces were combined, suspended in sample buffer (98% H2O, 2% acetonitrile and 0.1% formic acid) and analyzed by LC-MS. Peptides generated with trypsin on-bead digestion were subjected to LC-MS analysis: 1.5 µL of each peptide sample were separated with nano-flow LC using an RSLCnano Ultimate 3000 system (Thermo Fisher Scientific).

    Article Title: The Proteolysis Adaptor, NblA, Binds to the N-terminus of β-phycocyanin: Implications for the Mechanism of Phycobilisome Degradation
    Article Snippet: LysC (Wako Chemicals, Richmond, VA) stock solution (2 μL of 0.5 μg/μL) was added to each cross-linked sample at 37 °C for 2 h. The protein solution was diluted into 100 mM Tris (Sigma-Aldrich, St. Louis, MO) and incubated with trypsin overnight at 37 °C. .. LC-MS/MS with an Ultimate 3000 Nano LC system (Thermo Scientific Dionex, Sunnyvale, CA) attached on-line to a Q Exactive Plus mass spectrometer (Thermo Fisher, Waltham, MA) was used to analyze the cross-linked sample digests.

    Article Title: Controlled Measurement and Comparative Analysis of Cellular Components in E. coli Reveals Broad Regulatory Changes in Response to Glucose Starvation
    Article Snippet: Following incubation, iodoacetamide was added to a concentration of 25 mM and samples were incubated at room temperature in the dark for 30 min. .. For LC-MS/MS analysis, peptides were subjected to separation by C18 reverse phase chromatography on a Dionex Ultimate 3000 RSLCnano UHPLC system (Thermo Scientific).

    Mass Spectrometry:

    Article Title: Characterization of the Canine MHC Class I DLA-88*50101 Peptide Binding Motif as a Prerequisite for Canine T Cell Immunotherapy
    Article Snippet: .. An UltiMate 3000 RSLCnano nano-HPLC system coupled online to an LTQ Orbitrap XL mass spectrometer (both Thermo Scientific) was applied. ..

    Article Title: Marine Bacteria, A Source for Alginolytic Enzyme to Disrupt Pseudomonas aeruginosa Biofilms
    Article Snippet: .. The samples were transferred to a 300 µL HPLC vial and subject to analysis by LC-MS/MS on a VelosPRO orbitrap mass spectrometer (Thermo Fisher Scientific) equipped with an UltiMate 3000 Nano-LC system (Thermo Fisher Scientific). .. Chromatographic separation of the digests was performed on PicoFRIT C18 self-packed 75 mm x 60 cm capillary column (New Objective, Woburn, MA) at a flow rate of 300 µL/min.

    Article Title: Podocalyxin‐like protein promotes gastric cancer progression through interacting with RUN and FYVE domain containing 1 protein, et al. Podocalyxin‐like protein promotes gastric cancer progression through interacting with RUN and FYVE domain containing 1 protein
    Article Snippet: .. 2.8 Mass spectrometry and data analysis Samples were resuspended in 40 μL of aqueous formic acid, and 8 μg of each sample was analyzed using an Ultimate 3000 RSLCnano, coupled with an Orbitrap Elite mass spectrometer (Thermo Fisher, San Jose, CA, USA). .. Separations were performed using a Zorbax 300SB‐C18 column (Agilent Technologies, Santa Clara, CA, USA).

    Article Title: Proteomic Characterization of the Neural Ectoderm Fated Cell Clones in the Xenopus laevis Embryo by High-Resolution Mass Spectrometry
    Article Snippet: Paragraph title: Liquid Chromatography Mass Spectrometry. ... Separation used a nanoflow liquid chromatography system (Dionex Ultimate 3000 RSLCnano, Thermo) providing a 120 min gradient mixture from Buffer A (2% ACN, 0.1% FA) and Buffer B (100% ACN, 0.1% FA).

    Article Title: The landscape of transcription errors in eukaryotic cells
    Article Snippet: .. Tryptic digests were analyzed by LC–tandem MS (LC-MS/MS) on a Q Exactive HF mass spectrometer (Thermo Fisher Scientific) coupled to an UltiMate 3000 RSLCnano UPLC system (Dionex). ..

    Article Title: Metabolic crosstalk regulates Porphyromonas gingivalis colonization and virulence during oral polymicrobial Infection
    Article Snippet: For LC-MS/MS analysis, peptides were separated by reverse phase chromatography using an Acclaim C18 PepMap RSLC column (Dionex; Thermo Scientific, Waltham, MA) and reverse phase chromatography on a Dionex Ultimate 3000 RSLCnano UHPLC system (Thermo Scientific). .. Eluted peptides were directly injected into an Orbitrap Fusion mass spectrometer (Thermo Scientific) by nano-electrospray and subject to data-dependent tandem mass spectrometry, with full precursor ion scans (MS1) collected at 120,000 resolution.

    Article Title: The uremic toxin hippurate promotes endothelial dysfunction via the activation of Drp1-mediated mitochondrial fission
    Article Snippet: Serum hippurate was measured by liquid chromatography tandem mass spectrometry (LC/MS). .. Hippurate was separated by a Dionex Ultimate 3000 RSLCnano system (Thermo Fisher Scientific, USA) using a Hypersil Gold column (2.1 × 100 mm, inner diameter 1.9 µm, Thermo Fisher Scientific).

