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: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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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 hf mass spectrometer
    Ser 139 , Thr 206 , and Ser 213 are PKCβ-regulatory sites. A , for <t>mass</t> spectrometry, an in vitro kinase assay was performed with recombinant kinases and p66 as substrate and subjected to SDS-PAGE. The gel was stained with Coomassie or immunoblotted for p66 Ser 36 . B , the protein bands were excised from Coomassie-stained gel and digested with trypsin or Lys C. Both Tryptic ( C ) and Lys C ( D ) digests were analyzed by nano-HPLC coupled via an electrospray ionization interface to a <t>Q</t> <t>Exactive</t> <t>HF</t> mass <t>spectrometer.</t> Data analysis and peak area calculation were performed using Proteome Discoverer 1.4.1.14.
    Q Exactive Hf Mass Spectrometer, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 76 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher tribrid quadrupole orbitrap ion trap mass spectrometer
    Differential N-glycomics and proteomics of APL and APL-6 cells investigating the response of the cells towards ATRA treatment. (a) Overview of this experimental workflow for APL cells after DMSO and ATRA treatment respectively, showing that differential quantitative N-glycomics was performed by <t>tribrid</t> <t>orbitrap</t> mass spectrometer with CID fragmentation and differential quantitative proteomics was performed by hybrid orbitrap mass spectrometer with higher energy collisional dissociation (HCD) fragmentation. (b) Volcano plot of differential N-glycomics of APL-6-H vs APL-H. (c) Heat map of monosaccharide compositions present at significantly different abundance in APL-6-H vs APL-H. (d) Volcano plot of differential proteomics of APL-6 vs APL cells. (e) The quantitative comparison of differential N-glycan precursors and their related specific glucosidase, α-Glc II including Q14697 and P14314, in APL-6 vs APL cells.
    Tribrid Quadrupole Orbitrap Ion Trap Mass Spectrometer, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/tribrid quadrupole orbitrap ion trap mass spectrometer/product/Thermo Fisher
    Average 99 stars, based on 1 article reviews
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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
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    Ser 139 , Thr 206 , and Ser 213 are PKCβ-regulatory sites. A , for mass spectrometry, an in vitro kinase assay was performed with recombinant kinases and p66 as substrate and subjected to SDS-PAGE. The gel was stained with Coomassie or immunoblotted for p66 Ser 36 . B , the protein bands were excised from Coomassie-stained gel and digested with trypsin or Lys C. Both Tryptic ( C ) and Lys C ( D ) digests were analyzed by nano-HPLC coupled via an electrospray ionization interface to a Q Exactive HF mass spectrometer. Data analysis and peak area calculation were performed using Proteome Discoverer 1.4.1.14.

    Journal: The Journal of Biological Chemistry

    Article Title: Novel Insights into the PKCβ-dependent Regulation of the Oxidoreductase p66Shc *

    doi: 10.1074/jbc.M116.752766

    Figure Lengend Snippet: Ser 139 , Thr 206 , and Ser 213 are PKCβ-regulatory sites. A , for mass spectrometry, an in vitro kinase assay was performed with recombinant kinases and p66 as substrate and subjected to SDS-PAGE. The gel was stained with Coomassie or immunoblotted for p66 Ser 36 . B , the protein bands were excised from Coomassie-stained gel and digested with trypsin or Lys C. Both Tryptic ( C ) and Lys C ( D ) digests were analyzed by nano-HPLC coupled via an electrospray ionization interface to a Q Exactive HF mass spectrometer. Data analysis and peak area calculation were performed using Proteome Discoverer 1.4.1.14.

    Article Snippet: Tryptic digests were analyzed using an UltiMate 3000 nano-HPLC system (Thermo Scientific, Bremen, Germany) coupled to a Q Exactive Plus or Q Exactive HF mass spectrometer (Thermo Scientific) equipped with a Nanospray Flex ionization source.

