quadrupole orbitrapã¢â„⢠mass spectrometer  (Thermo Fisher)


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    Thermo Fisher quadrupole orbitrapã¢â„⢠mass spectrometer
    Quadrupole Orbitrapã¢â„⢠Mass Spectrometer, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 84/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/quadrupole orbitrapã¢â„⢠mass spectrometer/product/Thermo Fisher
    Average 84 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    quadrupole orbitrapã¢â„⢠mass spectrometer - by Bioz Stars, 2020-05
    84/100 stars

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    Article Title: Proteomic Changes in Mouse Spleen after Radiation-Induced Injury and its Modulation by Gamma-Tocotrienol
    Article Snippet: .. The LC was interfaced to a Quadrupole-Orbitrap™ Mass Spectrometer (Q-Exactive™; Thermo Fisher Scientific) via nano-electrospray ionization. ..

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    Thermo Fisher q exactive plus hybrid quadrupole orbitrap mass spectrometer
    A, initial identification of 79 Br- and 81 Br-containing BrdU-cross-linked A3G peptides aa 181–213 that matched predicted MS1 values. Tryptic peptides of A3G/BrdU cross-linked sample were analyzed on Q Exactive Plus Hybrid <t>Quadrupole-Orbitrap</t> mass spectrometer and searched for BrdU modifications, including 79 Br and 81 Br isotope difference with Compass software (Compass IsotopePattern, Bruker Daltonics). Panel a, 79 Br- and 81 Br-containing peptide peaks with m / z values in a range of 1111–1113, corresponding to the A3G peptide YYILLHIMLGEILRHSMDPPTFTFNFNNEPWVR (aa 181–213, m / z charge +4, one missed trypsin cleavage site) were identified ( panel b ) in a fraction eluted at 18.96 min followed by ( panel c ) Compass IsotopePattern analysis and ( panel d ) MS/MS fragmentation of this peptide that matched a predicted fragmentation pattern. It should be noted that due to the presence in the samples of other stable isotopes besides 79 Br and 81 Br, including 13 C (mostly) 2 H, and 15 N, the MS1 pattern of each shown A3G peptide analyzed by Xcalibur and Compass is represented by several peaks (typically 2–4, depending on peptide change, with decreasing relative intensity). As evident from Compass IsotopePattern analysis ( panel c ), we observed eight peptide peaks in an area of 1111–1113 m / z that at the charge 4+ and peak distance ∼0.5 m / z (not counting common 13 C-double peaks) may constitute two identical peptides that differ only by ∼2.0 m / z that corresponds to bromine-isotope difference of 79 Br and 81 Br in BrdU cross-linker. B, initial identification of 79 Br- and 81 Br-containing BrdU-cross-linked A3G peptides aa 314–326 that matched predicted MS1 values. Tryptic peptides of the A3G/BrdU cross-linked sample were analyzed on Q Exactive Plus Hybrid Quadrupole-Orbitrap mass spectrometer and searched for BrdU modifications including 79 Br and 81 Br isotope difference with Compass software (Compass IsotopePattern, Bruker Daltonics). Panel a, 79 Br- and 81 Br-containing peptide peaks with m / z values in a range of 663–665, corresponding to the A3G peptide IYDDQGRCQEGLR (aa 314–326, m / z charge +3, one missed trypsin cleavage site) were identified ( panel b ) in a fraction eluted at 12.26 min followed by ( panel c ) Compass IsotopePattern analysis and ( panel d ) MS/MS fragmentation of this peptide that matched a predicted fragmentation pattern. It should be noted that due to the presence in the samples of other stable isotopes besides 79 Br and 81 Br, including 13 C (mostly), 2 H, and 15 N, the MS1 pattern of each shown A3G peptide analyzed by Xcalibur and Compass is represented by several peaks (typically 2–4, depending on peptide change, with decreasing relative intensity). As evident from Compass IsotopePattern analysis ( panel c ), we observed six peptide peaks in an area of 663–665 m / z that at the charge 3+ and peak distance ∼0.67 m / z (not counting common 13 C-double peaks) may constitute two identical peptides that differ only by ∼2.0 m / z that correspond to BrdU-isotope difference of 79 Br and 81 Br in BrdU cross-linker.
    Q Exactive Plus Hybrid Quadrupole Orbitrap Mass Spectrometer, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 22 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/q exactive plus hybrid quadrupole orbitrap mass spectrometer/product/Thermo Fisher
    Average 99 stars, based on 22 article reviews
    Price from $9.99 to $1999.99
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    99
    Thermo Fisher hybrid quadrupole orbitrap mass spectrometer
    Quality control after cross-link identification at a 5% link FDR. (a) Results from cross-linking HSA with sulfo-SDA acquired on an Q Exactive and an LTQ <t>Orbitrap</t> Velos mass spectrometer. The line at 25 Å indicates the distance cutoff for links classified as long distance. The inlet shows the fraction of long-distance links (LDL) in each data set. (b) Score comparison between within-distance linkzs and LDL. LDL showed no significant (ns) deviation from the within-distance links (two-sided Mann–Whitney-U-test at α = 0.05).
    Hybrid Quadrupole Orbitrap Mass Spectrometer, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/hybrid quadrupole orbitrap mass spectrometer/product/Thermo Fisher
    Average 99 stars, based on 5 article reviews
    Price from $9.99 to $1999.99
    hybrid quadrupole orbitrap mass spectrometer - by Bioz Stars, 2020-05
    99/100 stars
      Buy from Supplier

