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  • 99
    Thermo Fisher orbitrap mass spectrometer
    Development of a quantitative high-resolution mass spectrometry to directly measure intracellular 5-AZA-CdR and AZA. ( a ) Chemical structures of cytidine, deoxycytidine, AZA and 5-AZA-CdR. ( b ) Schematic depicting intracellular metabolism of AZA. Following cellular uptake and phosphorylation, ~80% of AZA gets incorporated into RNA by RNA polymerases. The remaining fraction is converted into 5-AZA-CdR by ribonucleotide reductase and incorporated into DNA by DNA polymerases. ( c ) Representative high-resolution <t>Orbitrap</t> mass spectra at RT of 0.98 min, showing clear baseline separation between 5-AZA-CdR, 15N-dC and 13C-dC (left, with respective m/z values) despite their identical chromatographic retention times (right). ( d ) Schematic depicting the optimised method incorporating steps to improve sensitivity of detection of intracellular 5-AZA-CdR and AZA by LC–MS.
    Orbitrap Mass Spectrometer, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 2201 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/orbitrap mass spectrometer/product/Thermo Fisher
    Average 99 stars, based on 2201 article reviews
    Price from $9.99 to $1999.99
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    88
    PerkinElmer spectrometric determination nexion 300d mass spectrometer
    Development of a quantitative high-resolution mass spectrometry to directly measure intracellular 5-AZA-CdR and AZA. ( a ) Chemical structures of cytidine, deoxycytidine, AZA and 5-AZA-CdR. ( b ) Schematic depicting intracellular metabolism of AZA. Following cellular uptake and phosphorylation, ~80% of AZA gets incorporated into RNA by RNA polymerases. The remaining fraction is converted into 5-AZA-CdR by ribonucleotide reductase and incorporated into DNA by DNA polymerases. ( c ) Representative high-resolution <t>Orbitrap</t> mass spectra at RT of 0.98 min, showing clear baseline separation between 5-AZA-CdR, 15N-dC and 13C-dC (left, with respective m/z values) despite their identical chromatographic retention times (right). ( d ) Schematic depicting the optimised method incorporating steps to improve sensitivity of detection of intracellular 5-AZA-CdR and AZA by LC–MS.
    Spectrometric Determination Nexion 300d Mass Spectrometer, supplied by PerkinElmer, used in various techniques. Bioz Stars score: 88/100, based on 6 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/spectrometric determination nexion 300d mass spectrometer/product/PerkinElmer
    Average 88 stars, based on 6 article reviews
    Price from $9.99 to $1999.99
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    88/100 stars
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    94
    Thermo Fisher mass spectrometer
    Development of a quantitative high-resolution mass spectrometry to directly measure intracellular 5-AZA-CdR and AZA. ( a ) Chemical structures of cytidine, deoxycytidine, AZA and 5-AZA-CdR. ( b ) Schematic depicting intracellular metabolism of AZA. Following cellular uptake and phosphorylation, ~80% of AZA gets incorporated into RNA by RNA polymerases. The remaining fraction is converted into 5-AZA-CdR by ribonucleotide reductase and incorporated into DNA by DNA polymerases. ( c ) Representative high-resolution <t>Orbitrap</t> mass spectra at RT of 0.98 min, showing clear baseline separation between 5-AZA-CdR, 15N-dC and 13C-dC (left, with respective m/z values) despite their identical chromatographic retention times (right). ( d ) Schematic depicting the optimised method incorporating steps to improve sensitivity of detection of intracellular 5-AZA-CdR and AZA by LC–MS.
    Mass Spectrometer, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 94/100, based on 5373 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/mass spectrometer/product/Thermo Fisher
    Average 94 stars, based on 5373 article reviews
    Price from $9.99 to $1999.99
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    91
    Advion mass spectrometers
    Development of a quantitative high-resolution mass spectrometry to directly measure intracellular 5-AZA-CdR and AZA. ( a ) Chemical structures of cytidine, deoxycytidine, AZA and 5-AZA-CdR. ( b ) Schematic depicting intracellular metabolism of AZA. Following cellular uptake and phosphorylation, ~80% of AZA gets incorporated into RNA by RNA polymerases. The remaining fraction is converted into 5-AZA-CdR by ribonucleotide reductase and incorporated into DNA by DNA polymerases. ( c ) Representative high-resolution <t>Orbitrap</t> mass spectra at RT of 0.98 min, showing clear baseline separation between 5-AZA-CdR, 15N-dC and 13C-dC (left, with respective m/z values) despite their identical chromatographic retention times (right). ( d ) Schematic depicting the optimised method incorporating steps to improve sensitivity of detection of intracellular 5-AZA-CdR and AZA by LC–MS.
    Mass Spectrometers, supplied by Advion, used in various techniques. Bioz Stars score: 91/100, based on 17 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/mass spectrometers/product/Advion
    Average 91 stars, based on 17 article reviews
    Price from $9.99 to $1999.99
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    91
    Shimadzu Corporation mass spectrometers
    Development of a quantitative high-resolution mass spectrometry to directly measure intracellular 5-AZA-CdR and AZA. ( a ) Chemical structures of cytidine, deoxycytidine, AZA and 5-AZA-CdR. ( b ) Schematic depicting intracellular metabolism of AZA. Following cellular uptake and phosphorylation, ~80% of AZA gets incorporated into RNA by RNA polymerases. The remaining fraction is converted into 5-AZA-CdR by ribonucleotide reductase and incorporated into DNA by DNA polymerases. ( c ) Representative high-resolution <t>Orbitrap</t> mass spectra at RT of 0.98 min, showing clear baseline separation between 5-AZA-CdR, 15N-dC and 13C-dC (left, with respective m/z values) despite their identical chromatographic retention times (right). ( d ) Schematic depicting the optimised method incorporating steps to improve sensitivity of detection of intracellular 5-AZA-CdR and AZA by LC–MS.
