ltq-orbitrap mass spectrometer Search Results


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  • 99
    Thermo Fisher maldi ltq orbitrap mass spectrometer
    Workflow for MS imaging of Pseudonocardia on the ant propleural plate. a) Photograph and b) cartoon of Pseudonocardia on the ant exoskeleton. c) Grooves were cut into glass slides and double-sided tape was applied to the back of the slide. The ant thoraxes were removed and positioned into the groove of the slide with the propleural plate facing outward and even with the top of the slide. An additional thin strip of double-sided tape was applied below the propleural plate to stabilize and secure the thorax into place. d) Matrix was applied to the slide using an automatic sprayer. e) A laser was fired at the sample to ionize compounds of interest and introduce them into the mass spectrometer. f) An array of mass spectra was acquired using a <t>MALDI-LTQ</t> <t>Orbitrap</t> and g) compiled into MS images. Photo courtesy of Alex Wild.
    Maldi Ltq Orbitrap Mass Spectrometer, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 16 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    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: 99/100, based on 7725 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    Thermo Fisher ltq orbitrap fusion tribrid 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 Fusion Tribrid Mass Spectrometer, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 44 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    94
    Waters Corporation ltq orbitrap xl 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 Xl Mass Spectrometer, supplied by Waters Corporation, used in various techniques. Bioz Stars score: 94/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    Thermo Fisher ltq orbitrap xl hybrid mass spectrometer
    Schematic outline of proteomic analysis methodology. Sample processing, followed by strong cation exchange (SCX) and reverse-phase chromatography coupled online to an <t>LTQ-Orbitrap</t> mass spectrometer, and subsequent data analysis is outlined. CM, conditioned media; LC-MS/MS, liquid chromatography tandem mass spectrometry.
    Ltq Orbitrap Xl Hybrid Mass Spectrometer, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 1036 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    90
    Thermo Fisher orbitrap mass spectrometer
    Accuracies and discrimination power of the FlavonoidSearch system. ( a ) The accuracy of each search tool was evaluated using the area under the cumulative curve (AUCc) for a plot of cumulative ratio of queries ( Y -axis) to the efficiency of narrowing down to the correct answer ( X -axis). The cumulative curve will move closer to the upper left-hand corner of the figure when highly narrowed-down results are obtained for a high number of queries. Therefore, a high AUCc is indicative of high accuracy. Results are shown for data obtained in-house for flavonoid aglycones using ion trap (IT) and Fourier transform (FT) mass spectrometry (MS) of LTQ-FT and IT of <t>LTQ-Orbitrap</t> and spectra retrieved from MassBank and NIST14 searched with the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. ( b ) Differences in the frequency distributions of Jaccard indices for flavonoid aglycones (red bars) and other compounds (grey bars). The frequency represents the ratio of records with a range of Jaccard indices to all records that had a Jaccard index > 0. ( c ) A receiver operating characteristic curve of the discrimination test by a binary classification in ( b ), yielding an area under the curve (AUC) of 0.91. Results obtained with ITFT data from NIST14 are shown in ( b ) and ( c ).
    Orbitrap Mass Spectrometer, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 90/100, based on 1569 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    93
    Thermo Fisher ltq orbitrap elite etd mass spectrometer
    Accuracies and discrimination power of the FlavonoidSearch system. ( a ) The accuracy of each search tool was evaluated using the area under the cumulative curve (AUCc) for a plot of cumulative ratio of queries ( Y -axis) to the efficiency of narrowing down to the correct answer ( X -axis). The cumulative curve will move closer to the upper left-hand corner of the figure when highly narrowed-down results are obtained for a high number of queries. Therefore, a high AUCc is indicative of high accuracy. Results are shown for data obtained in-house for flavonoid aglycones using ion trap (IT) and Fourier transform (FT) mass spectrometry (MS) of LTQ-FT and IT of <t>LTQ-Orbitrap</t> and spectra retrieved from MassBank and NIST14 searched with the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. ( b ) Differences in the frequency distributions of Jaccard indices for flavonoid aglycones (red bars) and other compounds (grey bars). The frequency represents the ratio of records with a range of Jaccard indices to all records that had a Jaccard index > 0. ( c ) A receiver operating characteristic curve of the discrimination test by a binary classification in ( b ), yielding an area under the curve (AUC) of 0.91. Results obtained with ITFT data from NIST14 are shown in ( b ) and ( c ).
    Ltq Orbitrap Elite Etd Mass Spectrometer, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 93/100, based on 47 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    95
    Thermo Fisher electrospray ltq orbitrap discovery mass spectrometer
    Accuracies and discrimination power of the FlavonoidSearch system. ( a ) The accuracy of each search tool was evaluated using the area under the cumulative curve (AUCc) for a plot of cumulative ratio of queries ( Y -axis) to the efficiency of narrowing down to the correct answer ( X -axis). The cumulative curve will move closer to the upper left-hand corner of the figure when highly narrowed-down results are obtained for a high number of queries. Therefore, a high AUCc is indicative of high accuracy. Results are shown for data obtained in-house for flavonoid aglycones using ion trap (IT) and Fourier transform (FT) mass spectrometry (MS) of LTQ-FT and IT of <t>LTQ-Orbitrap</t> and spectra retrieved from MassBank and NIST14 searched with the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. ( b ) Differences in the frequency distributions of Jaccard indices for flavonoid aglycones (red bars) and other compounds (grey bars). The frequency represents the ratio of records with a range of Jaccard indices to all records that had a Jaccard index > 0. ( c ) A receiver operating characteristic curve of the discrimination test by a binary classification in ( b ), yielding an area under the curve (AUC) of 0.91. Results obtained with ITFT data from NIST14 are shown in ( b ) and ( c ).
    Electrospray Ltq Orbitrap Discovery Mass Spectrometer, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 95/100, based on 14 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    86
    Thermo Fisher ltq orbitrap classic tandem mass spectrometer
    Accuracies and discrimination power of the FlavonoidSearch system. ( a ) The accuracy of each search tool was evaluated using the area under the cumulative curve (AUCc) for a plot of cumulative ratio of queries ( Y -axis) to the efficiency of narrowing down to the correct answer ( X -axis). The cumulative curve will move closer to the upper left-hand corner of the figure when highly narrowed-down results are obtained for a high number of queries. Therefore, a high AUCc is indicative of high accuracy. Results are shown for data obtained in-house for flavonoid aglycones using ion trap (IT) and Fourier transform (FT) mass spectrometry (MS) of LTQ-FT and IT of <t>LTQ-Orbitrap</t> and spectra retrieved from MassBank and NIST14 searched with the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. ( b ) Differences in the frequency distributions of Jaccard indices for flavonoid aglycones (red bars) and other compounds (grey bars). The frequency represents the ratio of records with a range of Jaccard indices to all records that had a Jaccard index > 0. ( c ) A receiver operating characteristic curve of the discrimination test by a binary classification in ( b ), yielding an area under the curve (AUC) of 0.91. Results obtained with ITFT data from NIST14 are shown in ( b ) and ( c ).
