hybrid quadrupole orbitrap mass spectrometer  (Thermo Fisher)


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    Q Exactive Hybrid Quadrupole Orbitrap Mass Spectrometer
    Description:
    Identify quantify and confirm more compounds rapidly and with confidence using the Thermo Scientific Q Exactive Hybrid Quadrupole Orbitrap Mass Spectrometer This benchtop LC MS MS system combines quadruple precursor ion selection with high resolution accurate mass HRAM Orbitrap detection to deliver exceptional performance and versatility The Q Exactive Mass Spectrometer is equally useful for untargeted or targeted screening and a broad range of qualitative and quantitative applications in drug discovery proteomics environmental and food safety clinical research and forensic toxicology
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    Structured Review

    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).
    Identify quantify and confirm more compounds rapidly and with confidence using the Thermo Scientific Q Exactive Hybrid Quadrupole Orbitrap Mass Spectrometer This benchtop LC MS MS system combines quadruple precursor ion selection with high resolution accurate mass HRAM Orbitrap detection to deliver exceptional performance and versatility The Q Exactive Mass Spectrometer is equally useful for untargeted or targeted screening and a broad range of qualitative and quantitative applications in drug discovery proteomics environmental and food safety clinical research and forensic toxicology
    https://www.bioz.com/result/hybrid quadrupole orbitrap mass spectrometer/product/Thermo Fisher
    Average 99 stars, based on 119 article reviews
    Price from $9.99 to $1999.99
    hybrid quadrupole orbitrap mass spectrometer - by Bioz Stars, 2020-07
    99/100 stars

    Images

    1) Product Images from "Noncovalently Associated Peptides Observed during Liquid Chromatography-Mass Spectrometry and Their Effect on Cross-Link Analyses"

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

    Journal: Analytical Chemistry

    doi: 10.1021/acs.analchem.8b04037

    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).
    Figure Legend 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).

    Techniques Used: Mass Spectrometry, MANN-WHITNEY

    2) Product Images from "Noncovalently Associated Peptides Observed during Liquid Chromatography-Mass Spectrometry and Their Effect on Cross-Link Analyses"

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

    Journal: Analytical Chemistry

    doi: 10.1021/acs.analchem.8b04037

    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).
    Figure Legend 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).

    Techniques Used: Mass Spectrometry, MANN-WHITNEY

    3) Product Images from "Methylated Cytokinins from the Phytopathogen Rhodococcus fascians Mimic Plant Hormone Activity"

    Article Title: Methylated Cytokinins from the Phytopathogen Rhodococcus fascians Mimic Plant Hormone Activity

    Journal: Plant Physiology

    doi: 10.1104/pp.15.00787

    s produced by R. fascians mt s and fas4 isolated from filtrates of E. coli cultures expressing R. fascians fas4mt2 and fas4mt1mt2 , 1 -d 6 , 1 -d 6 (bottom) were analyzed with a hybrid quadrupole-Orbitrap mass spectrometer in the positive ion mode. Predicted fragmented structures are shown above the peaks.
    Figure Legend Snippet: s produced by R. fascians mt s and fas4 isolated from filtrates of E. coli cultures expressing R. fascians fas4mt2 and fas4mt1mt2 , 1 -d 6 , 1 -d 6 (bottom) were analyzed with a hybrid quadrupole-Orbitrap mass spectrometer in the positive ion mode. Predicted fragmented structures are shown above the peaks.

    Techniques Used: Produced, Isolation, Expressing, Mass Spectrometry

    4) Product Images from "Endogenous ocular lipids as potential modulators of intraocular pressure, et al. Endogenous ocular lipids as potential modulators of intraocular pressure"

    Article Title: Endogenous ocular lipids as potential modulators of intraocular pressure, et al. Endogenous ocular lipids as potential modulators of intraocular pressure

