q exactive plus hybrid quadrupole orbitrap mass spectrometer  (Thermo Fisher)


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    Q Exactive Focus Hybrid Quadrupole Orbitrap Mass Spectrometer
    Description:
    The sensitivity selectivity flexibility and ease of use provided by hybrid quadrupole Orbitrap mass spectrometers set the standard for screening quantitation identification and confirmation of targeted and untargeted compounds The Thermo Scientific Q Exactive Focus hybrid quadrupole Orbitrap MS makes this power accessible to environmental food safety clinical research forensic toxicology and pharmaceutical labs challenged by growing sample volumes and constrained by strict budgets The Q Exactive Focus system simplifies method development saving time and decreasing costs while reliably delivering unsurpassed results
    Catalog Number:
    iqlaaegaapfalgmbhe
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    Applications:
    Industrial & Applied Science|Industrial Mass Spectrometry
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    Instruments and Equipment
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    Structured Review

    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.
    The sensitivity selectivity flexibility and ease of use provided by hybrid quadrupole Orbitrap mass spectrometers set the standard for screening quantitation identification and confirmation of targeted and untargeted compounds The Thermo Scientific Q Exactive Focus hybrid quadrupole Orbitrap MS makes this power accessible to environmental food safety clinical research forensic toxicology and pharmaceutical labs challenged by growing sample volumes and constrained by strict budgets The Q Exactive Focus system simplifies method development saving time and decreasing costs while reliably delivering unsurpassed results
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    Images

    1) Product Images from "DNA mutagenic activity and capacity for HIV-1 restriction of the cytidine deaminase APOBEC3G depend on whether DNA or RNA binds to tyrosine 315"

    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

    Journal: The Journal of Biological Chemistry

    doi: 10.1074/jbc.M116.767889

    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.
    Figure Legend 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.

    Techniques Used: 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.
    Figure Legend 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.

    Techniques Used: Modification, Mass Spectrometry

    2) Product Images from "Impacts of Penicillin Binding Protein 2 Inactivation on β-Lactamase Expression and Muropeptide Profile in Stenotrophomonas maltophilia"

    Article Title: Impacts of Penicillin Binding Protein 2 Inactivation on β-Lactamase Expression and Muropeptide Profile in Stenotrophomonas maltophilia

    Journal: mSystems

    doi: 10.1128/mSystems.00077-17

    Quantitative LC-MS analysis of periplasmic muropeptides from wild-type KJ and mrdA mutant strain KJΔ mrdA . The LC-MS total ion chromatograms (TICs) of periplasmic muropeptide analysis of wild-type KJ and the mrdA mutant strain, KJΔ mrdA were determined by reverse-phase ultraperformance liquid chromatography coupled to a high-resolution hybrid Orbitrap mass spectrometer. A full list of periplasmic muropeptides is provided in Table S3 . An equal amount of purified N -acetylglucosaminyl- N -acetylmuramyl- l -alanyl- d -glutamic acid in its reduced form (GlcNAc-MurNAc dipeptide; M2), which was only observed in total muropeptides ( Fig. 5 ), was spiked in both wild-type KJ and the KJΔ mrdA strain as an internal standard to quantify the periplasmic muropeptides.
    Figure Legend Snippet: Quantitative LC-MS analysis of periplasmic muropeptides from wild-type KJ and mrdA mutant strain KJΔ mrdA . The LC-MS total ion chromatograms (TICs) of periplasmic muropeptide analysis of wild-type KJ and the mrdA mutant strain, KJΔ mrdA were determined by reverse-phase ultraperformance liquid chromatography coupled to a high-resolution hybrid Orbitrap mass spectrometer. A full list of periplasmic muropeptides is provided in Table S3 . An equal amount of purified N -acetylglucosaminyl- N -acetylmuramyl- l -alanyl- d -glutamic acid in its reduced form (GlcNAc-MurNAc dipeptide; M2), which was only observed in total muropeptides ( Fig. 5 ), was spiked in both wild-type KJ and the KJΔ mrdA strain as an internal standard to quantify the periplasmic muropeptides.