    Ltq Orbitrap Classic Tandem Mass Spectrometer, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 86/100, based on 8 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher ltq velos orbitrap etd mass spectrometer
    Accuracies and discrimination power of the FlavonoidSearch system. ( a ) The accuracy of each search tool was evaluated using the area under the cumulative curve (AUCc) for a plot of cumulative ratio of queries ( Y -axis) to the efficiency of narrowing down to the correct answer ( X -axis). The cumulative curve will move closer to the upper left-hand corner of the figure when highly narrowed-down results are obtained for a high number of queries. Therefore, a high AUCc is indicative of high accuracy. Results are shown for data obtained in-house for flavonoid aglycones using ion trap (IT) and Fourier transform (FT) mass spectrometry (MS) of LTQ-FT and IT of <t>LTQ-Orbitrap</t> and spectra retrieved from MassBank and NIST14 searched with the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. ( b ) Differences in the frequency distributions of Jaccard indices for flavonoid aglycones (red bars) and other compounds (grey bars). The frequency represents the ratio of records with a range of Jaccard indices to all records that had a Jaccard index > 0. ( c ) A receiver operating characteristic curve of the discrimination test by a binary classification in ( b ), yielding an area under the curve (AUC) of 0.91. Results obtained with ITFT data from NIST14 are shown in ( b ) and ( c ).
    Ltq Velos Orbitrap Etd Mass Spectrometer, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 92/100, based on 11 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    86
    Thermo Fisher ltq orbitrap classic mass spectrometer system
    Accuracies and discrimination power of the FlavonoidSearch system. ( a ) The accuracy of each search tool was evaluated using the area under the cumulative curve (AUCc) for a plot of cumulative ratio of queries ( Y -axis) to the efficiency of narrowing down to the correct answer ( X -axis). The cumulative curve will move closer to the upper left-hand corner of the figure when highly narrowed-down results are obtained for a high number of queries. Therefore, a high AUCc is indicative of high accuracy. Results are shown for data obtained in-house for flavonoid aglycones using ion trap (IT) and Fourier transform (FT) mass spectrometry (MS) of LTQ-FT and IT of <t>LTQ-Orbitrap</t> and spectra retrieved from MassBank and NIST14 searched with the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. ( b ) Differences in the frequency distributions of Jaccard indices for flavonoid aglycones (red bars) and other compounds (grey bars). The frequency represents the ratio of records with a range of Jaccard indices to all records that had a Jaccard index > 0. ( c ) A receiver operating characteristic curve of the discrimination test by a binary classification in ( b ), yielding an area under the curve (AUC) of 0.91. Results obtained with ITFT data from NIST14 are shown in ( b ) and ( c ).
    Ltq Orbitrap Classic Mass Spectrometer System, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 86/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    88
    Thermo Fisher usingan ltq velos orbitrap mass spectrometer
    Accuracies and discrimination power of the FlavonoidSearch system. ( a ) The accuracy of each search tool was evaluated using the area under the cumulative curve (AUCc) for a plot of cumulative ratio of queries ( Y -axis) to the efficiency of narrowing down to the correct answer ( X -axis). The cumulative curve will move closer to the upper left-hand corner of the figure when highly narrowed-down results are obtained for a high number of queries. Therefore, a high AUCc is indicative of high accuracy. Results are shown for data obtained in-house for flavonoid aglycones using ion trap (IT) and Fourier transform (FT) mass spectrometry (MS) of LTQ-FT and IT of <t>LTQ-Orbitrap</t> and spectra retrieved from MassBank and NIST14 searched with the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. ( b ) Differences in the frequency distributions of Jaccard indices for flavonoid aglycones (red bars) and other compounds (grey bars). The frequency represents the ratio of records with a range of Jaccard indices to all records that had a Jaccard index > 0. ( c ) A receiver operating characteristic curve of the discrimination test by a binary classification in ( b ), yielding an area under the curve (AUC) of 0.91. Results obtained with ITFT data from NIST14 are shown in ( b ) and ( c ).
    Usingan Ltq Velos Orbitrap Mass Spectrometer, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 88/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    84
    Thermo Fisher discovery model ltq orbitrap mass spectrometer
    Accuracies and discrimination power of the FlavonoidSearch system. ( a ) The accuracy of each search tool was evaluated using the area under the cumulative curve (AUCc) for a plot of cumulative ratio of queries ( Y -axis) to the efficiency of narrowing down to the correct answer ( X -axis). The cumulative curve will move closer to the upper left-hand corner of the figure when highly narrowed-down results are obtained for a high number of queries. Therefore, a high AUCc is indicative of high accuracy. Results are shown for data obtained in-house for flavonoid aglycones using ion trap (IT) and Fourier transform (FT) mass spectrometry (MS) of LTQ-FT and IT of <t>LTQ-Orbitrap</t> and spectra retrieved from MassBank and NIST14 searched with the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. ( b ) Differences in the frequency distributions of Jaccard indices for flavonoid aglycones (red bars) and other compounds (grey bars). The frequency represents the ratio of records with a range of Jaccard indices to all records that had a Jaccard index > 0. ( c ) A receiver operating characteristic curve of the discrimination test by a binary classification in ( b ), yielding an area under the curve (AUC) of 0.91. Results obtained with ITFT data from NIST14 are shown in ( b ) and ( c ).
    Discovery Model Ltq Orbitrap Mass Spectrometer, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 84/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher ltq orbitrap elite mass spectrometer system
    Accuracies and discrimination power of the FlavonoidSearch system. ( a ) The accuracy of each search tool was evaluated using the area under the cumulative curve (AUCc) for a plot of cumulative ratio of queries ( Y -axis) to the efficiency of narrowing down to the correct answer ( X -axis). The cumulative curve will move closer to the upper left-hand corner of the figure when highly narrowed-down results are obtained for a high number of queries. Therefore, a high AUCc is indicative of high accuracy. Results are shown for data obtained in-house for flavonoid aglycones using ion trap (IT) and Fourier transform (FT) mass spectrometry (MS) of LTQ-FT and IT of <t>LTQ-Orbitrap</t> and spectra retrieved from MassBank and NIST14 searched with the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. ( b ) Differences in the frequency distributions of Jaccard indices for flavonoid aglycones (red bars) and other compounds (grey bars). The frequency represents the ratio of records with a range of Jaccard indices to all records that had a Jaccard index > 0. ( c ) A receiver operating characteristic curve of the discrimination test by a binary classification in ( b ), yielding an area under the curve (AUC) of 0.91. Results obtained with ITFT data from NIST14 are shown in ( b ) and ( c ).
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    Image Search Results