    Article Title: microRNA regulatory circuits in a mouse model of inherited retinal degeneration
    Article Snippet: .. LC-MS/MS analysis was carried out on an Ultimate3000 nano HPLC system (Dionex, Sunnyvale, CA, USA) coupled to a LTQ OrbitrapXL mass spectrometer (Thermo Fisher Scientific Inc., Waltham, MA, USA) . .. MS spectra were acquired in OrbitrapXL and up to 10 of the most abundant peptide ions selected for fragmentation in the linear ion trap.

    Article Title: Omega-3 fatty acid deficiency disrupts endocytosis, neuritogenesis, and mitochondrial protein pathways in the mouse hippocampus
    Article Snippet: .. Each of the 16 samples were run in triplicate, on a Thermo Scientific LTQ ORBITRAP XL mass spectrometer connected to an Dionex Ultimate 3000 (RSLCnano) chromatography system. .. Each sample was loaded onto Biobasic Picotip Emitter (120 mm length, 75 μm ID) packed in house with Reprocil Pur C18 (1.9 μm) reverse phase media column, and was separated by an increasing acetonitrile gradient, using a 56 min reverse phase gradient at a flow rate of 250 nL/min.

    Article Title: The Proteolysis Adaptor, NblA, Binds to the N-terminus of β-phycocyanin: Implications for the Mechanism of Phycobilisome Degradation
    Article Snippet: .. LC-MS/MS with an Ultimate 3000 Nano LC system (Thermo Scientific Dionex, Sunnyvale, CA) attached on-line to a Q Exactive Plus mass spectrometer (Thermo Fisher, Waltham, MA) was used to analyze the cross-linked sample digests. .. A 5 μL aliquot of each sample was loaded onto a guard column (Acclaim PepMap100, 100 μm × 2 cm, C18, 5 μm, 100 Å; Thermo Scientific Dionex) in Solvent A (water with 0.1% formic acid), and the peptides in the sample were separated on a custom-packed C18 reversed-phase column (Magic, 0.075 mm ×150 mm, 5 μm, 120 Å, Michrom Bioresources, Inc., Auburn, CA) at a flow rate of 4.5 μL/min.

    Article Title: Controlled Measurement and Comparative Analysis of Cellular Components in E. coli Reveals Broad Regulatory Changes in Response to Glucose Starvation
    Article Snippet: For LC-MS/MS analysis, peptides were subjected to separation by C18 reverse phase chromatography on a Dionex Ultimate 3000 RSLCnano UHPLC system (Thermo Scientific). .. Eluted peptides were directly injected into an Orbitrap Elite mass spectrometer (Thermo Scientific) by nano-electrospray and subject to data-dependent tandem mass spectrometry, with full precursor ion scans (MS1) collected at 60,0000 resolution.

    Article Title: Comparative venom-gland transcriptomics and venom proteomics of four Sidewinder Rattlesnake (Crotalus cerastes) lineages reveal little differential expression despite individual variation
    Article Snippet: .. For the LCMS/MS run, a 2 μ L aliquot was analyzed using an externally calibrated Thermo Q Exactive HF (high-resolution electrospray tandem mass spectrometer) in conjunction with Dionex UltiMate3000 RSLCnano System. ..

    Article Title: JASPer controls interphase histone H3S10 phosphorylation by chromosomal kinase JIL-1 in Drosophila
    Article Snippet: Paragraph title: Mass spectrometry and data analysis ... For LC-MS/MS purposes, desalted peptides were injected in an Ultimate 3000 RSLCnano system (Thermo), separated in a 15-cm analytical column (75 μm ID home-packed with ReproSil-Pur C18-AQ 2.4 μm from Dr. Maisch) with a 50-min gradient from 5 to 60% acetonitrile in 0.1% formic acid.

    Modification:

    Article Title: Itaconate is an anti-inflammatory metabolite that activates Nrf2 via alkylation of KEAP1
    Article Snippet: Paragraph title: Analysis of KEAP1 modification by OI ... Digested protein samples were analysed in an Orbitrap Fusion Lumos coupled to a UPLC ultimate 3000 RSLCnano System (both Thermo Fisher).

    High Performance Liquid Chromatography:

    Article Title: Marine Bacteria, A Source for Alginolytic Enzyme to Disrupt Pseudomonas aeruginosa Biofilms
    Article Snippet: .. The samples were transferred to a 300 µL HPLC vial and subject to analysis by LC-MS/MS on a VelosPRO orbitrap mass spectrometer (Thermo Fisher Scientific) equipped with an UltiMate 3000 Nano-LC system (Thermo Fisher Scientific). .. Chromatographic separation of the digests was performed on PicoFRIT C18 self-packed 75 mm x 60 cm capillary column (New Objective, Woburn, MA) at a flow rate of 300 µL/min.