    Techniques Used: Liquid Chromatography with Mass Spectroscopy, Mutagenesis, Liquid Chromatography, Mass Spectrometry, Purification

    LC-MS analysis results for total muropeptides from wild-type KJ and the mrdA mutant, KJΔ mrdA . (A) The LC-MS total ion chromatogram (TIC) of wild-type KJ and mutant KJΔ mrdA , determined via reversed-phase ultraperformance liquid chromatography coupled to a high-resolution hybrid Orbitrap mass spectrometer. (Inset) Enlargement of the region where M4N is eluted. (The extracted ion chromatogram [EIC] of M4 and M4N are shown in Fig. S3 in the supplemental material.) (B) The ratios of the top 10 muropeptide compositions in wild-type KJ and KJΔ mrdA mutant strain. (The full list of identified muropeptides is provided in Table S2 ). *, P
    Figure Legend Snippet: LC-MS analysis results for total muropeptides from wild-type KJ and the mrdA mutant, KJΔ mrdA . (A) The LC-MS total ion chromatogram (TIC) of wild-type KJ and mutant KJΔ mrdA , determined via reversed-phase ultraperformance liquid chromatography coupled to a high-resolution hybrid Orbitrap mass spectrometer. (Inset) Enlargement of the region where M4N is eluted. (The extracted ion chromatogram [EIC] of M4 and M4N are shown in Fig. S3 in the supplemental material.) (B) The ratios of the top 10 muropeptide compositions in wild-type KJ and KJΔ mrdA mutant strain. (The full list of identified muropeptides is provided in Table S2 ). *, P

    Techniques Used: Liquid Chromatography with Mass Spectroscopy, Mutagenesis, Liquid Chromatography, Mass Spectrometry

    3) Product Images from "Improved discrimination of asymmetric and symmetric arginine dimethylation by optimization of the normalized collision energy in LC-MS proteomics"

    Article Title: Improved discrimination of asymmetric and symmetric arginine dimethylation by optimization of the normalized collision energy in LC-MS proteomics

    Journal: bioRxiv

    doi: 10.1101/2020.02.14.949255

    Higher NCE improves generation of NL ions in synthetic ADMA and SDMA peptides. A) Mechanism of neutral loss of dimethylamine and monomethylamine from ADMA and SDMA, respectively. B) Total number of DMA PSMs from a dataset of synthetic ADMA and SDMA peptides. The proportion of PSMs displaying either an ADMA or SDMA neutral loss in the HCD cell of an Orbitrap Fusion Lumos are shown for each NCE. C) Total number of unique peptides with assignable ADMA or SDMA neutral loss for each NCE. D) Violin plot of the number of NL ions present in DMA PSMs for each NCE. Each point represents a PSM with a corresponding number of NL ions observed in that spectra.
    Figure Legend Snippet: Higher NCE improves generation of NL ions in synthetic ADMA and SDMA peptides. A) Mechanism of neutral loss of dimethylamine and monomethylamine from ADMA and SDMA, respectively. B) Total number of DMA PSMs from a dataset of synthetic ADMA and SDMA peptides. The proportion of PSMs displaying either an ADMA or SDMA neutral loss in the HCD cell of an Orbitrap Fusion Lumos are shown for each NCE. C) Total number of unique peptides with assignable ADMA or SDMA neutral loss for each NCE. D) Violin plot of the number of NL ions present in DMA PSMs for each NCE. Each point represents a PSM with a corresponding number of NL ions observed in that spectra.

    Techniques Used:

    4) Product Images from "Hybrid Quadrupole-Orbitrap Mass Spectrometry for Quantitative Measurement of Quorum Sensing Inhibition"

    Article Title: Hybrid Quadrupole-Orbitrap Mass Spectrometry for Quantitative Measurement of Quorum Sensing Inhibition