    Workflow for MS imaging of Pseudonocardia on the ant propleural plate. a) Photograph and b) cartoon of Pseudonocardia on the ant exoskeleton. c) Grooves were cut into glass slides and double-sided tape was applied to the back of the slide. The ant thoraxes were removed and positioned into the groove of the slide with the propleural plate facing outward and even with the top of the slide. An additional thin strip of double-sided tape was applied below the propleural plate to stabilize and secure the thorax into place. d) Matrix was applied to the slide using an automatic sprayer. e) A laser was fired at the sample to ionize compounds of interest and introduce them into the mass spectrometer. f) An array of mass spectra was acquired using a MALDI-LTQ Orbitrap and g) compiled into MS images. Photo courtesy of Alex Wild.

    Journal: ACS chemical biology

    Article Title: Imaging with Mass Spectrometry of Bacteria on the Exoskeleton of Fungus-Growing Ants

    doi: 10.1021/acschembio.7b00038

    Figure Lengend Snippet: Workflow for MS imaging of Pseudonocardia on the ant propleural plate. a) Photograph and b) cartoon of Pseudonocardia on the ant exoskeleton. c) Grooves were cut into glass slides and double-sided tape was applied to the back of the slide. The ant thoraxes were removed and positioned into the groove of the slide with the propleural plate facing outward and even with the top of the slide. An additional thin strip of double-sided tape was applied below the propleural plate to stabilize and secure the thorax into place. d) Matrix was applied to the slide using an automatic sprayer. e) A laser was fired at the sample to ionize compounds of interest and introduce them into the mass spectrometer. f) An array of mass spectra was acquired using a MALDI-LTQ Orbitrap and g) compiled into MS images. Photo courtesy of Alex Wild.

    Article Snippet: A MALDI- LTQ Orbitrap mass spectrometer (Thermo Scientific) equipped with an N2 laser (spot diameter of 75 μ m) was used in positive ion mode for MSI.

    Techniques: Mass Spectrometry, Imaging, Stripping Membranes, Introduce

    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

    Full scan spectra of protein mixtures: MALDI-TOF spectrum of histone mixture, 10 mg/mL (a), HRAM MAI-Orbitrap spectrum of histone mixture, 1 mg/mL (b) and HRAM MAI-Orbitrap spectrum of rat brain protein extract.

    Journal: Analytical and bioanalytical chemistry

    Article Title: Coupling Matrix-Assisted Ionization with High Resolution Mass Spectrometry and Electron Transfer Dissociation to Characterize Intact Proteins and Post-Translational Modifications

    doi: 10.1007/s00216-017-0611-4

    Figure Lengend Snippet: Full scan spectra of protein mixtures: MALDI-TOF spectrum of histone mixture, 10 mg/mL (a), HRAM MAI-Orbitrap spectrum of histone mixture, 1 mg/mL (b) and HRAM MAI-Orbitrap spectrum of rat brain protein extract.

    Article Snippet: In the comparison study, the MALDI and MAI (MALDI) spectra were acquired on MALDI-LTQ-Orbitrap XL mass spectrometer (Thermo Scientific, Bremen, Germany), which is also a hybrid ion-trap-Orbitrap mass spectrometer but with MALDI source.