    Article Title: microRNA regulatory circuits in a mouse model of inherited retinal degeneration
    Article Snippet: .. LC-MS/MS analysis was carried out on an Ultimate3000 nano HPLC system (Dionex, Sunnyvale, CA, USA) coupled to a LTQ OrbitrapXL mass spectrometer (Thermo Fisher Scientific Inc., Waltham, MA, USA) . .. MS spectra were acquired in OrbitrapXL and up to 10 of the most abundant peptide ions selected for fragmentation in the linear ion trap.

    Article Title: Omega-3 fatty acid deficiency disrupts endocytosis, neuritogenesis, and mitochondrial protein pathways in the mouse hippocampus
    Article Snippet: Samples were resuspended in Solution A (HPLC grade water, 2% acetonitrile, 0.5% acetic acid) where by 1 μg of protein digest (5 μl) was injected per LC-MS/MS run. .. Each of the 16 samples were run in triplicate, on a Thermo Scientific LTQ ORBITRAP XL mass spectrometer connected to an Dionex Ultimate 3000 (RSLCnano) chromatography system.

    Article Title: JASPer controls interphase histone H3S10 phosphorylation by chromosomal kinase JIL-1 in Drosophila
    Article Snippet: For LC-MS/MS purposes, desalted peptides were injected in an Ultimate 3000 RSLCnano system (Thermo), separated in a 15-cm analytical column (75 μm ID home-packed with ReproSil-Pur C18-AQ 2.4 μm from Dr. Maisch) with a 50-min gradient from 5 to 60% acetonitrile in 0.1% formic acid. .. The effluent from the HPLC was directly electrosprayed into a Q Exactive HF (Thermo) operated in data-dependent mode to automatically switch between full scan MS and MS/MS acquisition.

    Flow Cytometry:

    Article Title: Marine Bacteria, A Source for Alginolytic Enzyme to Disrupt Pseudomonas aeruginosa Biofilms
    Article Snippet: The samples were transferred to a 300 µL HPLC vial and subject to analysis by LC-MS/MS on a VelosPRO orbitrap mass spectrometer (Thermo Fisher Scientific) equipped with an UltiMate 3000 Nano-LC system (Thermo Fisher Scientific). .. Chromatographic separation of the digests was performed on PicoFRIT C18 self-packed 75 mm x 60 cm capillary column (New Objective, Woburn, MA) at a flow rate of 300 µL/min.

    Article Title: Metabolic crosstalk regulates Porphyromonas gingivalis colonization and virulence during oral polymicrobial Infection
    Article Snippet: For LC-MS/MS analysis, peptides were separated by reverse phase chromatography using an Acclaim C18 PepMap RSLC column (Dionex; Thermo Scientific, Waltham, MA) and reverse phase chromatography on a Dionex Ultimate 3000 RSLCnano UHPLC system (Thermo Scientific). .. Peptides were eluted using a 5–40% acetonitrile gradient over 90 min at 300 nL/min flow rate.

    Article Title: Cytoplasmic retention and degradation of a mitotic inducer enable plant infection by a pathogenic fungus
    Article Snippet: The eluates of the five upper and the five lower gel pieces were combined, suspended in sample buffer (98% H2O, 2% acetonitrile and 0.1% formic acid) and analyzed by LC-MS. Peptides generated with trypsin on-bead digestion were subjected to LC-MS analysis: 1.5 µL of each peptide sample were separated with nano-flow LC using an RSLCnano Ultimate 3000 system (Thermo Fisher Scientific). .. Peptides were loaded for 5 min with 0.07% trifluoroacetic acid on an Acclaim PepMap 100 pre-column (100 µm x 2 cm, C18, 3 µm, 100 Å; Thermo Fisher Scientific) with a flow rate of 20 µL/min.

    Article Title: Omega-3 fatty acid deficiency disrupts endocytosis, neuritogenesis, and mitochondrial protein pathways in the mouse hippocampus
    Article Snippet: Each of the 16 samples were run in triplicate, on a Thermo Scientific LTQ ORBITRAP XL mass spectrometer connected to an Dionex Ultimate 3000 (RSLCnano) chromatography system. .. Each sample was loaded onto Biobasic Picotip Emitter (120 mm length, 75 μm ID) packed in house with Reprocil Pur C18 (1.9 μm) reverse phase media column, and was separated by an increasing acetonitrile gradient, using a 56 min reverse phase gradient at a flow rate of 250 nL/min.

    Article Title: The Proteolysis Adaptor, NblA, Binds to the N-terminus of β-phycocyanin: Implications for the Mechanism of Phycobilisome Degradation
    Article Snippet: LC-MS/MS with an Ultimate 3000 Nano LC system (Thermo Scientific Dionex, Sunnyvale, CA) attached on-line to a Q Exactive Plus mass spectrometer (Thermo Fisher, Waltham, MA) was used to analyze the cross-linked sample digests. .. A 5 μL aliquot of each sample was loaded onto a guard column (Acclaim PepMap100, 100 μm × 2 cm, C18, 5 μm, 100 Å; Thermo Scientific Dionex) in Solvent A (water with 0.1% formic acid), and the peptides in the sample were separated on a custom-packed C18 reversed-phase column (Magic, 0.075 mm ×150 mm, 5 μm, 120 Å, Michrom Bioresources, Inc., Auburn, CA) at a flow rate of 4.5 μL/min.