    Techniques: Mass Spectrometry, In Vitro, Kinase Assay, Recombinant, SDS Page, Staining, High Performance Liquid Chromatography

    Metformin Prevents Tumor-Cell-Induced Stabilization of HIF1α in Mesothelial Cells (A) Mass spectrometry (MS) analysis of mesothelial cells (HPMCs) co-cultured with OvCa cells and treated with metformin (1 mM, 48 h). Cell lysates were collected and measured on a Q Exactive HF mass spectrometer, and the quantification of proteins significantly altered by metformin is shown by volcano plot (Perseus), with the significantly altered proteins highlighted in red. Significance was defined by a false discovery rate (FDR) of 0.05 and an S 0 value of 0.05 (n = 4 patients in triplicate). (B) Unsupervised hierarchical clustering (Perseus) was performed on the dataset from (A), assessing hypoxia-related proteins in HPMCs following exposure to TYKnu OvCa co-culture in the presence or absence of metformin (1 mM, 48 h) (n = 4 patients per group in triplicate). (C) Western blot of HIF1α and HIF2α protein expression in HPMCs following exposure to TYKnu OvCa co-culture in the presence of metformin (1 mM, 48 h) (representative blot from n = 2 patients in duplicate). (D) Western blot of HIF1α protein expression in HPMCs expressing constitutively stable HIF1α (P402A/P564A substitutions) ± metformin (1 mM, 48 h) (representative blot from n = 2 patients in duplicate). (E) qRT-PCR of IL-8 (left) and CCL2 (right) mRNA expression in HPMCs transfected with constitutively stable HIF1α (P402A/P564A) with or without metformin (1 mM) (n = 2 patients in duplicate). (F) Invasion of TYKnu OvCa cells (36 h) in 3D culture with metformin (pretreatment of HPMCs with 250 μM for 72 h) in the presence of N -oxalylglycine (OG, 1 mM) and 2-oxoglutarate (2-oxo, 5 mM) (n = 2 patients per group in triplicate). (G) Invasion of TYKnu OvCa cells (36 h) in 3D culture containing control or HPMCs expressing constitutively stable HIF1α (P402A/P564A) treated with metformin (pretreatment of HPMCs with 250 μM for 72 h), with concurrent exposure to IL-8RA/CXCR1 neutralizing antibody (150 ng/mL) during the invasion assay (n = 2 patients in duplicate). (H) Western blot of HIF1α and CAIX expression in normal/benign omental explants from patients using metformin for diabetes compared to control patients without diabetes not using metformin. Rightside, densitometry (area under the curve [AUC]) of western immunoblot bands of HIF1α and CAIX was quantified and normalized to vinculin (n = 3 patients per group in duplicate). (I) CAIX immunohistochemical staining in primary ovarian and omental tumors from patients with OvCa who were using metformin for diabetes compared to non-diabetic patients with OvCa not taking metformin. Quantification of primary tumor (n = 15 and 18 for control and metformin, respectively) or omental metastasis (n = 15 and 12 for control and metformin, respectively) was performed using ImageScope software. Images are representative and were taken at 20× magnification; scale bar represents 100 μm. Data represent mean values ± SDs. *p

    Journal: Cell reports

    Article Title: Mesothelial Cell HIF1α Expression Is Metabolically Downregulated by Metformin to Prevent Oncogenic Tumor-Stromal Crosstalk