    Journal: Journal of microbiological methods

    doi: 10.1016/j.mimet.2016.05.024

    Flow diagram for the newly developed mass spectrometry-based assay for monitoring quorum sensing inhibition. 1. Bacteria are cultured in the presence of inhibitors or controls in triplicate wells in a 96 well plate format. 2. OD 600 is monitored for the bacterial cultures at 1 hr intervals to check for growth inhibition or growth delays. 3. Bacterial cultures are filtered (using a 96-well plate compatible filter) and the filtrate (spent broth) is analyzed directly using an ultraperformance liquid chromatograph coupled to a Q-exactive Orbitrap mass spectrometer (UPLC-MS). 4. Plots of AIP peak area versus time are used to quantitatively measure quorum sensing inhibition.
    Figure Legend Snippet: Flow diagram for the newly developed mass spectrometry-based assay for monitoring quorum sensing inhibition. 1. Bacteria are cultured in the presence of inhibitors or controls in triplicate wells in a 96 well plate format. 2. OD 600 is monitored for the bacterial cultures at 1 hr intervals to check for growth inhibition or growth delays. 3. Bacterial cultures are filtered (using a 96-well plate compatible filter) and the filtrate (spent broth) is analyzed directly using an ultraperformance liquid chromatograph coupled to a Q-exactive Orbitrap mass spectrometer (UPLC-MS). 4. Plots of AIP peak area versus time are used to quantitatively measure quorum sensing inhibition.

    Techniques Used: Flow Cytometry, Mass Spectrometry, Inhibition, Cell Culture

    5) Product Images from "Impacts of Penicillin Binding Protein 2 Inactivation on β-Lactamase Expression and Muropeptide Profile in Stenotrophomonas maltophilia"

    Article Title: Impacts of Penicillin Binding Protein 2 Inactivation on β-Lactamase Expression and Muropeptide Profile in Stenotrophomonas maltophilia

    Journal: mSystems

    doi: 10.1128/mSystems.00077-17

    Quantitative LC-MS analysis of periplasmic muropeptides from wild-type KJ and mrdA mutant strain KJΔ mrdA . The LC-MS total ion chromatograms (TICs) of periplasmic muropeptide analysis of wild-type KJ and the mrdA mutant strain, KJΔ mrdA were determined by reverse-phase ultraperformance liquid chromatography coupled to a high-resolution hybrid Orbitrap mass spectrometer. A full list of periplasmic muropeptides is provided in Table S3 . An equal amount of purified N -acetylglucosaminyl- N -acetylmuramyl- l -alanyl- d -glutamic acid in its reduced form (GlcNAc-MurNAc dipeptide; M2), which was only observed in total muropeptides ( Fig. 5 ), was spiked in both wild-type KJ and the KJΔ mrdA strain as an internal standard to quantify the periplasmic muropeptides.
    Figure Legend Snippet: Quantitative LC-MS analysis of periplasmic muropeptides from wild-type KJ and mrdA mutant strain KJΔ mrdA . The LC-MS total ion chromatograms (TICs) of periplasmic muropeptide analysis of wild-type KJ and the mrdA mutant strain, KJΔ mrdA were determined by reverse-phase ultraperformance liquid chromatography coupled to a high-resolution hybrid Orbitrap mass spectrometer. A full list of periplasmic muropeptides is provided in Table S3 . An equal amount of purified N -acetylglucosaminyl- N -acetylmuramyl- l -alanyl- d -glutamic acid in its reduced form (GlcNAc-MurNAc dipeptide; M2), which was only observed in total muropeptides ( Fig. 5 ), was spiked in both wild-type KJ and the KJΔ mrdA strain as an internal standard to quantify the periplasmic muropeptides.

    Techniques Used: Liquid Chromatography with Mass Spectroscopy, Mutagenesis, Liquid Chromatography, Mass Spectrometry, Purification

    LC-MS analysis results for total muropeptides from wild-type KJ and the mrdA mutant, KJΔ mrdA . (A) The LC-MS total ion chromatogram (TIC) of wild-type KJ and mutant KJΔ mrdA , determined via reversed-phase ultraperformance liquid chromatography coupled to a high-resolution hybrid Orbitrap mass spectrometer. (Inset) Enlargement of the region where M4N is eluted. (The extracted ion chromatogram [EIC] of M4 and M4N are shown in Fig. S3 in the supplemental material.) (B) The ratios of the top 10 muropeptide compositions in wild-type KJ and KJΔ mrdA mutant strain. (The full list of identified muropeptides is provided in Table S2 ). *, P
    Figure Legend Snippet: LC-MS analysis results for total muropeptides from wild-type KJ and the mrdA mutant, KJΔ mrdA . (A) The LC-MS total ion chromatogram (TIC) of wild-type KJ and mutant KJΔ mrdA , determined via reversed-phase ultraperformance liquid chromatography coupled to a high-resolution hybrid Orbitrap mass spectrometer. (Inset) Enlargement of the region where M4N is eluted. (The extracted ion chromatogram [EIC] of M4 and M4N are shown in Fig. S3 in the supplemental material.) (B) The ratios of the top 10 muropeptide compositions in wild-type KJ and KJΔ mrdA mutant strain. (The full list of identified muropeptides is provided in Table S2 ). *, P

    Techniques Used: Liquid Chromatography with Mass Spectroscopy, Mutagenesis, Liquid Chromatography, Mass Spectrometry

    Related Articles

    Mass Spectrometry:

    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
    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). ..