    Techniques:

    (A) Scheme of the methods used to analyze BMSCs Proteins identification was done on an orbitrap LTQ XL with a protein threshold of 99% (FDR 0.1%) and peptide threshold of 97% (FDR 0.1%) and contained at least 2 identified peptides as parameters ( Supplementary data 1 2 ). (B) Label free quantification of immune modulators, neurotrophic and growth factors and apoptotic molecules identified in conditioned media obtained from BMSCs, spinal cord lesion (SCI) or control (non injured) using Scaffold_4.0.6.1. Label-free quantification was done on top3 of the total ion current (TIC). (BMP 1: Bone morphogenic protein 1, Cdh13: T-Cadherin, CLEC11a: C-type lectin domain family 11 member A CTGF: connective tissue growth factor, Epha 3: Ephrin A isoform 3, Epdr1: Ependymin related protein 1, FAM3C: family with sequence similarity 3, member C Gal 1: galectin 1; GAP-43: Growth associated protein 43, Ltbp: Latent TGF-beta binding protein, IgFbp 7: Insulin growth factor binding protein 7, MIF: macrophage inhibiting factor, PDGF: Platelet derived growth factor, PGF: placenta growth factor, spondin 2, SPARC, TIMP-1: Tissue inhibitor metalloproteinase 1 2).

    Journal: Scientific Reports

    Article Title: Modulation properties of factors released by bone marrow stromal cells on activated microglia: an in vitro study

    doi: 10.1038/srep07514

    Figure Lengend Snippet: (A) Scheme of the methods used to analyze BMSCs Proteins identification was done on an orbitrap LTQ XL with a protein threshold of 99% (FDR 0.1%) and peptide threshold of 97% (FDR 0.1%) and contained at least 2 identified peptides as parameters ( Supplementary data 1 2 ). (B) Label free quantification of immune modulators, neurotrophic and growth factors and apoptotic molecules identified in conditioned media obtained from BMSCs, spinal cord lesion (SCI) or control (non injured) using Scaffold_4.0.6.1. Label-free quantification was done on top3 of the total ion current (TIC). (BMP 1: Bone morphogenic protein 1, Cdh13: T-Cadherin, CLEC11a: C-type lectin domain family 11 member A CTGF: connective tissue growth factor, Epha 3: Ephrin A isoform 3, Epdr1: Ependymin related protein 1, FAM3C: family with sequence similarity 3, member C Gal 1: galectin 1; GAP-43: Growth associated protein 43, Ltbp: Latent TGF-beta binding protein, IgFbp 7: Insulin growth factor binding protein 7, MIF: macrophage inhibiting factor, PDGF: Platelet derived growth factor, PGF: placenta growth factor, spondin 2, SPARC, TIMP-1: Tissue inhibitor metalloproteinase 1 2).

    Article Snippet: The chromatography system was coupled to a Thermo Scientific LTQ-Orbitrap XL mass spectrometer programmed to acquire in data-dependent mode.

    Techniques: Sequencing, Binding Assay, Derivative Assay

    Rationale and experimental design. A , Confirmation of Δ hik33 growth phenotype under photoautotrophic condition. The deletion of hik33 ), which also contains the photo of the cell culture. B , The WCLs of the WT and Δ hik33 strains of Synechocystis were separated into the membrane (Mem) and the soluble (Sol) fractions. Proteins extracted from either fraction and the WCL were subsequently separated by SDS-PAGE and visualized with Coomassie blue staining. C , Schematic representation of the workflow for the quantitative analysis of the Δ hik33 proteome. Total proteins were extracted from the WCLs of three biological replicates of the WT and Δ hik33 and digested with trypsin. The tryptic peptides were labeled with 6-plex TMT reagents in the order as indicated. The labeled peptides were mixed together with an equal molar ratio, and separated into 15 fractions with RP-HPLC. The peptides in each fraction were quantitatively analyzed by LC-MS/MS using a LTQ-Orbitrap-Elite mass spectrometer.

    Journal: Molecular & Cellular Proteomics : MCP

    Article Title: Translating Divergent Environmental Stresses into a Common Proteome Response through the Histidine Kinase 33 (Hik33) in a Model Cyanobacterium *

    doi: 10.1074/mcp.M116.068080

    Figure Lengend Snippet: Rationale and experimental design. A , Confirmation of Δ hik33 growth phenotype under photoautotrophic condition. The deletion of hik33 ), which also contains the photo of the cell culture. B , The WCLs of the WT and Δ hik33 strains of Synechocystis were separated into the membrane (Mem) and the soluble (Sol) fractions. Proteins extracted from either fraction and the WCL were subsequently separated by SDS-PAGE and visualized with Coomassie blue staining. C , Schematic representation of the workflow for the quantitative analysis of the Δ hik33 proteome. Total proteins were extracted from the WCLs of three biological replicates of the WT and Δ hik33 and digested with trypsin. The tryptic peptides were labeled with 6-plex TMT reagents in the order as indicated. The labeled peptides were mixed together with an equal molar ratio, and separated into 15 fractions with RP-HPLC. The peptides in each fraction were quantitatively analyzed by LC-MS/MS using a LTQ-Orbitrap-Elite mass spectrometer.

    Article Snippet: For MS analysis, the peptides were resuspended in 0.1% formic acid (FA) and analyzed by a LTQ Orbitrap Elite mass spectrometer (Thermo Scientific) coupled online to an Easy-nLC 1000 in the data-dependent mode.

    Techniques: Cell Culture, SDS Page, Staining, Labeling, High Performance Liquid Chromatography, Liquid Chromatography with Mass Spectroscopy, Mass Spectrometry

    Partial sequence (162–174) is present in unprocessed ABCA3 and missing in processed protein form. A : Intensity profiles of an m/z range corresponding to the monoisotopic peak of the doubly-charged ion at m/z 819.885 ( m/z window ±5 ppm) for 190 kDa and 170 kDa gel bands acquired in Orbitrap. B : Identification of the ABCA3 tryptic peptide comprising amino acid residues 162–174 of the precursor protein and containing methionine sulfoxide at position 164. MS/MS spectra after CID fragmentation measured in the LTQ ion trap are shown. Major b and y ions are labelled on the spectra and all fragment ions obtained are marked on the identified sequence. The ion at m/z 811 corresponds to the loss of water from the parent ion.