    85
    Thermo Fisher linear quadrupole ion trap ltq orbitrap mass spectrometer
    Workflow to identify lipid raft-associated proteins. Stable isotopic labeling of amino acids in cell culture (SILAC) labeled SH-SY5Y cells left untreated or exposed to 400 nM okadaic acid for 50 min before mixed in a ratio 1:1 in 0.7% Triton X-100/MES buffer. After centrifugation in a sucrose gradient, 10 fractions of 0.5 mL were collected. The lipid raft fractions were identified by Western blotting using flotillin as a lipid raft marker. Fractions containing flotillin were pooled prior to removal of lipids by chloroform/methanol extraction, followed by acetone precipitation. Proteins were separated by SDS-PAGE. Proteins were in-gel digested with trypsin, and peptides were purified either with (1) C18 or (2) IMAC/TiO 2 and analyzed on <t>LTQ-Orbitrap.</t> Proteins were identified with Mascot (ver. 2.2) and quantified using MaxQuant (ver. 1.13).
    Linear Quadrupole Ion Trap Ltq Orbitrap Mass Spectrometer, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 85/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/linear quadrupole ion trap ltq orbitrap mass spectrometer/product/Thermo Fisher
    Average 85 stars, based on 1 article reviews
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    linear quadrupole ion trap ltq orbitrap mass spectrometer - by Bioz Stars, 2020-05
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    A, initial identification of 79 Br- and 81 Br-containing BrdU-cross-linked A3G peptides aa 181–213 that matched predicted MS1 values. Tryptic peptides of A3G/BrdU cross-linked sample were analyzed on Q Exactive Plus Hybrid Quadrupole-Orbitrap mass spectrometer and searched for BrdU modifications, including 79 Br and 81 Br isotope difference with Compass software (Compass IsotopePattern, Bruker Daltonics). Panel a, 79 Br- and 81 Br-containing peptide peaks with m / z values in a range of 1111–1113, corresponding to the A3G peptide YYILLHIMLGEILRHSMDPPTFTFNFNNEPWVR (aa 181–213, m / z charge +4, one missed trypsin cleavage site) were identified ( panel b ) in a fraction eluted at 18.96 min followed by ( panel c ) Compass IsotopePattern analysis and ( panel d ) MS/MS fragmentation of this peptide that matched a predicted fragmentation pattern. It should be noted that due to the presence in the samples of other stable isotopes besides 79 Br and 81 Br, including 13 C (mostly) 2 H, and 15 N, the MS1 pattern of each shown A3G peptide analyzed by Xcalibur and Compass is represented by several peaks (typically 2–4, depending on peptide change, with decreasing relative intensity). As evident from Compass IsotopePattern analysis ( panel c ), we observed eight peptide peaks in an area of 1111–1113 m / z that at the charge 4+ and peak distance ∼0.5 m / z (not counting common 13 C-double peaks) may constitute two identical peptides that differ only by ∼2.0 m / z that corresponds to bromine-isotope difference of 79 Br and 81 Br in BrdU cross-linker. B, initial identification of 79 Br- and 81 Br-containing BrdU-cross-linked A3G peptides aa 314–326 that matched predicted MS1 values. Tryptic peptides of the A3G/BrdU cross-linked sample were analyzed on Q Exactive Plus Hybrid Quadrupole-Orbitrap mass spectrometer and searched for BrdU modifications including 79 Br and 81 Br isotope difference with Compass software (Compass IsotopePattern, Bruker Daltonics). Panel a, 79 Br- and 81 Br-containing peptide peaks with m / z values in a range of 663–665, corresponding to the A3G peptide IYDDQGRCQEGLR (aa 314–326, m / z charge +3, one missed trypsin cleavage site) were identified ( panel b ) in a fraction eluted at 12.26 min followed by ( panel c ) Compass IsotopePattern analysis and ( panel d ) MS/MS fragmentation of this peptide that matched a predicted fragmentation pattern. It should be noted that due to the presence in the samples of other stable isotopes besides 79 Br and 81 Br, including 13 C (mostly), 2 H, and 15 N, the MS1 pattern of each shown A3G peptide analyzed by Xcalibur and Compass is represented by several peaks (typically 2–4, depending on peptide change, with decreasing relative intensity). As evident from Compass IsotopePattern analysis ( panel c ), we observed six peptide peaks in an area of 663–665 m / z that at the charge 3+ and peak distance ∼0.67 m / z (not counting common 13 C-double peaks) may constitute two identical peptides that differ only by ∼2.0 m / z that correspond to BrdU-isotope difference of 79 Br and 81 Br in BrdU cross-linker.