    Journal: Journal of Cellular and Molecular Medicine

    doi: 10.1111/jcmm.14975

    Representative chromatogram and mass spectra of AH lipids. A, Chromatogram from Acela HPLC that was coupled with high‐resolution Q‐Exactive Orbitrap mass spectrometer. Five samples each for glaucoma and control or normal (as indicated) are depicted by different colours. B, Representative mass spectrogram. Product ion spectra of negative ion phospholipids from AH samples
    Figure Legend Snippet: Representative chromatogram and mass spectra of AH lipids. A, Chromatogram from Acela HPLC that was coupled with high‐resolution Q‐Exactive Orbitrap mass spectrometer. Five samples each for glaucoma and control or normal (as indicated) are depicted by different colours. B, Representative mass spectrogram. Product ion spectra of negative ion phospholipids from AH samples

    Techniques Used: High Performance Liquid Chromatography, Mass Spectrometry

    Related Articles

    High Performance Liquid Chromatography:

    Article Title: Cmr1/WDR76 defines a nuclear genotoxic stress body linking genome integrity and protein quality control
    Article Snippet: .. Peptide fractions were analysed on a quadrupole Orbitrap mass spectrometer (Q-Exactive, Thermo Scientific) equipped with a nanoflow HPLC system (Thermo Scientific) . .. Raw data files were analysed using MaxQuant software (version 1.2.2.9) .

    Mass Spectrometry:

    Article Title: Evaluation of the Nutritional Quality of Chinese Kale (Brassica alboglabra Bailey) Using UHPLC-Quadrupole-Orbitrap MS/MS-Based Metabolomics
    Article Snippet: .. Mass spectrometry analysis was performed on a Q Exactive Quadrupole-Orbitrap mass spectrometer (Thermo Fisher Scientific, Bremen, Germany), which was equipped with a heated electrospray ionization source II (HESI-II) operating in negative ionization mode. .. The optimised ionization source and MS parameters were set as follows: spray voltage at 3.0 kV, sheath gas at 35 arbitrary units, auxiliary gas at 10 arbitrary units, capillary temperature at 350 °C, heater temperature at 400 °C, and S-lens radio frequency level at 50.

    Article Title: Mass spectrometry captures off-target drug binding and provides mechanistic insights into the human metalloprotease ZMPSTE24
    Article Snippet: .. QExactive High-resolution mass spectrometry was performed using a modified QExactive hybrid quadrupole-Orbitrap mass spectrometer (Thermo Fisher Scientific, Bremen, Germany) optimised for transmission of high m/z ions (Heck Nat Methods) and analysis of membrane proteins . .. Modifications included a lower frequency RF applied to the quadrupole, higher pressures in the HCD cell, and modified electronics for extended frequency range detection on the Orbitrap.

    Article Title: Noncovalently Associated Peptides Observed during Liquid Chromatography-Mass Spectrometry and Their Effect on Cross-Link Analyses
    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). .. In both cases, peptides were loaded directly onto a spray analytical column (75 μm inner diameter, 8 μm opening, 250 mm length; New Objectives, Woburn, MA) packed with C18 material (ReproSil-Pur C18-AQ 3 μm; Dr. Maisch GmbH, Ammerbuch-Entringen, Germany) using an air pressure pump (Proxeon Biosystems).

    Article Title: Noncovalently Associated Peptides Observed during Liquid Chromatography-Mass Spectrometry and Their Effect on Cross-Link Analyses
    Article Snippet: .. We observed surprising differences when comparing the identified cross-links using data acquired on two different mass spectrometers: a hybrid linear ion trap-Orbitrap mass spectrometer (LTQ Orbitrap Velos, Thermo Fisher Scientific) and a hybrid quadrupole-Orbitrap mass spectrometer (Q Exactive, Thermo Fisher Scientific). ..

    Article Title: Engineered FGF19 eliminates bile acid toxicity and lipotoxicity leading to resolution of steatohepatitis and fibrosis in mice
    Article Snippet: .. The samples were reconstituted in isopropyl alcohol/methanol (1:1 volume per volume) for liquid chromatography–mass spectrometry (LC‐MS) analysis on an Ultimate 3000 ultrahigh‐performance LC system coupled to a Q Exactive hybrid quadrupole‐Orbitrap MS (Thermo Fisher Scientific). ..