    Article Title: Controlled Measurement and Comparative Analysis of Cellular Components in E. coli Reveals Broad Regulatory Changes in Response to Glucose Starvation
    Article Snippet: For LC-MS/MS analysis, peptides were subjected to separation by C18 reverse phase chromatography on a Dionex Ultimate 3000 RSLCnano UHPLC system (Thermo Scientific). .. Peptides were loaded onto an Acclaim C18 PepMap RSLC column (Dionex; Thermo Scientific) and eluted using a 5–40% acetonitrile gradient over 250 min at 300 nl/min flow rate.

    Chromatography:

    Article Title: The landscape of transcription errors in eukaryotic cells
    Article Snippet: Paragraph title: Multidimensional high-performance liquid chromatography–mass spectrometry analysis ... Tryptic digests were analyzed by LC–tandem MS (LC-MS/MS) on a Q Exactive HF mass spectrometer (Thermo Fisher Scientific) coupled to an UltiMate 3000 RSLCnano UPLC system (Dionex).

    Article Title: Omega-3 fatty acid deficiency disrupts endocytosis, neuritogenesis, and mitochondrial protein pathways in the mouse hippocampus
    Article Snippet: .. Each of the 16 samples were run in triplicate, on a Thermo Scientific LTQ ORBITRAP XL mass spectrometer connected to an Dionex Ultimate 3000 (RSLCnano) chromatography system. .. Each sample was loaded onto Biobasic Picotip Emitter (120 mm length, 75 μm ID) packed in house with Reprocil Pur C18 (1.9 μm) reverse phase media column, and was separated by an increasing acetonitrile gradient, using a 56 min reverse phase gradient at a flow rate of 250 nL/min.

    Qubit Protein Assay:

    Article Title: Comparative venom-gland transcriptomics and venom proteomics of four Sidewinder Rattlesnake (Crotalus cerastes) lineages reveal little differential expression despite individual variation
    Article Snippet: We first quantified venom protein samples using the Qubit Protein Assay kit with a Qubit 1.0 Fluorometer (Thermo Fisher Scientific). .. For the LCMS/MS run, a 2 μ L aliquot was analyzed using an externally calibrated Thermo Q Exactive HF (high-resolution electrospray tandem mass spectrometer) in conjunction with Dionex UltiMate3000 RSLCnano System.

    Cell Culture:

    Article Title: Metabolic crosstalk regulates Porphyromonas gingivalis colonization and virulence during oral polymicrobial Infection
    Article Snippet: In brief, bacteria were cultured to mid-log phase and reacted for 18 h with pABA (1 mg/mL) or vehicle control. .. For LC-MS/MS analysis, peptides were separated by reverse phase chromatography using an Acclaim C18 PepMap RSLC column (Dionex; Thermo Scientific, Waltham, MA) and reverse phase chromatography on a Dionex Ultimate 3000 RSLCnano UHPLC system (Thermo Scientific).

    SDS Page:

    Article Title: Cytoplasmic retention and degradation of a mitotic inducer enable plant infection by a pathogenic fungus
    Article Snippet: After separation of the protein samples by SDS-PAGE and Coomassie Brilliant Blue R250 (Serva, 17525, Heidelberg, Germany) staining and distaining of the SDS-Gel was performed and each lane was cut into 10 pieces. .. The eluates of the five upper and the five lower gel pieces were combined, suspended in sample buffer (98% H2O, 2% acetonitrile and 0.1% formic acid) and analyzed by LC-MS. Peptides generated with trypsin on-bead digestion were subjected to LC-MS analysis: 1.5 µL of each peptide sample were separated with nano-flow LC using an RSLCnano Ultimate 3000 system (Thermo Fisher Scientific).

    Generated:

    Article Title: Proteomic Characterization of the Neural Ectoderm Fated Cell Clones in the Xenopus laevis Embryo by High-Resolution Mass Spectrometry
    Article Snippet: Separation used a nanoflow liquid chromatography system (Dionex Ultimate 3000 RSLCnano, Thermo) providing a 120 min gradient mixture from Buffer A (2% ACN, 0.1% FA) and Buffer B (100% ACN, 0.1% FA). .. The electrospray was generated at 2.5 kV using a pulled fused silica capillary as emitter (10 μ m tip, New Objective, Woburn, MA).

    Article Title: Cytoplasmic retention and degradation of a mitotic inducer enable plant infection by a pathogenic fungus
    Article Snippet: .. The eluates of the five upper and the five lower gel pieces were combined, suspended in sample buffer (98% H2O, 2% acetonitrile and 0.1% formic acid) and analyzed by LC-MS. Peptides generated with trypsin on-bead digestion were subjected to LC-MS analysis: 1.5 µL of each peptide sample were separated with nano-flow LC using an RSLCnano Ultimate 3000 system (Thermo Fisher Scientific). .. Peptides were loaded for 5 min with 0.07% trifluoroacetic acid on an Acclaim PepMap 100 pre-column (100 µm x 2 cm, C18, 3 µm, 100 Å; Thermo Fisher Scientific) with a flow rate of 20 µL/min.