    Journal: The Journal of Biological Chemistry

    Article Title: DNA mutagenic activity and capacity for HIV-1 restriction of the cytidine deaminase APOBEC3G depend on whether DNA or RNA binds to tyrosine 315

    doi: 10.1074/jbc.M116.767889

    Figure Lengend Snippet: A, initial identification of 79 Br- and 81 Br-containing BrdU-cross-linked A3G peptides aa 181–213 that matched predicted MS1 values. Tryptic peptides of A3G/BrdU cross-linked sample were analyzed on Q Exactive Plus Hybrid Quadrupole-Orbitrap mass spectrometer and searched for BrdU modifications, including 79 Br and 81 Br isotope difference with Compass software (Compass IsotopePattern, Bruker Daltonics). Panel a, 79 Br- and 81 Br-containing peptide peaks with m / z values in a range of 1111–1113, corresponding to the A3G peptide YYILLHIMLGEILRHSMDPPTFTFNFNNEPWVR (aa 181–213, m / z charge +4, one missed trypsin cleavage site) were identified ( panel b ) in a fraction eluted at 18.96 min followed by ( panel c ) Compass IsotopePattern analysis and ( panel d ) MS/MS fragmentation of this peptide that matched a predicted fragmentation pattern. It should be noted that due to the presence in the samples of other stable isotopes besides 79 Br and 81 Br, including 13 C (mostly) 2 H, and 15 N, the MS1 pattern of each shown A3G peptide analyzed by Xcalibur and Compass is represented by several peaks (typically 2–4, depending on peptide change, with decreasing relative intensity). As evident from Compass IsotopePattern analysis ( panel c ), we observed eight peptide peaks in an area of 1111–1113 m / z that at the charge 4+ and peak distance ∼0.5 m / z (not counting common 13 C-double peaks) may constitute two identical peptides that differ only by ∼2.0 m / z that corresponds to bromine-isotope difference of 79 Br and 81 Br in BrdU cross-linker. B, initial identification of 79 Br- and 81 Br-containing BrdU-cross-linked A3G peptides aa 314–326 that matched predicted MS1 values. Tryptic peptides of the A3G/BrdU cross-linked sample were analyzed on Q Exactive Plus Hybrid Quadrupole-Orbitrap mass spectrometer and searched for BrdU modifications including 79 Br and 81 Br isotope difference with Compass software (Compass IsotopePattern, Bruker Daltonics). Panel a, 79 Br- and 81 Br-containing peptide peaks with m / z values in a range of 663–665, corresponding to the A3G peptide IYDDQGRCQEGLR (aa 314–326, m / z charge +3, one missed trypsin cleavage site) were identified ( panel b ) in a fraction eluted at 12.26 min followed by ( panel c ) Compass IsotopePattern analysis and ( panel d ) MS/MS fragmentation of this peptide that matched a predicted fragmentation pattern. It should be noted that due to the presence in the samples of other stable isotopes besides 79 Br and 81 Br, including 13 C (mostly), 2 H, and 15 N, the MS1 pattern of each shown A3G peptide analyzed by Xcalibur and Compass is represented by several peaks (typically 2–4, depending on peptide change, with decreasing relative intensity). As evident from Compass IsotopePattern analysis ( panel c ), we observed six peptide peaks in an area of 663–665 m / z that at the charge 3+ and peak distance ∼0.67 m / z (not counting common 13 C-double peaks) may constitute two identical peptides that differ only by ∼2.0 m / z that correspond to BrdU-isotope difference of 79 Br and 81 Br in BrdU cross-linker.