    Article Title: Impacts of Penicillin Binding Protein 2 Inactivation on β-Lactamase Expression and Muropeptide Profile in Stenotrophomonas maltophilia
    Article Snippet: .. The fractions were collected every 30 s. The purity of each fraction was checked with a Q Exactive Plus hybrid quadrupole-orbitrap mass spectrometer (Thermo Fisher Scientific, USA). ..

    Article Title: Hybrid Quadrupole-Orbitrap Mass Spectrometry for Quantitative Measurement of Quorum Sensing Inhibition
    Article Snippet: .. Liquid chromatography-mass spectrometry was performed using an Aquity ultra-high performance liquid chromatography (UPLC) system (Waters Corporation, Milford, MA) coupled to a Q Exactive Plus Hybrid Quadrupole-Orbitrap mass spectrometer (Thermo Fisher Scientific, Waltham, MA). ..

    Article Title: Identification of Candidate Cyclin-dependent kinase 1 (Cdk1) Substrates in Mitosis by Quantitative Phosphoproteomics *
    Article Snippet: .. Phosphopeptides were analyzed on a Q-Exactive Plus hybrid quadrupole Orbitrap mass spectrometer (ThermoFisher Scientific) equipped with an Easy-nLC 1000 (ThermoFisher Scientific) and nanospray source (ThermoFisher Scientific). .. Peptides were resuspended in 5% methanol/1% formic acid and loaded on to a trap column (1 cm length, 100 μm inner diameter, ReproSil, C18 AQ 5 μm 120 Å pore (Dr. Maisch, Ammerbuch, Germany)) vented to waste via a micro-tee and eluted across a fritless analytical resolving column (35 cm length, 100 μm inner diameter, ReproSil, C18 AQ 3 μm 120 Å pore) pulled in-house (Sutter P-2000, Sutter Instruments, San Francisco, CA) with a 60 min gradient of 5–30% LC-MS buffer B (LC-MS buffer A: 0.0625% formic acid, 3% ACN; LC-MS buffer B: 0.0625% formic acid, 95% ACN).

    Article Title: Impacts of Penicillin Binding Protein 2 Inactivation on β-Lactamase Expression and Muropeptide Profile in Stenotrophomonas maltophilia
    Article Snippet: .. A Dionex UltiMate 3000 UHPLC system coupled with a Q Exactive Plus hybrid quadrupole-orbitrap mass spectrometer (Thermo Fisher Scientific, USA) was used for LC-MS analysis. ..

    Article Title: Integrative Analysis of Proteome and Ubiquitylome Reveals Unique Features of Lysosomal and Endocytic Pathways in Gefitinib‐Resistant Non‐Small Cell Lung Cancer Cells
    Article Snippet: .. The gradient comprised an increase from 6% to 22% of solvent B (0.1% FA in 98% ACN) for 26 min, 22–35% for 8 min, and climbing to 80% in 3 min then holding at 80% for the last 3 min, all at a constant flow rate of 300 nL min−1 on an EASY‐nLC 1000 UPLC system, the resulting peptides were analyzed by Q Exactive Plus hybrid quadrupole‐Orbitrap mass spectrometer (ThermoFisher Scientific). .. The peptides were subjected to NSI source followed by MS/MS in Q Exactive Plus (Thermo) coupled online to the UPLC.

    Article Title: More Is Not Always Better: Evaluation of 1D and 2D-LC-MS/MS Methods for Metaproteomics
    Article Snippet: .. An EASY-Spray source connected the analytical column to a Q Exactive Plus hybrid quadrupole-Orbitrap mass spectrometer (Thermo Fisher Scientific). .. Elution and separation of peptides on the analytical column was achieved at a flow rate of 225 nl min−1 using a gradient of eluent A (0.1% formic acid) and eluent B (0.1% formic acid, 80% acetonitrile) with the times as specified in .