    Tandem Mass Spectroscopy:

    Article Title: Marine Bacteria, A Source for Alginolytic Enzyme to Disrupt Pseudomonas aeruginosa Biofilms
    Article Snippet: The samples were transferred to a 300 µL HPLC vial and subject to analysis by LC-MS/MS on a VelosPRO orbitrap mass spectrometer (Thermo Fisher Scientific) equipped with an UltiMate 3000 Nano-LC system (Thermo Fisher Scientific). .. MS and MS/MS data were acquired using a data-dependent acquisition method in which a full scan was obtained at a resolution of 30,000, followed by ten consecutive MS/MS spectra in both higher-energy collisional dissociation (HCD) and collision-induced dissociation (CID) mode (normalized collision energy 36%).

    Article Title: JASPer controls interphase histone H3S10 phosphorylation by chromosomal kinase JIL-1 in Drosophila
    Article Snippet: For LC-MS/MS purposes, desalted peptides were injected in an Ultimate 3000 RSLCnano system (Thermo), separated in a 15-cm analytical column (75 μm ID home-packed with ReproSil-Pur C18-AQ 2.4 μm from Dr. Maisch) with a 50-min gradient from 5 to 60% acetonitrile in 0.1% formic acid. .. The effluent from the HPLC was directly electrosprayed into a Q Exactive HF (Thermo) operated in data-dependent mode to automatically switch between full scan MS and MS/MS acquisition.

    Sequencing:

    Article Title: Cytoplasmic retention and degradation of a mitotic inducer enable plant infection by a pathogenic fungus
    Article Snippet: A digest with trypsin NB sequencing grade (Serva, 37283.01, Heidelberg, Germany) was performed with each gel piece over night at 37°C. .. The eluates of the five upper and the five lower gel pieces were combined, suspended in sample buffer (98% H2O, 2% acetonitrile and 0.1% formic acid) and analyzed by LC-MS. Peptides generated with trypsin on-bead digestion were subjected to LC-MS analysis: 1.5 µL of each peptide sample were separated with nano-flow LC using an RSLCnano Ultimate 3000 system (Thermo Fisher Scientific).

    Sonication:

    Article Title: Omega-3 fatty acid deficiency disrupts endocytosis, neuritogenesis, and mitochondrial protein pathways in the mouse hippocampus
    Article Snippet: Following solubilisation of samples by sonication in triethylammonium bicarbonate (TEAB; Sigma), 50 μg of protein from each of the 8 n-3 Adq and 8n-3 Def samples was denatured for 10 min at 80°C in the presence of 1% RapiGest (Waters). .. Each of the 16 samples were run in triplicate, on a Thermo Scientific LTQ ORBITRAP XL mass spectrometer connected to an Dionex Ultimate 3000 (RSLCnano) chromatography system.

    Injection:

    Article Title: Metabolic crosstalk regulates Porphyromonas gingivalis colonization and virulence during oral polymicrobial Infection
    Article Snippet: For LC-MS/MS analysis, peptides were separated by reverse phase chromatography using an Acclaim C18 PepMap RSLC column (Dionex; Thermo Scientific, Waltham, MA) and reverse phase chromatography on a Dionex Ultimate 3000 RSLCnano UHPLC system (Thermo Scientific). .. Eluted peptides were directly injected into an Orbitrap Fusion mass spectrometer (Thermo Scientific) by nano-electrospray and subject to data-dependent tandem mass spectrometry, with full precursor ion scans (MS1) collected at 120,000 resolution.

    Article Title: Omega-3 fatty acid deficiency disrupts endocytosis, neuritogenesis, and mitochondrial protein pathways in the mouse hippocampus
    Article Snippet: Samples were resuspended in Solution A (HPLC grade water, 2% acetonitrile, 0.5% acetic acid) where by 1 μg of protein digest (5 μl) was injected per LC-MS/MS run. .. Each of the 16 samples were run in triplicate, on a Thermo Scientific LTQ ORBITRAP XL mass spectrometer connected to an Dionex Ultimate 3000 (RSLCnano) chromatography system.

    Article Title: Controlled Measurement and Comparative Analysis of Cellular Components in E. coli Reveals Broad Regulatory Changes in Response to Glucose Starvation
    Article Snippet: For LC-MS/MS analysis, peptides were subjected to separation by C18 reverse phase chromatography on a Dionex Ultimate 3000 RSLCnano UHPLC system (Thermo Scientific). .. Eluted peptides were directly injected into an Orbitrap Elite mass spectrometer (Thermo Scientific) by nano-electrospray and subject to data-dependent tandem mass spectrometry, with full precursor ion scans (MS1) collected at 60,0000 resolution.

