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    Thermo Fisher exactive orbitrap mass spectrometer
    MS spectra (mass range: m/z 200–1000) by <t>Orbitrap</t> and MS/MS spectra (parent ion: m/z 316.1, mass range: 297.0–299.0 and 240.0–242.0) by TSQ for blank paper substrates subject to different treatments. (a) untreated 31 ET paper,
    Exactive Orbitrap Mass Spectrometer, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 1537 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/exactive orbitrap mass spectrometer/product/Thermo Fisher
    Average 99 stars, based on 1537 article reviews
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    exactive orbitrap mass spectrometer - by Bioz Stars, 2020-05
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    MS spectra (mass range: m/z 200–1000) by Orbitrap and MS/MS spectra (parent ion: m/z 316.1, mass range: 297.0–299.0 and 240.0–242.0) by TSQ for blank paper substrates subject to different treatments. (a) untreated 31 ET paper,

    Journal: The Analyst

    Article Title: Quantitative Paper Spray Mass Spectrometry Analysis of Drugs of Abuse

    doi: 10.1039/c3an00934c

    Figure Lengend Snippet: MS spectra (mass range: m/z 200–1000) by Orbitrap and MS/MS spectra (parent ion: m/z 316.1, mass range: 297.0–299.0 and 240.0–242.0) by TSQ for blank paper substrates subject to different treatments. (a) untreated 31 ET paper,

    Article Snippet: The MS spectra were recorded using an Exactive Orbitrap mass spectrometer (Exactive, Thermo Scientific, CA).

    Techniques: Mass Spectrometry

    Workflow of TMT quantitative shotgun proteomic analysis. Proteins extracted from rice leaves were reduced, alkylased, precipitated and digested before being labelled with Tandem Mass Tags. Labelled samples were pooled, fractionated by SCX and then analysed on a Q Exactive Orbitrap mass spectrometer. Raw data generated from the mass spectrometer were processed using Proteome Discover v1.4 and Mascot. The search results were further analysed by the TMTPrePro software package.

    Journal: Data in Brief

    Article Title: Label-free and isobaric tandem mass tag (TMT) multiplexed quantitative proteomic data of two contrasting rice cultivars exposed to drought stress and recovery

    doi: 10.1016/j.dib.2018.12.041

    Figure Lengend Snippet: Workflow of TMT quantitative shotgun proteomic analysis. Proteins extracted from rice leaves were reduced, alkylased, precipitated and digested before being labelled with Tandem Mass Tags. Labelled samples were pooled, fractionated by SCX and then analysed on a Q Exactive Orbitrap mass spectrometer. Raw data generated from the mass spectrometer were processed using Proteome Discover v1.4 and Mascot. The search results were further analysed by the TMTPrePro software package.

    Article Snippet: These fractions were desalted using C18 OMIX® tips (Agilent) and analysed on a Q Exactive Orbitrap mass spectrometer (Thermo Scientific) coupled to an EASY-nLC1000 (Thermo Scientific).

    Techniques: Mass Spectrometry, Generated, Software

    Overlay of extracted ion chromatograms (EICs) of HT2/T2 plant metabolites. ( a ) Overlaid EICs of HT2 metabolites based on HT2-treated oat sample (time point full-ripening) and Table 1 ; ( b ) overlaid EICs of T2 metabolites based on T2-treated oat samples (time point full-ripening and accumulated time points marked with an asterisk) and Table 2 . Oat panicles were treated with a 1/1 mixture of non-labelled and uniformly 13 C-labelled toxin, extracted and analysed by LC-Orbitrap-MS in positive and negative ion mode and MetExtract II software. Non-labelled metabolite form is depicted with positive intensity (up) and corresponding 13 C-labelled metabolite form with negative intensity (down). HT2, HT-2 toxin; T2, T-2 toxin.