    Article Title: Quantification of Cardiovascular Disease Biomarkers in Human Platelets by Targeted Mass Spectrometry
    Article Snippet: .. The nanoHPLC was coupled to a Q Exactive Hybrid Quadrupole-Orbitrap Plus mass spectrometer (Thermo Scientific) and eluting peptides were ionized directly via a silica emitter (FS360-20-10-D-20, New Objective, Ringoes, NJ, USA) of the nanoESI source. .. Peptides of interest were analyzed using a scheduled parallel reaction monitoring method, which was performed with a resolution of 17,500, a maximum injection time of 50 ms, and an automatic gain control (AGC) value of 3 × 106 .

    Article Title: Methylated Cytokinins from the Phytopathogen Rhodococcus fascians Mimic Plant Hormone Activity
    Article Snippet: .. Purified s from E. coli liquid culture filtrates were analyzed by Q-Exactive (Thermo Scientific), a hybrid quadrupole-Orbitrap mass spectrometer in the positive ion mode, and fragmented structures were predicted with Mass Frontier (Thermo Scientific). .. Spectra were recorded on an AVANCE ll-700 spectrometer (Bruker) equipped with an inverse triple resonance cryogenic probe with a z -axis gradient operating at 700.154 MHz for 1 H (176.061 for 13 C).

    Article Title: Cmr1/WDR76 defines a nuclear genotoxic stress body linking genome integrity and protein quality control
    Article Snippet: .. Peptide fractions were analysed on a quadrupole Orbitrap mass spectrometer (Q-Exactive, Thermo Scientific) equipped with a nanoflow HPLC system (Thermo Scientific) . .. Raw data files were analysed using MaxQuant software (version 1.2.2.9) .

    Chromatography:

    Article Title: Engineered FGF19 eliminates bile acid toxicity and lipotoxicity leading to resolution of steatohepatitis and fibrosis in mice
    Article Snippet: .. The samples were reconstituted in isopropyl alcohol/methanol (1:1 volume per volume) for liquid chromatography–mass spectrometry (LC‐MS) analysis on an Ultimate 3000 ultrahigh‐performance LC system coupled to a Q Exactive hybrid quadrupole‐Orbitrap MS (Thermo Fisher Scientific). ..

    Purification:

    Article Title: Methylated Cytokinins from the Phytopathogen Rhodococcus fascians Mimic Plant Hormone Activity
    Article Snippet: .. Purified s from E. coli liquid culture filtrates were analyzed by Q-Exactive (Thermo Scientific), a hybrid quadrupole-Orbitrap mass spectrometer in the positive ion mode, and fragmented structures were predicted with Mass Frontier (Thermo Scientific). .. Spectra were recorded on an AVANCE ll-700 spectrometer (Bruker) equipped with an inverse triple resonance cryogenic probe with a z -axis gradient operating at 700.154 MHz for 1 H (176.061 for 13 C).

    Liquid Chromatography with Mass Spectroscopy:

    Article Title: Engineered FGF19 eliminates bile acid toxicity and lipotoxicity leading to resolution of steatohepatitis and fibrosis in mice
    Article Snippet: .. The samples were reconstituted in isopropyl alcohol/methanol (1:1 volume per volume) for liquid chromatography–mass spectrometry (LC‐MS) analysis on an Ultimate 3000 ultrahigh‐performance LC system coupled to a Q Exactive hybrid quadrupole‐Orbitrap MS (Thermo Fisher Scientific). ..

    Transmission Assay:

    Article Title: Mass spectrometry captures off-target drug binding and provides mechanistic insights into the human metalloprotease ZMPSTE24
    Article Snippet: .. QExactive High-resolution mass spectrometry was performed using a modified QExactive hybrid quadrupole-Orbitrap mass spectrometer (Thermo Fisher Scientific, Bremen, Germany) optimised for transmission of high m/z ions (Heck Nat Methods) and analysis of membrane proteins . .. Modifications included a lower frequency RF applied to the quadrupole, higher pressures in the HCD cell, and modified electronics for extended frequency range detection on the Orbitrap.

    Modification:

    Article Title: Mass spectrometry captures off-target drug binding and provides mechanistic insights into the human metalloprotease ZMPSTE24
    Article Snippet: .. QExactive High-resolution mass spectrometry was performed using a modified QExactive hybrid quadrupole-Orbitrap mass spectrometer (Thermo Fisher Scientific, Bremen, Germany) optimised for transmission of high m/z ions (Heck Nat Methods) and analysis of membrane proteins . .. Modifications included a lower frequency RF applied to the quadrupole, higher pressures in the HCD cell, and modified electronics for extended frequency range detection on the Orbitrap.