    Journal: PLoS ONE

    Article Title: Analysis of the Proteolytic Processing of ABCA3: Identification of Cleavage Site and Involved Proteases

    doi: 10.1371/journal.pone.0152594

    Figure Lengend Snippet: Partial sequence (162–174) is present in unprocessed ABCA3 and missing in processed protein form. A : Intensity profiles of an m/z range corresponding to the monoisotopic peak of the doubly-charged ion at m/z 819.885 ( m/z window ±5 ppm) for 190 kDa and 170 kDa gel bands acquired in Orbitrap. B : Identification of the ABCA3 tryptic peptide comprising amino acid residues 162–174 of the precursor protein and containing methionine sulfoxide at position 164. MS/MS spectra after CID fragmentation measured in the LTQ ion trap are shown. Major b and y ions are labelled on the spectra and all fragment ions obtained are marked on the identified sequence. The ion at m/z 811 corresponds to the loss of water from the parent ion.

    Article Snippet: Mass spectrometric analysis was performed on an LTQ-Orbitrap Discovery mass spectrometer (Thermo Fisher Scientific, Bremen, Germany) operated in a data dependent mode in which each full MS scan (m/z 200–1,450) acquired in Orbitrap with resolution of R = 30,000 (m/z 400) was followed by five MS/MS scans where the five most abundant molecular ions were dynamically selected and fragmented by collision-induced dissociation (CID) using a normalized collision energy of 35% in the LTQ ion trap.

    Techniques: Sequencing, Mass Spectrometry

    Flowchart of the label-free quantification approach. Protein digests of lysates of IECs were prepared from six mice per time point and analyzed in duplicate on the LTQ-Orbitrap, as described in the Experimental Procedures. Raw data sets were processed

    Journal: Molecular & Cellular Proteomics : MCP

    Article Title: Time-resolved Quantitative Proteome Analysis of In Vivo

    doi: 10.1074/mcp.M110.005231

    Figure Lengend Snippet: Flowchart of the label-free quantification approach. Protein digests of lysates of IECs were prepared from six mice per time point and analyzed in duplicate on the LTQ-Orbitrap, as described in the Experimental Procedures. Raw data sets were processed

    Article Snippet: Protein digests were analyzed in duplicate using a LC-ESI-MS/MS system consisting of a Rheos Allegro pump (Thermo Fisher Scientific, Waltham, MA), a PAL HTC autosampler (CTC Analytics, Zwingen, Switzerland), and an LTQ-XL Orbitrap mass spectrometer (Thermo Fisher Scientific, Waltham, MA) equipped with a nano-ESI source from the same supplier.

    Techniques: Mouse Assay

    SILAC workflow. A combined strategy involving RNAi against Cdc7, SDS-PAGE protein fractionation, LC–MS/MS data acquisition with a LTQ-Orbitrap (Thermo Fisher Scientific), and downstream bioinformatics for identification, quantification, and functional annotation was applied in this study.

    Journal: Journal of proteome research

    Article Title: Quantitative Proteomics Reveals a “Poised Quiescence” Cellular State after Triggering the DNA Replication Origin Activation Checkpoint

    doi: 10.1021/pr100678k

    Figure Lengend Snippet: SILAC workflow. A combined strategy involving RNAi against Cdc7, SDS-PAGE protein fractionation, LC–MS/MS data acquisition with a LTQ-Orbitrap (Thermo Fisher Scientific), and downstream bioinformatics for identification, quantification, and functional annotation was applied in this study.

    Article Snippet: LC–MS/MS was performed with an LTQ-Orbitrap Classic mass spectrometer (Thermo Fisher Scientific, U.K.).

    Techniques: SDS Page, Fractionation, Liquid Chromatography with Mass Spectroscopy, Mass Spectrometry, Functional Assay

    MS/MS spectra illustrating similar fragmentation profiles of Subunit 1 peptide GTGHFIGIYEVR from representative pertussis toxin (B) and pertussis toxoid (C). Nano Liquid Chromatography MS/MS were performed using the LTQ-Orbitrap on tryptic peptides obtained from pertussis toxin B and pertussis toxoid C. The MS/MS data was searched against the NCBI database and the peptide spectrum was analyzed [comparing relative peak intensity (0–100%) versus mass/charge (0 to 1500)] using the Scaffold software. The red and blue lines represent y- and b-ion distribution peaks, respectively.

    Journal: Journal of Biomedicine and Biotechnology

    Article Title: Mass Spectrometric Analysis of Multiple Pertussis Toxins and Toxoids

    doi: 10.1155/2010/942365

    Figure Lengend Snippet: MS/MS spectra illustrating similar fragmentation profiles of Subunit 1 peptide GTGHFIGIYEVR from representative pertussis toxin (B) and pertussis toxoid (C). Nano Liquid Chromatography MS/MS were performed using the LTQ-Orbitrap on tryptic peptides obtained from pertussis toxin B and pertussis toxoid C. The MS/MS data was searched against the NCBI database and the peptide spectrum was analyzed [comparing relative peak intensity (0–100%) versus mass/charge (0 to 1500)] using the Scaffold software. The red and blue lines represent y- and b-ion distribution peaks, respectively.

    Article Snippet: Peptides were nano-electrosprayed into an LTQ Orbitrap tandem mass spectrometer (Thermo Scientific, San Jose, CA).