    Journal: Toxins

    Article Title: Metabolism of HT-2 Toxin and T-2 Toxin in Oats

    doi: 10.3390/toxins8120364

    Figure Lengend Snippet: Overlay of extracted ion chromatograms (EICs) of HT2/T2 plant metabolites. ( a ) Overlaid EICs of HT2 metabolites based on HT2-treated oat sample (time point full-ripening) and Table 1 ; ( b ) overlaid EICs of T2 metabolites based on T2-treated oat samples (time point full-ripening and accumulated time points marked with an asterisk) and Table 2 . Oat panicles were treated with a 1/1 mixture of non-labelled and uniformly 13 C-labelled toxin, extracted and analysed by LC-Orbitrap-MS in positive and negative ion mode and MetExtract II software. Non-labelled metabolite form is depicted with positive intensity (up) and corresponding 13 C-labelled metabolite form with negative intensity (down). HT2, HT-2 toxin; T2, T-2 toxin.

    Article Snippet: Qualitative Screening Experiment Measurements of 12 C/13 C-toxin- and mock-treated samples were performed with an UltiMate 3000 HPLC system combined with an Exactive Plus Orbitrap mass spectrometer (Thermo Fisher Scientific, Bremen, Germany).

    Techniques: Mass Spectrometry, Software

    Development of a quantitative high-resolution mass spectrometry to directly measure intracellular 5-AZA-CdR and AZA. ( a ) Chemical structures of cytidine, deoxycytidine, AZA and 5-AZA-CdR. ( b ) Schematic depicting intracellular metabolism of AZA. Following cellular uptake and phosphorylation, ~80% of AZA gets incorporated into RNA by RNA polymerases. The remaining fraction is converted into 5-AZA-CdR by ribonucleotide reductase and incorporated into DNA by DNA polymerases. ( c ) Representative high-resolution Orbitrap mass spectra at RT of 0.98 min, showing clear baseline separation between 5-AZA-CdR, 15N-dC and 13C-dC (left, with respective m/z values) despite their identical chromatographic retention times (right). ( d ) Schematic depicting the optimised method incorporating steps to improve sensitivity of detection of intracellular 5-AZA-CdR and AZA by LC–MS.

    Journal: Leukemia

    Article Title: AZA-MS: a novel multiparameter mass spectrometry method to determine the intracellular dynamics of azacitidine therapy in vivo

    doi: 10.1038/leu.2017.340

    Figure Lengend Snippet: Development of a quantitative high-resolution mass spectrometry to directly measure intracellular 5-AZA-CdR and AZA. ( a ) Chemical structures of cytidine, deoxycytidine, AZA and 5-AZA-CdR. ( b ) Schematic depicting intracellular metabolism of AZA. Following cellular uptake and phosphorylation, ~80% of AZA gets incorporated into RNA by RNA polymerases. The remaining fraction is converted into 5-AZA-CdR by ribonucleotide reductase and incorporated into DNA by DNA polymerases. ( c ) Representative high-resolution Orbitrap mass spectra at RT of 0.98 min, showing clear baseline separation between 5-AZA-CdR, 15N-dC and 13C-dC (left, with respective m/z values) despite their identical chromatographic retention times (right). ( d ) Schematic depicting the optimised method incorporating steps to improve sensitivity of detection of intracellular 5-AZA-CdR and AZA by LC–MS.

    Article Snippet: Mass spectrometry and data analysis LC–MS analysis was performed utilising an ultra-high-performance liquid chromatography system (Dionex u3000 system, Thermo Fisher Scientific) interfaced to an Orbitrap mass spectrometer (Q Exactive Plus, Thermo Fisher Scientific) using a heated electrospray interface operated in the positive ion mode.