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  • 99
    Thermo Fisher q exactive hybrid quadrupole orbitrap mass spectrometer
    Principles of discovery and targeted proteomics approaches. Major steps of discovery and targeted mass spectrometry analyses are schematized. Discovery proteomics (top panel) characterizes the global composition of a protein sample. With the <t>quadrupole-orbitrap</t> technology, peptide ions within a small window of mass-to-charge (m/z) ratio are isolated in the first quadrupole (Q1) and then fragmented in a collision cell; all ion fragments are finally monitored in the orbitrap analyzer. The processing of resulting MS/MS spectra allows identifying the proteins initially present in the samples (not shown). Targeted proteomics (bottom panel) precisely quantifies a predefined set of proteins. The SRM methodology first selects peptide ions representative of the proteins of interest in the first quadrupole (Q1); they are fragmented in the second quadrupole (Q2); finally, predefined representative ion fragments (F1, F2 and F3) are recorded in the last quadrupole (Q3). The reconstitution of each peptide elution profile, named SRM trace, allows for the integration and quantification of its abundance. The PRM methodology is similar to the SRM pipeline but the last quantification step is not restricted to a predefined set of fragment ions and can consider all of them, recorded in the Orbitrap analyzer
    Q Exactive Hybrid Quadrupole Orbitrap Mass Spectrometer, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 560 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/q exactive hybrid quadrupole orbitrap mass spectrometer/product/Thermo Fisher
    Average 99 stars, based on 560 article reviews
    Price from $9.99 to $1999.99
    q exactive hybrid quadrupole orbitrap mass spectrometer - by Bioz Stars, 2020-07
    99/100 stars
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    99
    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 170 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 170 article reviews
    Price from $9.99 to $1999.99
    q exactive plus hybrid quadrupole orbitrap mass spectrometer - by Bioz Stars, 2020-07
    99/100 stars
      Buy from Supplier

    Image Search Results


    Principles of discovery and targeted proteomics approaches. Major steps of discovery and targeted mass spectrometry analyses are schematized. Discovery proteomics (top panel) characterizes the global composition of a protein sample. With the quadrupole-orbitrap technology, peptide ions within a small window of mass-to-charge (m/z) ratio are isolated in the first quadrupole (Q1) and then fragmented in a collision cell; all ion fragments are finally monitored in the orbitrap analyzer. The processing of resulting MS/MS spectra allows identifying the proteins initially present in the samples (not shown). Targeted proteomics (bottom panel) precisely quantifies a predefined set of proteins. The SRM methodology first selects peptide ions representative of the proteins of interest in the first quadrupole (Q1); they are fragmented in the second quadrupole (Q2); finally, predefined representative ion fragments (F1, F2 and F3) are recorded in the last quadrupole (Q3). The reconstitution of each peptide elution profile, named SRM trace, allows for the integration and quantification of its abundance. The PRM methodology is similar to the SRM pipeline but the last quantification step is not restricted to a predefined set of fragment ions and can consider all of them, recorded in the Orbitrap analyzer

    Journal: Epigenetics & Chromatin

    Article Title: Systematic quantitative analysis of H2A and H2B variants by targeted proteomics

    doi: 10.1186/s13072-017-0172-y

    Figure Lengend Snippet: Principles of discovery and targeted proteomics approaches. Major steps of discovery and targeted mass spectrometry analyses are schematized. Discovery proteomics (top panel) characterizes the global composition of a protein sample. With the quadrupole-orbitrap technology, peptide ions within a small window of mass-to-charge (m/z) ratio are isolated in the first quadrupole (Q1) and then fragmented in a collision cell; all ion fragments are finally monitored in the orbitrap analyzer. The processing of resulting MS/MS spectra allows identifying the proteins initially present in the samples (not shown). Targeted proteomics (bottom panel) precisely quantifies a predefined set of proteins. The SRM methodology first selects peptide ions representative of the proteins of interest in the first quadrupole (Q1); they are fragmented in the second quadrupole (Q2); finally, predefined representative ion fragments (F1, F2 and F3) are recorded in the last quadrupole (Q3). The reconstitution of each peptide elution profile, named SRM trace, allows for the integration and quantification of its abundance. The PRM methodology is similar to the SRM pipeline but the last quantification step is not restricted to a predefined set of fragment ions and can consider all of them, recorded in the Orbitrap analyzer

    Article Snippet: PRM analyses of histones on a Q-Exactive Instrument PRM analyses were performed using a Q-Exactive hybrid quadrupole-orbitrap mass spectrometer (Thermo Fisher Scientific).