    Techniques: Mass Spectrometry, Liquid Chromatography, Software

    Merged network map showing endothelin-1-induced changes in the fetal cardiomyocyte proteome Primary fetal cardiomyocytes were treated with control or endothelin-1 (10 nM) for 24 hours. Protein expression analysis was performed in fetal cardiomyocytes by TMT-LC-MS/MS analysis with a LTQ-Orbitrap-Velos instrument. IPA pathway analysis revealed five separate sub-networks for endothelin-1-modulated proteins. Panel A depicts a merged network of all detected proteins with their subcellular distribution. Panel B is the key.

    Journal: Current topics in medicinal chemistry

    Article Title: Proteomic Analysis of Endothelin-1 Targets in the Regulation of Cardiomyocyte Proliferation

    doi: 10.2174/1568026617666161116142417

    Figure Lengend Snippet: Merged network map showing endothelin-1-induced changes in the fetal cardiomyocyte proteome Primary fetal cardiomyocytes were treated with control or endothelin-1 (10 nM) for 24 hours. Protein expression analysis was performed in fetal cardiomyocytes by TMT-LC-MS/MS analysis with a LTQ-Orbitrap-Velos instrument. IPA pathway analysis revealed five separate sub-networks for endothelin-1-modulated proteins. Panel A depicts a merged network of all detected proteins with their subcellular distribution. Panel B is the key.

    Article Snippet: Quantitation of SCX fractionated TMT-labeled peptides was performed on the Thermo LTQ-Orbitrap Pro mass spectrometer.

    Techniques: Expressing, Liquid Chromatography with Mass Spectroscopy, Mass Spectrometry, Indirect Immunoperoxidase Assay

    (−) ESI-Q-TOF-MS/MS and LTQ-Orbitrap-MS n ( n = 3–4) spectra of PF 1 in group A and the fragmentation pathways proposed for PF 1 . Q-TOF-MS ( A ), Q-TOF-MS 2 ( B ), LTQ-Orbitrap-MS 3 of the ions at m / z 233.0852 from m / z 367.1205 ( C ), LTQ-Orbitrap-MS 3 of the ions at m / z 309.0417 from m / z 367.1205 ( D ), LTQ-Orbitrap-MS 4 of the ions at m / z 265.0599 from m / z 309.0417 ( E ), and the proposed fragmentation pathways for PF 1 ( F ). RDA: retro Diels–Alder.

    Journal: Molecules

    Article Title: Characterization and Identification of Prenylated Flavonoids from Artocarpus heterophyllus Lam. Roots by Quadrupole Time-Of-Flight and Linear Trap Quadrupole Orbitrap Mass Spectrometry

    doi: 10.3390/molecules24244591

    Figure Lengend Snippet: (−) ESI-Q-TOF-MS/MS and LTQ-Orbitrap-MS n ( n = 3–4) spectra of PF 1 in group A and the fragmentation pathways proposed for PF 1 . Q-TOF-MS ( A ), Q-TOF-MS 2 ( B ), LTQ-Orbitrap-MS 3 of the ions at m / z 233.0852 from m / z 367.1205 ( C ), LTQ-Orbitrap-MS 3 of the ions at m / z 309.0417 from m / z 367.1205 ( D ), LTQ-Orbitrap-MS 4 of the ions at m / z 265.0599 from m / z 309.0417 ( E ), and the proposed fragmentation pathways for PF 1 ( F ). RDA: retro Diels–Alder.

    Article Snippet: The multistage mass spectrometry data were obtained using a Thermo Fisher LTQ-Orbitrap Electrostatic Mass Spectrometer (Thermo Fisher Scientific, Bremen, Germany).

    Techniques: Mass Spectrometry

    (−)ESI-Q-TOF-MS/MS and LTQ-Orbitrap-MS n ( n = 3–4) spectra of PF 10 in group B and the fragmentation pathways proposed for PF 10 . Q-TOF-MS ( A ), Q-TOF-MS 2 ( B ), LTQ-Orbitrap-MS 3 of the ions at m / z 361.0731 from m / z 417.1358 ( C ), LTQ-Orbitrap-MS 4 of the ions at m / z 343.0523 from m / z 361.073 ( D ), and the proposed fragmentation pathways for PF 10 ( E ). RDA: retro Diels–Alder.

    Journal: Molecules

    Article Title: Characterization and Identification of Prenylated Flavonoids from Artocarpus heterophyllus Lam. Roots by Quadrupole Time-Of-Flight and Linear Trap Quadrupole Orbitrap Mass Spectrometry

    doi: 10.3390/molecules24244591

    Figure Lengend Snippet: (−)ESI-Q-TOF-MS/MS and LTQ-Orbitrap-MS n ( n = 3–4) spectra of PF 10 in group B and the fragmentation pathways proposed for PF 10 . Q-TOF-MS ( A ), Q-TOF-MS 2 ( B ), LTQ-Orbitrap-MS 3 of the ions at m / z 361.0731 from m / z 417.1358 ( C ), LTQ-Orbitrap-MS 4 of the ions at m / z 343.0523 from m / z 361.073 ( D ), and the proposed fragmentation pathways for PF 10 ( E ). RDA: retro Diels–Alder.

    Article Snippet: The multistage mass spectrometry data were obtained using a Thermo Fisher LTQ-Orbitrap Electrostatic Mass Spectrometer (Thermo Fisher Scientific, Bremen, Germany).