    Techniques: Mass Spectrometry, Liquid Chromatography with Mass Spectroscopy

    Identification of processed POMC peptides by LC-MS/MS. A) Schematic workflow for the quantification of POMC-derived peptides from hPSC-derived hypothalamic neurons. B) Liquid chromatographs of samples from hPSC-derived hypothalamic neurons (top), compared with stable isotope-labelled synthetic d-α-MSH(1-13), β-MSH(1-18) and β-EP (1-31) (bottom). Note that heavy isotope-labelled reference peptides have identical retention times as endogenous peptides but have slightly higher mass-to-charge (m/z) ratios, and that m/z values measured from Orbitrap and triple quadrupole mass spectrometers may differ. C) Schematic of human POMC protein and relevant dibasic cleavage sites (blue), expected POMC-derived peptides, and those peptides detected in hPSC-derived hypothalamic cultures by LC-MS/MS. Detected peptides included γ 1 -MSH (Lys- γ 1 -MSH), d-α-MSH(1-13), β-MSH(1-18) and β-EP (1-31). Quantified peptides are indicated in green. D) Summary of POMC-derived peptides detected by LC-MS/MS, where the colour intensity represents the relative abundance of each peptide species. Repl., replicates. Other abbreviations are as in Figure 1 .

    Journal: Molecular Metabolism

    Article Title: Quantitative mass spectrometry for human melanocortin peptides in vitro and in vivo suggests prominent roles for β-MSH and desacetyl α-MSH in energy homeostasis

    doi: 10.1016/j.molmet.2018.08.006

    Figure Lengend Snippet: Identification of processed POMC peptides by LC-MS/MS. A) Schematic workflow for the quantification of POMC-derived peptides from hPSC-derived hypothalamic neurons. B) Liquid chromatographs of samples from hPSC-derived hypothalamic neurons (top), compared with stable isotope-labelled synthetic d-α-MSH(1-13), β-MSH(1-18) and β-EP (1-31) (bottom). Note that heavy isotope-labelled reference peptides have identical retention times as endogenous peptides but have slightly higher mass-to-charge (m/z) ratios, and that m/z values measured from Orbitrap and triple quadrupole mass spectrometers may differ. C) Schematic of human POMC protein and relevant dibasic cleavage sites (blue), expected POMC-derived peptides, and those peptides detected in hPSC-derived hypothalamic cultures by LC-MS/MS. Detected peptides included γ 1 -MSH (Lys- γ 1 -MSH), d-α-MSH(1-13), β-MSH(1-18) and β-EP (1-31). Quantified peptides are indicated in green. D) Summary of POMC-derived peptides detected by LC-MS/MS, where the colour intensity represents the relative abundance of each peptide species. Repl., replicates. Other abbreviations are as in Figure 1 .

    Article Snippet: 2.9 Peptide discovery by LC-MS/MS Peptide extracts were run using nano-flow-based separation and electrospray approaches on a Thermo Fisher Ultimate 3000 nano-LC system coupled to a Q Exactive Plus Orbitrap mass spectrometer (ThermoScientific, San Jose, USA) as described previously .

    Techniques: Liquid Chromatography with Mass Spectroscopy, Mass Spectrometry, Derivative Assay

    The identification of a patient-specific protein signature in pancreatic juice. Protein quantitation was performed using isobaric labeling with TMT and LC-MS/MS analysis on an LTQ-Orbitrap Velos mass spectrometer. A : An unsupervised clustering analysis identified clearly different expression patterns in CEL -mutation carriers compared with controls with analyses performed by an investigator (F.M.) blinded to the samples. B : Log 2 plot of secretin-stimulated duodenal protein abundances and ratios of levels in the three CEL -mutation carriers compared with the three controls. Note the lack of skewed distribution of pancreatic proteins in the log 2 plot, indicating that a majority of the proteins had been detected despite degradation. Using “no-enzyme”-specific searches, we identified 757 proteins in the secretin-stimulated duodenal juice, of which 115 proteins were pancreatic specific based on a previous report ( 17 ). C : Immunoblot validation examples of proteins identified with stippled lines indicate gel crops. In addition to the three diabetic CEL -mutation carriers (D1, D2, D3) and three nonfamily controls (N1, N2, N3), we also added secretin-stimulated duodenal juice samples from two prediabetic CEL -mutation carriers (P1, P2) and from the CEL -mutation carrier with the KRAS -mutated pancreatic ductal adenocarcinoma (C1). D : Visualization of the MAPK-targeted proteins identified by Biobase ExPlain 3.0 tool and alphanumeric codes referring to PubMed identification in Supplementary Table 3 . E : Heat map demonstrating differential clustering of kinase activities in the secretin-stimulated duodenal juice and pancreatic tissue of CEL -mutation carriers and controls. F : Vertical bar graphs showing significant differences in kinase activities for PKC, CH1, and CH2 in secretin-stimulated duodenal juice. The multiplexed kinase activity assay allows the absolute quantitation of kinase activities by measuring the amount of phosphorylation of 60 peptide substrates with known motifs for many kinases. Vertical bar graphs showing differences in kinase activities for PKC, CH1, CH2, and MAPK in secretin-stimulated duodenal juice. PDAC, pancreatic ductal adenocarcinoma; mut, mutation; log 2 ratio, log 2 of the ratio of MS abundance for the sum of the three controls divided by the sum of the three diabetic mutation carriers; log 2 total, log 2 of the total MS abundance for a protein as the sum of the abundances of three controls and the three diabetic mutation carriers.