    Article Snippet: MS analysis of tryptic peptides was performed using either an LTQ Orbitrap XL or Q Exactive Plus Hybrid Quadrupole-Orbitrap mass spectrometer (Thermo Fisher Scientific).

    Techniques: Mass Spectrometry, Software

    Identification of A3G tyrosines 181 ( top panel ) and 315 ( bottom panel ) as cross-linked residues to 25-nt BrdU-modified ssDNA. UV light-induced cross-linking was performed with assembled A3G-ssDNA complex, and the cross-linked product was separated onto SDS-polyacrylamide gel and in-gel digested with trypsin. A3G tryptic peptides were analyzed on Q Exactive Plus Hybrid Quadrupole-Orbitrap mass spectrometer and searched with Mascot for amino acid residue BrdU modifications. Shown are A3G peptide MS/MS fragmentation spectra: aa 181–194 with BrdU-modified Tyr-181 ( A ) and aa 314–320 with BrdU-modified Tyr-315 ( B ). Peptide sequences are shown on the right . Most abundant b and y ion values and their m / z charge are marked on the spectra (no charge is shown for +1 fragment values). The positions of the BrdU-cross-linked fragments on the spectra are indicated with arrows . The complete list of identified b and y (1+ (monoisotopic) and 2+ mass/charge values). Abs. Int., absorbance intensity.

    Journal: The Journal of Biological Chemistry

    Article Title: DNA mutagenic activity and capacity for HIV-1 restriction of the cytidine deaminase APOBEC3G depend on whether DNA or RNA binds to tyrosine 315

    doi: 10.1074/jbc.M116.767889

    Figure Lengend Snippet: Identification of A3G tyrosines 181 ( top panel ) and 315 ( bottom panel ) as cross-linked residues to 25-nt BrdU-modified ssDNA. UV light-induced cross-linking was performed with assembled A3G-ssDNA complex, and the cross-linked product was separated onto SDS-polyacrylamide gel and in-gel digested with trypsin. A3G tryptic peptides were analyzed on Q Exactive Plus Hybrid Quadrupole-Orbitrap mass spectrometer and searched with Mascot for amino acid residue BrdU modifications. Shown are A3G peptide MS/MS fragmentation spectra: aa 181–194 with BrdU-modified Tyr-181 ( A ) and aa 314–320 with BrdU-modified Tyr-315 ( B ). Peptide sequences are shown on the right . Most abundant b and y ion values and their m / z charge are marked on the spectra (no charge is shown for +1 fragment values). The positions of the BrdU-cross-linked fragments on the spectra are indicated with arrows . The complete list of identified b and y (1+ (monoisotopic) and 2+ mass/charge values). Abs. Int., absorbance intensity.

    Article Snippet: MS analysis of tryptic peptides was performed using either an LTQ Orbitrap XL or Q Exactive Plus Hybrid Quadrupole-Orbitrap mass spectrometer (Thermo Fisher Scientific).