    Techniques: Mass Spectrometry

    (−)ESI-Q-TOF-MS/MS and LTQ-Orbitrap-MS n ( n = 3–4) spectra of PF 12 in group B and the fragmentation pathways proposed for PF 12 . Q-TOF-MS ( A ), Q-TOF-MS 2 ( B ), LTQ-Orbitrap-MS 3 of the ions at m / z 445.1296 from m / z 501.1939 ( C ), LTQ-Orbitrap-MS 4 of the ions at m / z 427.0927 from at m / z 445.1296 ( D ), LTQ-Orbitrap-MS 3 of the ions at m / z 485.1631 from m / z 501.1939 ( E ), LTQ-Orbitrap-MS 4 of the ions at m / z 429.1201 from m / z 485.1631 ( F ), and the proposed fragmentation pathways for PF 12 ( G ).

    Journal: Molecules

    Article Title: Characterization and Identification of Prenylated Flavonoids from Artocarpus heterophyllus Lam. Roots by Quadrupole Time-Of-Flight and Linear Trap Quadrupole Orbitrap Mass Spectrometry

    doi: 10.3390/molecules24244591

    Figure Lengend Snippet: (−)ESI-Q-TOF-MS/MS and LTQ-Orbitrap-MS n ( n = 3–4) spectra of PF 12 in group B and the fragmentation pathways proposed for PF 12 . Q-TOF-MS ( A ), Q-TOF-MS 2 ( B ), LTQ-Orbitrap-MS 3 of the ions at m / z 445.1296 from m / z 501.1939 ( C ), LTQ-Orbitrap-MS 4 of the ions at m / z 427.0927 from at m / z 445.1296 ( D ), LTQ-Orbitrap-MS 3 of the ions at m / z 485.1631 from m / z 501.1939 ( E ), LTQ-Orbitrap-MS 4 of the ions at m / z 429.1201 from m / z 485.1631 ( F ), and the proposed fragmentation pathways for PF 12 ( G ).

    Article Snippet: The multistage mass spectrometry data were obtained using a Thermo Fisher LTQ-Orbitrap Electrostatic Mass Spectrometer (Thermo Fisher Scientific, Bremen, Germany).

    Techniques: Mass Spectrometry

    (−) ESI-Q-TOF-MS/MS and LTQ-Orbitrap-MS n ( n = 3–4) spectra of PF 4 in group B and the fragmentation pathways proposed for PF 4 . Q-TOF-MS ( A ), Q-TOF-MS 2 ( B ), LTQ-Orbitrap-MS 3 of the ions at m / z 297.0395 from m / z 421.1644 ( C ), LTQ-Orbitrap-MS 4 of the ions at m / z 253.0483 from m / z 297.0395 ( D ), and the proposed fragmentation pathways for PF 4 ( E ).

    Journal: Molecules

    Article Title: Characterization and Identification of Prenylated Flavonoids from Artocarpus heterophyllus Lam. Roots by Quadrupole Time-Of-Flight and Linear Trap Quadrupole Orbitrap Mass Spectrometry

    doi: 10.3390/molecules24244591

    Figure Lengend Snippet: (−) ESI-Q-TOF-MS/MS and LTQ-Orbitrap-MS n ( n = 3–4) spectra of PF 4 in group B and the fragmentation pathways proposed for PF 4 . Q-TOF-MS ( A ), Q-TOF-MS 2 ( B ), LTQ-Orbitrap-MS 3 of the ions at m / z 297.0395 from m / z 421.1644 ( C ), LTQ-Orbitrap-MS 4 of the ions at m / z 253.0483 from m / z 297.0395 ( D ), and the proposed fragmentation pathways for PF 4 ( E ).

    Article Snippet: The multistage mass spectrometry data were obtained using a Thermo Fisher LTQ-Orbitrap Electrostatic Mass Spectrometer (Thermo Fisher Scientific, Bremen, Germany).

    Techniques: Mass Spectrometry

    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

    Coomassie stained SDS-PAGE Gel of tissue extracts showing protein loading and gel slices used to evaluate target peptides on Thermo LTQ Orbitrap MS/MS. The predicted location of the 35 candidate biomarkers, based on molecular weights, are illustrated

    Journal: Clinical chemistry

    Article Title: Candidate Serum Biomarkers for Prostate Adenocarcinoma Identified by mRNA Differences in Prostate Tissue and Verified with Protein Measurements in Tissue and Blood

    doi: 10.1373/clinchem.2011.171637

    Figure Lengend Snippet: Coomassie stained SDS-PAGE Gel of tissue extracts showing protein loading and gel slices used to evaluate target peptides on Thermo LTQ Orbitrap MS/MS. The predicted location of the 35 candidate biomarkers, based on molecular weights, are illustrated

    Article Snippet: MS/MS using nano-flow liquid chromatography electrospray on a ThermoFinnigan LTQ Orbitrap Hybrid Mass Spectrometer (ThermoElectron Bremen, Germany) was used to look for the targeted peptides for each gel band.

    Techniques: Staining, SDS Page, Mass Spectrometry

    Profiling cell surface sialoglycoproteins via the bio-orthogonal chemical reporter strategy combined with quantitative shotgun proteomics. The strategy consists of six steps: 1) metabolic labeling of cells with Ac 4 ManNAz; 2) chemoselective conjugation of azide-labeled glycans with a biotin-linked phosphine; 3) cell lysis; 4) affinity enrichment of the biotin-tagged proteins on streptavidin-conjugated beads; 5) on-beads trypsin digestion of affinity-captured sialoglycoproteins; 6) identification using high-performance liquid chromatography tandem mass spectrometry (LC-MS/MS) analysis using a nano-LC-LTQ Orbitrap mass spectrometer platform and sequence database searching, and quantitative differential analysis of the sialoglycoproteins using label-free analysis with DIFFTAL (DIFferential Fourier-Transform AnaLysis) software algorithm.