    Journal: Diabetes

    Article Title: Carboxyl-Ester Lipase Maturity-Onset Diabetes of the Young Is Associated With Development of Pancreatic Cysts and Upregulated MAPK Signaling in Secretin-Stimulated Duodenal Fluid

    doi: 10.2337/db13-1012

    Figure Lengend Snippet: The identification of a patient-specific protein signature in pancreatic juice. Protein quantitation was performed using isobaric labeling with TMT and LC-MS/MS analysis on an LTQ-Orbitrap Velos mass spectrometer. A : An unsupervised clustering analysis identified clearly different expression patterns in CEL -mutation carriers compared with controls with analyses performed by an investigator (F.M.) blinded to the samples. B : Log 2 plot of secretin-stimulated duodenal protein abundances and ratios of levels in the three CEL -mutation carriers compared with the three controls. Note the lack of skewed distribution of pancreatic proteins in the log 2 plot, indicating that a majority of the proteins had been detected despite degradation. Using “no-enzyme”-specific searches, we identified 757 proteins in the secretin-stimulated duodenal juice, of which 115 proteins were pancreatic specific based on a previous report ( 17 ). C : Immunoblot validation examples of proteins identified with stippled lines indicate gel crops. In addition to the three diabetic CEL -mutation carriers (D1, D2, D3) and three nonfamily controls (N1, N2, N3), we also added secretin-stimulated duodenal juice samples from two prediabetic CEL -mutation carriers (P1, P2) and from the CEL -mutation carrier with the KRAS -mutated pancreatic ductal adenocarcinoma (C1). D : Visualization of the MAPK-targeted proteins identified by Biobase ExPlain 3.0 tool and alphanumeric codes referring to PubMed identification in Supplementary Table 3 . E : Heat map demonstrating differential clustering of kinase activities in the secretin-stimulated duodenal juice and pancreatic tissue of CEL -mutation carriers and controls. F : Vertical bar graphs showing significant differences in kinase activities for PKC, CH1, and CH2 in secretin-stimulated duodenal juice. The multiplexed kinase activity assay allows the absolute quantitation of kinase activities by measuring the amount of phosphorylation of 60 peptide substrates with known motifs for many kinases. Vertical bar graphs showing differences in kinase activities for PKC, CH1, CH2, and MAPK in secretin-stimulated duodenal juice. PDAC, pancreatic ductal adenocarcinoma; mut, mutation; log 2 ratio, log 2 of the ratio of MS abundance for the sum of the three controls divided by the sum of the three diabetic mutation carriers; log 2 total, log 2 of the total MS abundance for a protein as the sum of the abundances of three controls and the three diabetic mutation carriers.

    Article Snippet: The peptides from proteolytic degradation assays were analyzed by liquid chromatography (LC)-MS on a high-resolution Exactive Orbitrap mass spectrometer (Thermo Scientific, Rockford, IL).

    Techniques: Protein Quantitation, Labeling, Liquid Chromatography with Mass Spectroscopy, Mass Spectrometry, Expressing, Mutagenesis, Kinase Assay, Quantitation Assay