    Techniques: Modification, Mass Spectrometry

    Quality control after cross-link identification at a 5% link FDR. (a) Results from cross-linking HSA with sulfo-SDA acquired on an Q Exactive and an LTQ Orbitrap Velos mass spectrometer. The line at 25 Å indicates the distance cutoff for links classified as long distance. The inlet shows the fraction of long-distance links (LDL) in each data set. (b) Score comparison between within-distance linkzs and LDL. LDL showed no significant (ns) deviation from the within-distance links (two-sided Mann–Whitney-U-test at α = 0.05).

    Journal: Analytical Chemistry

    Article Title: Noncovalently Associated Peptides Observed during Liquid Chromatography-Mass Spectrometry and Their Effect on Cross-Link Analyses

    doi: 10.1021/acs.analchem.8b04037

    Figure Lengend Snippet: Quality control after cross-link identification at a 5% link FDR. (a) Results from cross-linking HSA with sulfo-SDA acquired on an Q Exactive and an LTQ Orbitrap Velos mass spectrometer. The line at 25 Å indicates the distance cutoff for links classified as long distance. The inlet shows the fraction of long-distance links (LDL) in each data set. (b) Score comparison between within-distance linkzs and LDL. LDL showed no significant (ns) deviation from the within-distance links (two-sided Mann–Whitney-U-test at α = 0.05).

    Article Snippet: Peptides were analyzed on either a hybrid linear ion trap/Orbitrap mass spectrometer (LTQ Orbitrap Velos, Thermo Fisher Scientific) or a hybrid quadrupole/Orbitrap mass spectrometer (Q Exactive, Thermo Fisher Scientific).

    Techniques: Mass Spectrometry, MANN-WHITNEY

    Workflow to identify lipid raft-associated proteins. Stable isotopic labeling of amino acids in cell culture (SILAC) labeled SH-SY5Y cells left untreated or exposed to 400 nM okadaic acid for 50 min before mixed in a ratio 1:1 in 0.7% Triton X-100/MES buffer. After centrifugation in a sucrose gradient, 10 fractions of 0.5 mL were collected. The lipid raft fractions were identified by Western blotting using flotillin as a lipid raft marker. Fractions containing flotillin were pooled prior to removal of lipids by chloroform/methanol extraction, followed by acetone precipitation. Proteins were separated by SDS-PAGE. Proteins were in-gel digested with trypsin, and peptides were purified either with (1) C18 or (2) IMAC/TiO 2 and analyzed on LTQ-Orbitrap. Proteins were identified with Mascot (ver. 2.2) and quantified using MaxQuant (ver. 1.13).

    Journal: Marine Drugs

    Article Title: Identification of Dynamic Changes in Proteins Associated with the Cellular Cytoskeleton after Exposure to Okadaic Acid

    doi: 10.3390/md11061763

    Figure Lengend Snippet: Workflow to identify lipid raft-associated proteins. Stable isotopic labeling of amino acids in cell culture (SILAC) labeled SH-SY5Y cells left untreated or exposed to 400 nM okadaic acid for 50 min before mixed in a ratio 1:1 in 0.7% Triton X-100/MES buffer. After centrifugation in a sucrose gradient, 10 fractions of 0.5 mL were collected. The lipid raft fractions were identified by Western blotting using flotillin as a lipid raft marker. Fractions containing flotillin were pooled prior to removal of lipids by chloroform/methanol extraction, followed by acetone precipitation. Proteins were separated by SDS-PAGE. Proteins were in-gel digested with trypsin, and peptides were purified either with (1) C18 or (2) IMAC/TiO 2 and analyzed on LTQ-Orbitrap. Proteins were identified with Mascot (ver. 2.2) and quantified using MaxQuant (ver. 1.13).

    Article Snippet: For general lipid raft proteome mapping, the peptides were separated on a Dionex Ultimate 3000 nano-LC system (Sunnyvale, CA, USA) coupled to a linear quadrupole ion trap (LTQ-Orbitrap) mass spectrometer (Thermo Scientific).

    Techniques: Isotopic Labeling, Cell Culture, Labeling, Centrifugation, Western Blot, Marker, SDS Page, Purification