    Article Title: Comparative venom-gland transcriptomics and venom proteomics of four Sidewinder Rattlesnake (Crotalus cerastes) lineages reveal little differential expression despite individual variation
    Article Snippet: To initiate the mass spectrometry run, the resulting dried and digested tryptic peptides were resuspended in 0.1% formic acid at a final concentration of 250 ng/μ L. Three digested Escherichia coli proteins-purchased from Abcam at known concentrations and mixed in the specified proportions (1000×) prior to digestion-were used as internal standards: 25 fmol of P00811 (Beta-lactamase ampC), 250 fmol of P31658 (Protein deglycase 1), and 2500 fmol of P31697 (Chaperone protein FimC) per injection. .. For the LCMS/MS run, a 2 μ L aliquot was analyzed using an externally calibrated Thermo Q Exactive HF (high-resolution electrospray tandem mass spectrometer) in conjunction with Dionex UltiMate3000 RSLCnano System.

    Article Title: JASPer controls interphase histone H3S10 phosphorylation by chromosomal kinase JIL-1 in Drosophila
    Article Snippet: .. For LC-MS/MS purposes, desalted peptides were injected in an Ultimate 3000 RSLCnano system (Thermo), separated in a 15-cm analytical column (75 μm ID home-packed with ReproSil-Pur C18-AQ 2.4 μm from Dr. Maisch) with a 50-min gradient from 5 to 60% acetonitrile in 0.1% formic acid. .. The effluent from the HPLC was directly electrosprayed into a Q Exactive HF (Thermo) operated in data-dependent mode to automatically switch between full scan MS and MS/MS acquisition.

    Binding Assay:

    Article Title: JASPer controls interphase histone H3S10 phosphorylation by chromosomal kinase JIL-1 in Drosophila
    Article Snippet: Mass spectrometry and data analysis Whole IPs were used for trypsin digestion and mass spectrometry (IP/MS) identification of binding partners. .. For LC-MS/MS purposes, desalted peptides were injected in an Ultimate 3000 RSLCnano system (Thermo), separated in a 15-cm analytical column (75 μm ID home-packed with ReproSil-Pur C18-AQ 2.4 μm from Dr. Maisch) with a 50-min gradient from 5 to 60% acetonitrile in 0.1% formic acid.

    Isolation:

    Article Title: JASPer controls interphase histone H3S10 phosphorylation by chromosomal kinase JIL-1 in Drosophila
    Article Snippet: For LC-MS/MS purposes, desalted peptides were injected in an Ultimate 3000 RSLCnano system (Thermo), separated in a 15-cm analytical column (75 μm ID home-packed with ReproSil-Pur C18-AQ 2.4 μm from Dr. Maisch) with a 50-min gradient from 5 to 60% acetonitrile in 0.1% formic acid. .. The 10 most intense peptide ions with charge states between 2 and 5 were sequentially isolated to a target value of 1 × 105 , and fragmented at 27% normalized collision energy.

    Purification:

    Article Title: Omega-3 fatty acid deficiency disrupts endocytosis, neuritogenesis, and mitochondrial protein pathways in the mouse hippocampus
    Article Snippet: Digestion with trypsin (Promega; 1μg/μl) was carried out overnight at 37°C, and Tryptic peptides were purified using ZipTips (Millipore) according to the manufacturer's instructions. .. Each of the 16 samples were run in triplicate, on a Thermo Scientific LTQ ORBITRAP XL mass spectrometer connected to an Dionex Ultimate 3000 (RSLCnano) chromatography system.

    Reversed-phase Chromatography:

    Article Title: Metabolic crosstalk regulates Porphyromonas gingivalis colonization and virulence during oral polymicrobial Infection
    Article Snippet: .. For LC-MS/MS analysis, peptides were separated by reverse phase chromatography using an Acclaim C18 PepMap RSLC column (Dionex; Thermo Scientific, Waltham, MA) and reverse phase chromatography on a Dionex Ultimate 3000 RSLCnano UHPLC system (Thermo Scientific). .. Peptides were eluted using a 5–40% acetonitrile gradient over 90 min at 300 nL/min flow rate.

    Article Title: Cytoplasmic retention and degradation of a mitotic inducer enable plant infection by a pathogenic fungus
    Article Snippet: The eluates of the five upper and the five lower gel pieces were combined, suspended in sample buffer (98% H2O, 2% acetonitrile and 0.1% formic acid) and analyzed by LC-MS. Peptides generated with trypsin on-bead digestion were subjected to LC-MS analysis: 1.5 µL of each peptide sample were separated with nano-flow LC using an RSLCnano Ultimate 3000 system (Thermo Fisher Scientific). .. Separation of peptides was done with reverse phase chromatography on an Acclaim PepMap RSLC column (75 µm x 50 cm, C18, 3 µm, 100 Å; Thermo Fisher Scientific) at a flow rate of 300 nL/min.

    Article Title: Controlled Measurement and Comparative Analysis of Cellular Components in E. coli Reveals Broad Regulatory Changes in Response to Glucose Starvation
    Article Snippet: .. For LC-MS/MS analysis, peptides were subjected to separation by C18 reverse phase chromatography on a Dionex Ultimate 3000 RSLCnano UHPLC system (Thermo Scientific). .. Peptides were loaded onto an Acclaim C18 PepMap RSLC column (Dionex; Thermo Scientific) and eluted using a 5–40% acetonitrile gradient over 250 min at 300 nl/min flow rate.