    Article Title: Horizontal acquisition of a patchwork Calvin cycle by symbiotic and free-living Campylobacterota (formerly Epsilonproteobacteria)
    Article Snippet: .. An Easy-Spray source connected the analytical column to a Q Exactive Plus hybrid quadrupole-Orbitrap mass spectrometer (Thermo Fisher Scientific). .. Separation of peptides on the analytical column was achieved at a flow rate of 225 nl min−1 using a 460 min gradient going from 98% buffer A (0.1% formic acid) to 31% buffer B (0.1% formic acid, 80% acetonitrile) in 363 min, then to 50% B in 70 min, to 99% B in 1 min and ending with 99% B. Electrospray ionization was used to ionize eluting peptides.

    Flow Cytometry:

    Article Title: Integrative Analysis of Proteome and Ubiquitylome Reveals Unique Features of Lysosomal and Endocytic Pathways in Gefitinib‐Resistant Non‐Small Cell Lung Cancer Cells
    Article Snippet: .. The gradient comprised an increase from 6% to 22% of solvent B (0.1% FA in 98% ACN) for 26 min, 22–35% for 8 min, and climbing to 80% in 3 min then holding at 80% for the last 3 min, all at a constant flow rate of 300 nL min−1 on an EASY‐nLC 1000 UPLC system, the resulting peptides were analyzed by Q Exactive Plus hybrid quadrupole‐Orbitrap mass spectrometer (ThermoFisher Scientific). .. The peptides were subjected to NSI source followed by MS/MS in Q Exactive Plus (Thermo) coupled online to the UPLC.

    Chromatography:

    Article Title: Hybrid Quadrupole-Orbitrap Mass Spectrometry for Quantitative Measurement of Quorum Sensing Inhibition
    Article Snippet: .. Liquid chromatography-mass spectrometry was performed using an Aquity ultra-high performance liquid chromatography (UPLC) system (Waters Corporation, Milford, MA) coupled to a Q Exactive Plus Hybrid Quadrupole-Orbitrap mass spectrometer (Thermo Fisher Scientific, Waltham, MA). ..

    Liquid Chromatography with Mass Spectroscopy:

    Article Title: Impacts of Penicillin Binding Protein 2 Inactivation on β-Lactamase Expression and Muropeptide Profile in Stenotrophomonas maltophilia
    Article Snippet: .. A Dionex UltiMate 3000 UHPLC system coupled with a Q Exactive Plus hybrid quadrupole-orbitrap mass spectrometer (Thermo Fisher Scientific, USA) was used for LC-MS analysis. ..

    Liquid Chromatography:

    Article Title: Hybrid Quadrupole-Orbitrap Mass Spectrometry for Quantitative Measurement of Quorum Sensing Inhibition
    Article Snippet: .. Liquid chromatography-mass spectrometry was performed using an Aquity ultra-high performance liquid chromatography (UPLC) system (Waters Corporation, Milford, MA) coupled to a Q Exactive Plus Hybrid Quadrupole-Orbitrap mass spectrometer (Thermo Fisher Scientific, Waltham, MA). ..

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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
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    99
    Thermo Fisher q exactive hybrid quadrupole orbitrap plus mass spectrometer
    Quantification of platelet proteins by an internal standard curve. ( A ) Proteomics workflow. The prepared peptide samples were separated by nanoHPLC and measured subsequently with nanoESI-MS parallel reaction monitoring (PRM). Peptides of interest were isolated sequentially in a quadrupole, then fragmented, and finally peptide fragments detected in an <t>orbitrap</t> mass analyzer; ( B ) Distribution of endogenous concentration of quantified proteins. In total, 133 peptides corresponding to 99 proteins in human platelets were quantified; ( C ) Quantification of Integrin alpha-2 (ITA2) via an internal calibration curve and least squares linear regression. The dots represent the measured areas of the quantifier transition of the stable isotope-labeled (black) and endogenous peptides (red) plotted against the known or determined peptide concentration. Plotted in grey is the straight line fitted to the measured area under the curve of the quantifier transition of stable isotope-labeled peptide using least squares linear regression.
    Q Exactive Hybrid Quadrupole Orbitrap Plus Mass Spectrometer, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/q exactive hybrid quadrupole orbitrap plus mass spectrometer/product/Thermo Fisher
    Average 99 stars, based on 3 article reviews
    Price from $9.99 to $1999.99
    q exactive hybrid quadrupole orbitrap plus mass spectrometer - by Bioz Stars, 2020-07
    99/100 stars
      Buy from Supplier