    doi: 10.1016/j.celrep.2019.11.079

    Figure Lengend Snippet: Metformin Prevents Tumor-Cell-Induced Stabilization of HIF1α in Mesothelial Cells (A) Mass spectrometry (MS) analysis of mesothelial cells (HPMCs) co-cultured with OvCa cells and treated with metformin (1 mM, 48 h). Cell lysates were collected and measured on a Q Exactive HF mass spectrometer, and the quantification of proteins significantly altered by metformin is shown by volcano plot (Perseus), with the significantly altered proteins highlighted in red. Significance was defined by a false discovery rate (FDR) of 0.05 and an S 0 value of 0.05 (n = 4 patients in triplicate). (B) Unsupervised hierarchical clustering (Perseus) was performed on the dataset from (A), assessing hypoxia-related proteins in HPMCs following exposure to TYKnu OvCa co-culture in the presence or absence of metformin (1 mM, 48 h) (n = 4 patients per group in triplicate). (C) Western blot of HIF1α and HIF2α protein expression in HPMCs following exposure to TYKnu OvCa co-culture in the presence of metformin (1 mM, 48 h) (representative blot from n = 2 patients in duplicate). (D) Western blot of HIF1α protein expression in HPMCs expressing constitutively stable HIF1α (P402A/P564A substitutions) ± metformin (1 mM, 48 h) (representative blot from n = 2 patients in duplicate). (E) qRT-PCR of IL-8 (left) and CCL2 (right) mRNA expression in HPMCs transfected with constitutively stable HIF1α (P402A/P564A) with or without metformin (1 mM) (n = 2 patients in duplicate). (F) Invasion of TYKnu OvCa cells (36 h) in 3D culture with metformin (pretreatment of HPMCs with 250 μM for 72 h) in the presence of N -oxalylglycine (OG, 1 mM) and 2-oxoglutarate (2-oxo, 5 mM) (n = 2 patients per group in triplicate). (G) Invasion of TYKnu OvCa cells (36 h) in 3D culture containing control or HPMCs expressing constitutively stable HIF1α (P402A/P564A) treated with metformin (pretreatment of HPMCs with 250 μM for 72 h), with concurrent exposure to IL-8RA/CXCR1 neutralizing antibody (150 ng/mL) during the invasion assay (n = 2 patients in duplicate). (H) Western blot of HIF1α and CAIX expression in normal/benign omental explants from patients using metformin for diabetes compared to control patients without diabetes not using metformin. Rightside, densitometry (area under the curve [AUC]) of western immunoblot bands of HIF1α and CAIX was quantified and normalized to vinculin (n = 3 patients per group in duplicate). (I) CAIX immunohistochemical staining in primary ovarian and omental tumors from patients with OvCa who were using metformin for diabetes compared to non-diabetic patients with OvCa not taking metformin. Quantification of primary tumor (n = 15 and 18 for control and metformin, respectively) or omental metastasis (n = 15 and 12 for control and metformin, respectively) was performed using ImageScope software. Images are representative and were taken at 20× magnification; scale bar represents 100 μm. Data represent mean values ± SDs. *p

    Article Snippet: Q-Exactive HF mass spectrometer coupled to EASY-nLC 1000 HPLC system (ThermoFisher) was used to perform label-free shotgun proteomics as previously described in detail ( ).

    Techniques: Mass Spectrometry, Cell Culture, Co-Culture Assay, Western Blot, Expressing, Quantitative RT-PCR, Transfection, Invasion Assay, Immunohistochemistry, Staining, Software

    Differential N-glycomics and proteomics of APL and APL-6 cells investigating the response of the cells towards ATRA treatment. (a) Overview of this experimental workflow for APL cells after DMSO and ATRA treatment respectively, showing that differential quantitative N-glycomics was performed by tribrid orbitrap mass spectrometer with CID fragmentation and differential quantitative proteomics was performed by hybrid orbitrap mass spectrometer with higher energy collisional dissociation (HCD) fragmentation. (b) Volcano plot of differential N-glycomics of APL-6-H vs APL-H. (c) Heat map of monosaccharide compositions present at significantly different abundance in APL-6-H vs APL-H. (d) Volcano plot of differential proteomics of APL-6 vs APL cells. (e) The quantitative comparison of differential N-glycan precursors and their related specific glucosidase, α-Glc II including Q14697 and P14314, in APL-6 vs APL cells.

    Journal: bioRxiv

    Article Title: An improved comprehensive strategy for deep and quantitative N-glycomics based on optimization of sample preparation, isotope-based data quality control and quantification, new N-glycan libraries and new algorithms

    doi: 10.1101/2020.10.15.340638

    Figure Lengend Snippet: Differential N-glycomics and proteomics of APL and APL-6 cells investigating the response of the cells towards ATRA treatment. (a) Overview of this experimental workflow for APL cells after DMSO and ATRA treatment respectively, showing that differential quantitative N-glycomics was performed by tribrid orbitrap mass spectrometer with CID fragmentation and differential quantitative proteomics was performed by hybrid orbitrap mass spectrometer with higher energy collisional dissociation (HCD) fragmentation. (b) Volcano plot of differential N-glycomics of APL-6-H vs APL-H. (c) Heat map of monosaccharide compositions present at significantly different abundance in APL-6-H vs APL-H. (d) Volcano plot of differential proteomics of APL-6 vs APL cells. (e) The quantitative comparison of differential N-glycan precursors and their related specific glucosidase, α-Glc II including Q14697 and P14314, in APL-6 vs APL cells.

    Article Snippet: Derivative N-glycan ions were transferred to a tribrid quadrupole-orbitrap-ion trap mass spectrometer (Fusion, Thermo Fisher Scientific, Bremen, Germany).

    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