    Liquid Chromatography:

    Article Title: Marine Bacteria, A Source for Alginolytic Enzyme to Disrupt Pseudomonas aeruginosa Biofilms
    Article Snippet: Paragraph title: 4.9. Liquid Chromatography Tandem-Mass Spectrometry (LC-MS/MS) Enzyme Analysis ... The samples were transferred to a 300 µL HPLC vial and subject to analysis by LC-MS/MS on a VelosPRO orbitrap mass spectrometer (Thermo Fisher Scientific) equipped with an UltiMate 3000 Nano-LC system (Thermo Fisher Scientific).

    Article Title: Proteomic Characterization of the Neural Ectoderm Fated Cell Clones in the Xenopus laevis Embryo by High-Resolution Mass Spectrometry
    Article Snippet: .. Separation used a nanoflow liquid chromatography system (Dionex Ultimate 3000 RSLCnano, Thermo) providing a 120 min gradient mixture from Buffer A (2% ACN, 0.1% FA) and Buffer B (100% ACN, 0.1% FA). ..

    Article Title: The uremic toxin hippurate promotes endothelial dysfunction via the activation of Drp1-mediated mitochondrial fission
    Article Snippet: Serum hippurate was measured by liquid chromatography tandem mass spectrometry (LC/MS). .. Hippurate was separated by a Dionex Ultimate 3000 RSLCnano system (Thermo Fisher Scientific, USA) using a Hypersil Gold column (2.1 × 100 mm, inner diameter 1.9 µm, Thermo Fisher Scientific).

    Software:

    Article Title: microRNA regulatory circuits in a mouse model of inherited retinal degeneration
    Article Snippet: LC-MS/MS analysis was carried out on an Ultimate3000 nano HPLC system (Dionex, Sunnyvale, CA, USA) coupled to a LTQ OrbitrapXL mass spectrometer (Thermo Fisher Scientific Inc., Waltham, MA, USA) . .. Peptides were quantified using Progenesis QI (Waters, Milford, MA, USA) and identified with Mascot (version 2.5; Matrix Science, Boston, MA, USA) software.

    Selection:

    Article Title: Metabolic crosstalk regulates Porphyromonas gingivalis colonization and virulence during oral polymicrobial Infection
    Article Snippet: For LC-MS/MS analysis, peptides were separated by reverse phase chromatography using an Acclaim C18 PepMap RSLC column (Dionex; Thermo Scientific, Waltham, MA) and reverse phase chromatography on a Dionex Ultimate 3000 RSLCnano UHPLC system (Thermo Scientific). .. Monoisotopic precursor selection and charge-state screening were enabled, with ions of charge > +1 selected for collision-induced dissociation (CID).

    Article Title: Controlled Measurement and Comparative Analysis of Cellular Components in E. coli Reveals Broad Regulatory Changes in Response to Glucose Starvation
    Article Snippet: For LC-MS/MS analysis, peptides were subjected to separation by C18 reverse phase chromatography on a Dionex Ultimate 3000 RSLCnano UHPLC system (Thermo Scientific). .. Monoisotopic precursor selection and charge-state screening were enabled, with ions of charge > +1 selected for collision-induced dissociation (CID).

    Sample Prep:

    Article Title: Cytoplasmic retention and degradation of a mitotic inducer enable plant infection by a pathogenic fungus
    Article Snippet: Paragraph title: Proteomic sample preparation and LC-MS analysis of peptides ... The eluates of the five upper and the five lower gel pieces were combined, suspended in sample buffer (98% H2O, 2% acetonitrile and 0.1% formic acid) and analyzed by LC-MS. Peptides generated with trypsin on-bead digestion were subjected to LC-MS analysis: 1.5 µL of each peptide sample were separated with nano-flow LC using an RSLCnano Ultimate 3000 system (Thermo Fisher Scientific).

    Article Title: Omega-3 fatty acid deficiency disrupts endocytosis, neuritogenesis, and mitochondrial protein pathways in the mouse hippocampus
    Article Snippet: Paragraph title: Sample preparation and label free quantification using LC-MS/MS analysis ... Each of the 16 samples were run in triplicate, on a Thermo Scientific LTQ ORBITRAP XL mass spectrometer connected to an Dionex Ultimate 3000 (RSLCnano) chromatography system.

    Spectrophotometry:

    Article Title: The landscape of transcription errors in eukaryotic cells
    Article Snippet: The peptide concentrations were measured by ultraviolet spectrophotometry at 280 nm with an assumed extinction coefficient of 1.1 ml/cm per mg. Fifty micrograms of peptides from each sample was separated (0.3 ml/min at 30°C) using the following gradient (time, % B): 3 min, 0% B; 5 min, 6% B; 12 min, 14% B; 23 min, 26% B; 27 min, 34% B; 28 min, 65% B; 28.1 min, 100% B. .. Tryptic digests were analyzed by LC–tandem MS (LC-MS/MS) on a Q Exactive HF mass spectrometer (Thermo Fisher Scientific) coupled to an UltiMate 3000 RSLCnano UPLC system (Dionex).