    Image Search Results


    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

    Quantitative LC-MS analysis of periplasmic muropeptides from wild-type KJ and mrdA mutant strain KJΔ mrdA . The LC-MS total ion chromatograms (TICs) of periplasmic muropeptide analysis of wild-type KJ and the mrdA mutant strain, KJΔ mrdA were determined by reverse-phase ultraperformance liquid chromatography coupled to a high-resolution hybrid Orbitrap mass spectrometer. A full list of periplasmic muropeptides is provided in Table S3 . An equal amount of purified N -acetylglucosaminyl- N -acetylmuramyl- l -alanyl- d -glutamic acid in its reduced form (GlcNAc-MurNAc dipeptide; M2), which was only observed in total muropeptides ( Fig. 5 ), was spiked in both wild-type KJ and the KJΔ mrdA strain as an internal standard to quantify the periplasmic muropeptides.

    Journal: mSystems

    Article Title: Impacts of Penicillin Binding Protein 2 Inactivation on β-Lactamase Expression and Muropeptide Profile in Stenotrophomonas maltophilia

    doi: 10.1128/mSystems.00077-17

    Figure Lengend Snippet: Quantitative LC-MS analysis of periplasmic muropeptides from wild-type KJ and mrdA mutant strain KJΔ mrdA . The LC-MS total ion chromatograms (TICs) of periplasmic muropeptide analysis of wild-type KJ and the mrdA mutant strain, KJΔ mrdA were determined by reverse-phase ultraperformance liquid chromatography coupled to a high-resolution hybrid Orbitrap mass spectrometer. A full list of periplasmic muropeptides is provided in Table S3 . An equal amount of purified N -acetylglucosaminyl- N -acetylmuramyl- l -alanyl- d -glutamic acid in its reduced form (GlcNAc-MurNAc dipeptide; M2), which was only observed in total muropeptides ( Fig. 5 ), was spiked in both wild-type KJ and the KJΔ mrdA strain as an internal standard to quantify the periplasmic muropeptides.

    Article Snippet: The fractions were collected every 30 s. The purity of each fraction was checked with a Q Exactive Plus hybrid quadrupole-orbitrap mass spectrometer (Thermo Fisher Scientific, USA).

    Techniques: Liquid Chromatography with Mass Spectroscopy, Mutagenesis, Liquid Chromatography, Mass Spectrometry, Purification

    LC-MS analysis results for total muropeptides from wild-type KJ and the mrdA mutant, KJΔ mrdA . (A) The LC-MS total ion chromatogram (TIC) of wild-type KJ and mutant KJΔ mrdA , determined via reversed-phase ultraperformance liquid chromatography coupled to a high-resolution hybrid Orbitrap mass spectrometer. (Inset) Enlargement of the region where M4N is eluted. (The extracted ion chromatogram [EIC] of M4 and M4N are shown in Fig. S3 in the supplemental material.) (B) The ratios of the top 10 muropeptide compositions in wild-type KJ and KJΔ mrdA mutant strain. (The full list of identified muropeptides is provided in Table S2 ). *, P

    Journal: mSystems

    Article Title: Impacts of Penicillin Binding Protein 2 Inactivation on β-Lactamase Expression and Muropeptide Profile in Stenotrophomonas maltophilia

    doi: 10.1128/mSystems.00077-17

    Figure Lengend Snippet: LC-MS analysis results for total muropeptides from wild-type KJ and the mrdA mutant, KJΔ mrdA . (A) The LC-MS total ion chromatogram (TIC) of wild-type KJ and mutant KJΔ mrdA , determined via reversed-phase ultraperformance liquid chromatography coupled to a high-resolution hybrid Orbitrap mass spectrometer. (Inset) Enlargement of the region where M4N is eluted. (The extracted ion chromatogram [EIC] of M4 and M4N are shown in Fig. S3 in the supplemental material.) (B) The ratios of the top 10 muropeptide compositions in wild-type KJ and KJΔ mrdA mutant strain. (The full list of identified muropeptides is provided in Table S2 ). *, P

    Article Snippet: The fractions were collected every 30 s. The purity of each fraction was checked with a Q Exactive Plus hybrid quadrupole-orbitrap mass spectrometer (Thermo Fisher Scientific, USA).