    Techniques: Mass Spectrometry, Isolation

    Signature peptides used to quantify H2A and H2B variants by targeted proteomics. a Strategy used to select the signature peptides and validate their compatibility with targeted proteomic analysis. The sequences of 22 H2A and 3 H2B variants were obtained from our recently published list of mouse histone variants (MS_histone_DB, [ 8 ]). In silico digestion of these sequences produced a theoretical list of peptides, which were ranked according to their computed ESPP score, predictive of their compatibility with MS analysis [ 41 ]. Fifty-five peptides were selected and further analyzed to monitor the potential presence of post-translational modifications, which could interfere with their analysis by targeted proteomics. This analysis excluded seven of them (see Table 1 ). Then, heavy standard peptides, 13 C, 15 N-labeled, were synthesized and analyzed on different MS instruments (LTQ-Orbitrap Velos, QTRAP 5500) to acquire full MS/MS spectra and create spectral libraries. They were used to select up to five more intense SRM transitions for each peptide. b Selected signature peptides presented on their corresponding histone variants. They are presented as black bars and numbered according to Table 1 . Histone fold domains, also called globular domains, are presented as a rectangle for each histone, surrounded by N- and C-terminal tails. H2A (orange), H2B (red), H4 (green)

    Journal: Epigenetics & Chromatin

    Article Title: Systematic quantitative analysis of H2A and H2B variants by targeted proteomics

    doi: 10.1186/s13072-017-0172-y

    Figure Lengend Snippet: Signature peptides used to quantify H2A and H2B variants by targeted proteomics. a Strategy used to select the signature peptides and validate their compatibility with targeted proteomic analysis. The sequences of 22 H2A and 3 H2B variants were obtained from our recently published list of mouse histone variants (MS_histone_DB, [ 8 ]). In silico digestion of these sequences produced a theoretical list of peptides, which were ranked according to their computed ESPP score, predictive of their compatibility with MS analysis [ 41 ]. Fifty-five peptides were selected and further analyzed to monitor the potential presence of post-translational modifications, which could interfere with their analysis by targeted proteomics. This analysis excluded seven of them (see Table 1 ). Then, heavy standard peptides, 13 C, 15 N-labeled, were synthesized and analyzed on different MS instruments (LTQ-Orbitrap Velos, QTRAP 5500) to acquire full MS/MS spectra and create spectral libraries. They were used to select up to five more intense SRM transitions for each peptide. b Selected signature peptides presented on their corresponding histone variants. They are presented as black bars and numbered according to Table 1 . Histone fold domains, also called globular domains, are presented as a rectangle for each histone, surrounded by N- and C-terminal tails. H2A (orange), H2B (red), H4 (green)

    Article Snippet: PRM analyses of histones on a Q-Exactive Instrument PRM analyses were performed using a Q-Exactive hybrid quadrupole-orbitrap mass spectrometer (Thermo Fisher Scientific).

    Techniques: Mass Spectrometry, In Silico, Produced, Labeling, Synthesized

    The Q Exactive Hybrid Quadrupole-Orbitrap-MS spectrum of compound S in positive mode.

    Journal: Molecules

    Article Title: A Simple, Rapid, and Practical Method for Distinguishing Lonicerae Japonicae Flos from Lonicerae Flos

    doi: 10.3390/molecules24193455

    Figure Lengend Snippet: The Q Exactive Hybrid Quadrupole-Orbitrap-MS spectrum of compound S in positive mode.

    Article Snippet: An UltiMate 3000 UPLC system coupled to a Q Exactive Hybrid Quadrupole-Orbitrap Mass Spectrometer (Thermo Scientific, MA, USA) was used.

    Techniques: Mass Spectrometry

    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