    Concentration Assay:

    Article Title: Controlled Measurement and Comparative Analysis of Cellular Components in E. coli Reveals Broad Regulatory Changes in Response to Glucose Starvation
    Article Snippet: Following incubation, iodoacetamide was added to a concentration of 25 mM and samples were incubated at room temperature in the dark for 30 min. .. For LC-MS/MS analysis, peptides were subjected to separation by C18 reverse phase chromatography on a Dionex Ultimate 3000 RSLCnano UHPLC system (Thermo Scientific).

    Article Title: Comparative venom-gland transcriptomics and venom proteomics of four Sidewinder Rattlesnake (Crotalus cerastes) lineages reveal little differential expression despite individual variation
    Article Snippet: To initiate the mass spectrometry run, the resulting dried and digested tryptic peptides were resuspended in 0.1% formic acid at a final concentration of 250 ng/μ L. Three digested Escherichia coli proteins-purchased from Abcam at known concentrations and mixed in the specified proportions (1000×) prior to digestion-were used as internal standards: 25 fmol of P00811 (Beta-lactamase ampC), 250 fmol of P31658 (Protein deglycase 1), and 2500 fmol of P31697 (Chaperone protein FimC) per injection. .. For the LCMS/MS run, a 2 μ L aliquot was analyzed using an externally calibrated Thermo Q Exactive HF (high-resolution electrospray tandem mass spectrometer) in conjunction with Dionex UltiMate3000 RSLCnano System.

    Liquid Chromatography with Mass Spectroscopy:

    Article Title: The landscape of transcription errors in eukaryotic cells
    Article Snippet: The HRM (Hyper Reaction Monitoring) standard (catalog no. Pp-2001, Biognosys) was added to each sample before liquid chromatography–mass spectrometry (LC-MS) analysis. .. Tryptic digests were analyzed by LC–tandem MS (LC-MS/MS) on a Q Exactive HF mass spectrometer (Thermo Fisher Scientific) coupled to an UltiMate 3000 RSLCnano UPLC system (Dionex).

    Article Title: The uremic toxin hippurate promotes endothelial dysfunction via the activation of Drp1-mediated mitochondrial fission
    Article Snippet: Serum hippurate was measured by liquid chromatography tandem mass spectrometry (LC/MS). .. Hippurate was separated by a Dionex Ultimate 3000 RSLCnano system (Thermo Fisher Scientific, USA) using a Hypersil Gold column (2.1 × 100 mm, inner diameter 1.9 µm, Thermo Fisher Scientific).

    Article Title: Cytoplasmic retention and degradation of a mitotic inducer enable plant infection by a pathogenic fungus
    Article Snippet: .. The eluates of the five upper and the five lower gel pieces were combined, suspended in sample buffer (98% H2O, 2% acetonitrile and 0.1% formic acid) and analyzed by LC-MS. Peptides generated with trypsin on-bead digestion were subjected to LC-MS analysis: 1.5 µL of each peptide sample were separated with nano-flow LC using an RSLCnano Ultimate 3000 system (Thermo Fisher Scientific). .. Peptides were loaded for 5 min with 0.07% trifluoroacetic acid on an Acclaim PepMap 100 pre-column (100 µm x 2 cm, C18, 3 µm, 100 Å; Thermo Fisher Scientific) with a flow rate of 20 µL/min.

    Article Title: Comparative venom-gland transcriptomics and venom proteomics of four Sidewinder Rattlesnake (Crotalus cerastes) lineages reveal little differential expression despite individual variation
    Article Snippet: .. For the LCMS/MS run, a 2 μ L aliquot was analyzed using an externally calibrated Thermo Q Exactive HF (high-resolution electrospray tandem mass spectrometer) in conjunction with Dionex UltiMate3000 RSLCnano System. ..

    Staining:

    Article Title: Marine Bacteria, A Source for Alginolytic Enzyme to Disrupt Pseudomonas aeruginosa Biofilms
    Article Snippet: The excised gel slices stained with Coomassie blue G-250 were processed for LC-MS/MS as previously described [ ], with minor modifications. .. The samples were transferred to a 300 µL HPLC vial and subject to analysis by LC-MS/MS on a VelosPRO orbitrap mass spectrometer (Thermo Fisher Scientific) equipped with an UltiMate 3000 Nano-LC system (Thermo Fisher Scientific).

    Article Title: Cytoplasmic retention and degradation of a mitotic inducer enable plant infection by a pathogenic fungus
    Article Snippet: After separation of the protein samples by SDS-PAGE and Coomassie Brilliant Blue R250 (Serva, 17525, Heidelberg, Germany) staining and distaining of the SDS-Gel was performed and each lane was cut into 10 pieces. .. The eluates of the five upper and the five lower gel pieces were combined, suspended in sample buffer (98% H2O, 2% acetonitrile and 0.1% formic acid) and analyzed by LC-MS. Peptides generated with trypsin on-bead digestion were subjected to LC-MS analysis: 1.5 µL of each peptide sample were separated with nano-flow LC using an RSLCnano Ultimate 3000 system (Thermo Fisher Scientific).

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    Thermo Fisher ultimate3000 rslc nano hplc system
    Ultimate3000 Rslc Nano Hplc System, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 90/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 90 stars, based on 2 article reviews
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    ultimate3000 rslc nano hplc system - by Bioz Stars, 2020-02
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