    Journal: PLoS ONE

    Article Title: Identification of Novel Tumor-Associated Cell Surface Sialoglycoproteins in Human Glioblastoma Tumors Using Quantitative Proteomics

    doi: 10.1371/journal.pone.0110316

    Figure Lengend Snippet: Profiling cell surface sialoglycoproteins via the bio-orthogonal chemical reporter strategy combined with quantitative shotgun proteomics. The strategy consists of six steps: 1) metabolic labeling of cells with Ac 4 ManNAz; 2) chemoselective conjugation of azide-labeled glycans with a biotin-linked phosphine; 3) cell lysis; 4) affinity enrichment of the biotin-tagged proteins on streptavidin-conjugated beads; 5) on-beads trypsin digestion of affinity-captured sialoglycoproteins; 6) identification using high-performance liquid chromatography tandem mass spectrometry (LC-MS/MS) analysis using a nano-LC-LTQ Orbitrap mass spectrometer platform and sequence database searching, and quantitative differential analysis of the sialoglycoproteins using label-free analysis with DIFFTAL (DIFferential Fourier-Transform AnaLysis) software algorithm.

    Article Snippet: NanoLC-MS/MS analysis Peptide digests were analyzed on a on a Ultimate/Famos/Switchos suite of instruments (Dionex) connected to a hybrid LTQ Orbitrap mass spectrometer (Thermo Fisher Scientific) with the instruments setup and parameters described in .

    Techniques: Labeling, Conjugation Assay, Lysis, High Performance Liquid Chromatography, Mass Spectrometry, Liquid Chromatography with Mass Spectroscopy, Sequencing, Software

    Schematic outline of proteomic analysis methodology. Sample processing, followed by strong cation exchange (SCX) and reverse-phase chromatography coupled online to an LTQ-Orbitrap mass spectrometer, and subsequent data analysis is outlined. CM, conditioned media; LC-MS/MS, liquid chromatography tandem mass spectrometry.

    Journal: Molecular & Cellular Proteomics : MCP

    Article Title:

    doi: 10.1074/mcp.M111.008599

    Figure Lengend Snippet: Schematic outline of proteomic analysis methodology. Sample processing, followed by strong cation exchange (SCX) and reverse-phase chromatography coupled online to an LTQ-Orbitrap mass spectrometer, and subsequent data analysis is outlined. CM, conditioned media; LC-MS/MS, liquid chromatography tandem mass spectrometry.

    Article Snippet: The trap and analytical columns were operated on the EASY-nLC system (Proxeon Biosystems, Odense, Denmark), and this liquid chromatography setup was coupled online to an LTQ-Orbitrap XL hybrid mass spectrometer (Thermo Fisher Scientific, San Jose, California) using a nano-electrospray ionization (ESI) source (Proxeon Biosystems, Odense, Denmark).

    Techniques: Reversed-phase Chromatography, Mass Spectrometry, Liquid Chromatography with Mass Spectroscopy, Liquid Chromatography

    Accuracies and discrimination power of the FlavonoidSearch system. ( a ) The accuracy of each search tool was evaluated using the area under the cumulative curve (AUCc) for a plot of cumulative ratio of queries ( Y -axis) to the efficiency of narrowing down to the correct answer ( X -axis). The cumulative curve will move closer to the upper left-hand corner of the figure when highly narrowed-down results are obtained for a high number of queries. Therefore, a high AUCc is indicative of high accuracy. Results are shown for data obtained in-house for flavonoid aglycones using ion trap (IT) and Fourier transform (FT) mass spectrometry (MS) of LTQ-FT and IT of LTQ-Orbitrap and spectra retrieved from MassBank and NIST14 searched with the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. ( b ) Differences in the frequency distributions of Jaccard indices for flavonoid aglycones (red bars) and other compounds (grey bars). The frequency represents the ratio of records with a range of Jaccard indices to all records that had a Jaccard index > 0. ( c ) A receiver operating characteristic curve of the discrimination test by a binary classification in ( b ), yielding an area under the curve (AUC) of 0.91. Results obtained with ITFT data from NIST14 are shown in ( b ) and ( c ).

    Journal: Scientific Reports

    Article Title: FlavonoidSearch: A system for comprehensive flavonoid annotation by mass spectrometry

    doi: 10.1038/s41598-017-01390-3

    Figure Lengend Snippet: Accuracies and discrimination power of the FlavonoidSearch system. ( a ) The accuracy of each search tool was evaluated using the area under the cumulative curve (AUCc) for a plot of cumulative ratio of queries ( Y -axis) to the efficiency of narrowing down to the correct answer ( X -axis). The cumulative curve will move closer to the upper left-hand corner of the figure when highly narrowed-down results are obtained for a high number of queries. Therefore, a high AUCc is indicative of high accuracy. Results are shown for data obtained in-house for flavonoid aglycones using ion trap (IT) and Fourier transform (FT) mass spectrometry (MS) of LTQ-FT and IT of LTQ-Orbitrap and spectra retrieved from MassBank and NIST14 searched with the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. ( b ) Differences in the frequency distributions of Jaccard indices for flavonoid aglycones (red bars) and other compounds (grey bars). The frequency represents the ratio of records with a range of Jaccard indices to all records that had a Jaccard index > 0. ( c ) A receiver operating characteristic curve of the discrimination test by a binary classification in ( b ), yielding an area under the curve (AUC) of 0.91. Results obtained with ITFT data from NIST14 are shown in ( b ) and ( c ).

    Article Snippet: Chemicals Sources for the standard compounds, which were used for construction of the probable mass fragment database (FsDatabase) and evaluating the FsTool after analysis by a linear ion trap combined with an Orbitrap mass spectrometer (LTQ-Orbitrap, Thermo Fisher Scientific, Waltham, MA), are given in Supplementary Tables and , respectively.

    Techniques: Mass Spectrometry