    Techniques: Liquid Chromatography with Mass Spectroscopy, Mutagenesis, Liquid Chromatography, Mass Spectrometry

    Higher NCE improves generation of NL ions in synthetic ADMA and SDMA peptides. A) Mechanism of neutral loss of dimethylamine and monomethylamine from ADMA and SDMA, respectively. B) Total number of DMA PSMs from a dataset of synthetic ADMA and SDMA peptides. The proportion of PSMs displaying either an ADMA or SDMA neutral loss in the HCD cell of an Orbitrap Fusion Lumos are shown for each NCE. C) Total number of unique peptides with assignable ADMA or SDMA neutral loss for each NCE. D) Violin plot of the number of NL ions present in DMA PSMs for each NCE. Each point represents a PSM with a corresponding number of NL ions observed in that spectra.

    Journal: bioRxiv

    Article Title: Improved discrimination of asymmetric and symmetric arginine dimethylation by optimization of the normalized collision energy in LC-MS proteomics

    doi: 10.1101/2020.02.14.949255

    Figure Lengend Snippet: Higher NCE improves generation of NL ions in synthetic ADMA and SDMA peptides. A) Mechanism of neutral loss of dimethylamine and monomethylamine from ADMA and SDMA, respectively. B) Total number of DMA PSMs from a dataset of synthetic ADMA and SDMA peptides. The proportion of PSMs displaying either an ADMA or SDMA neutral loss in the HCD cell of an Orbitrap Fusion Lumos are shown for each NCE. C) Total number of unique peptides with assignable ADMA or SDMA neutral loss for each NCE. D) Violin plot of the number of NL ions present in DMA PSMs for each NCE. Each point represents a PSM with a corresponding number of NL ions observed in that spectra.

    Article Snippet: Mass Spectrometric Analysis All LC-MS experiments were performed on a nanoscale UHPLC system (EASY-nLC1200, Thermo Scientific) connected to an Q Exactive Plus hybrid quadrupole-Orbitrap mass spectrometer equipped with a nanoelectrospray source (Thermo Scientific).

    Techniques:

    Quantification of platelet proteins by an internal standard curve. ( A ) Proteomics workflow. The prepared peptide samples were separated by nanoHPLC and measured subsequently with nanoESI-MS parallel reaction monitoring (PRM). Peptides of interest were isolated sequentially in a quadrupole, then fragmented, and finally peptide fragments detected in an orbitrap mass analyzer; ( B ) Distribution of endogenous concentration of quantified proteins. In total, 133 peptides corresponding to 99 proteins in human platelets were quantified; ( C ) Quantification of Integrin alpha-2 (ITA2) via an internal calibration curve and least squares linear regression. The dots represent the measured areas of the quantifier transition of the stable isotope-labeled (black) and endogenous peptides (red) plotted against the known or determined peptide concentration. Plotted in grey is the straight line fitted to the measured area under the curve of the quantifier transition of stable isotope-labeled peptide using least squares linear regression.

    Journal: Proteomes

    Article Title: Quantification of Cardiovascular Disease Biomarkers in Human Platelets by Targeted Mass Spectrometry

    doi: 10.3390/proteomes5040031

    Figure Lengend Snippet: Quantification of platelet proteins by an internal standard curve. ( A ) Proteomics workflow. The prepared peptide samples were separated by nanoHPLC and measured subsequently with nanoESI-MS parallel reaction monitoring (PRM). Peptides of interest were isolated sequentially in a quadrupole, then fragmented, and finally peptide fragments detected in an orbitrap mass analyzer; ( B ) Distribution of endogenous concentration of quantified proteins. In total, 133 peptides corresponding to 99 proteins in human platelets were quantified; ( C ) Quantification of Integrin alpha-2 (ITA2) via an internal calibration curve and least squares linear regression. The dots represent the measured areas of the quantifier transition of the stable isotope-labeled (black) and endogenous peptides (red) plotted against the known or determined peptide concentration. Plotted in grey is the straight line fitted to the measured area under the curve of the quantifier transition of stable isotope-labeled peptide using least squares linear regression.

    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.

    Techniques: Mass Spectrometry, Isolation, Concentration Assay, Labeling