    Mass Spectrometers, supplied by Shimadzu Corporation, used in various techniques. Bioz Stars score: 91/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/mass spectrometers/product/Shimadzu Corporation
    Average 91 stars, based on 2 article reviews
    Price from $9.99 to $1999.99
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    85
    Bruker Corporation mass array mass spectrometer
    Development of a quantitative high-resolution mass spectrometry to directly measure intracellular 5-AZA-CdR and AZA. ( a ) Chemical structures of cytidine, deoxycytidine, AZA and 5-AZA-CdR. ( b ) Schematic depicting intracellular metabolism of AZA. Following cellular uptake and phosphorylation, ~80% of AZA gets incorporated into RNA by RNA polymerases. The remaining fraction is converted into 5-AZA-CdR by ribonucleotide reductase and incorporated into DNA by DNA polymerases. ( c ) Representative high-resolution <t>Orbitrap</t> mass spectra at RT of 0.98 min, showing clear baseline separation between 5-AZA-CdR, 15N-dC and 13C-dC (left, with respective m/z values) despite their identical chromatographic retention times (right). ( d ) Schematic depicting the optimised method incorporating steps to improve sensitivity of detection of intracellular 5-AZA-CdR and AZA by LC–MS.
    Mass Array Mass Spectrometer, supplied by Bruker Corporation, used in various techniques. Bioz Stars score: 85/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/mass array mass spectrometer/product/Bruker Corporation
    Average 85 stars, based on 4 article reviews
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    mass array mass spectrometer - by Bioz Stars, 2020-08
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    94
    Thermo Fisher process mass spectrometer
    Development of a quantitative high-resolution mass spectrometry to directly measure intracellular 5-AZA-CdR and AZA. ( a ) Chemical structures of cytidine, deoxycytidine, AZA and 5-AZA-CdR. ( b ) Schematic depicting intracellular metabolism of AZA. Following cellular uptake and phosphorylation, ~80% of AZA gets incorporated into RNA by RNA polymerases. The remaining fraction is converted into 5-AZA-CdR by ribonucleotide reductase and incorporated into DNA by DNA polymerases. ( c ) Representative high-resolution <t>Orbitrap</t> mass spectra at RT of 0.98 min, showing clear baseline separation between 5-AZA-CdR, 15N-dC and 13C-dC (left, with respective m/z values) despite their identical chromatographic retention times (right). ( d ) Schematic depicting the optimised method incorporating steps to improve sensitivity of detection of intracellular 5-AZA-CdR and AZA by LC–MS.
    Process Mass Spectrometer, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 94/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/process mass spectrometer/product/Thermo Fisher
    Average 94 stars, based on 4 article reviews
    Price from $9.99 to $1999.99
    process mass spectrometer - by Bioz Stars, 2020-08
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    91
    Agilent technologies mass spectrometers
    Development of a quantitative high-resolution mass spectrometry to directly measure intracellular 5-AZA-CdR and AZA. ( a ) Chemical structures of cytidine, deoxycytidine, AZA and 5-AZA-CdR. ( b ) Schematic depicting intracellular metabolism of AZA. Following cellular uptake and phosphorylation, ~80% of AZA gets incorporated into RNA by RNA polymerases. The remaining fraction is converted into 5-AZA-CdR by ribonucleotide reductase and incorporated into DNA by DNA polymerases. ( c ) Representative high-resolution <t>Orbitrap</t> mass spectra at RT of 0.98 min, showing clear baseline separation between 5-AZA-CdR, 15N-dC and 13C-dC (left, with respective m/z values) despite their identical chromatographic retention times (right). ( d ) Schematic depicting the optimised method incorporating steps to improve sensitivity of detection of intracellular 5-AZA-CdR and AZA by LC–MS.
    Mass Spectrometers, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 91/100, based on 49 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/mass spectrometers/product/Agilent technologies
    Average 91 stars, based on 49 article reviews
    Price from $9.99 to $1999.99
    mass spectrometers - by Bioz Stars, 2020-08
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    91
    Waters Corporation mass spectrometers
    Development of a quantitative high-resolution mass spectrometry to directly measure intracellular 5-AZA-CdR and AZA. ( a ) Chemical structures of cytidine, deoxycytidine, AZA and 5-AZA-CdR. ( b ) Schematic depicting intracellular metabolism of AZA. Following cellular uptake and phosphorylation, ~80% of AZA gets incorporated into RNA by RNA polymerases. The remaining fraction is converted into 5-AZA-CdR by ribonucleotide reductase and incorporated into DNA by DNA polymerases. ( c ) Representative high-resolution <t>Orbitrap</t> mass spectra at RT of 0.98 min, showing clear baseline separation between 5-AZA-CdR, 15N-dC and 13C-dC (left, with respective m/z values) despite their identical chromatographic retention times (right). ( d ) Schematic depicting the optimised method incorporating steps to improve sensitivity of detection of intracellular 5-AZA-CdR and AZA by LC–MS.
    Mass Spectrometers, supplied by Waters Corporation, used in various techniques. Bioz Stars score: 91/100, based on 42 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/mass spectrometers/product/Waters Corporation
    Average 91 stars, based on 42 article reviews
    Price from $9.99 to $1999.99
    mass spectrometers - by Bioz Stars, 2020-08
    91/100 stars
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    99
    Thermo Fisher tribrid mass spectrometer
    Metabolic Labeling and Workflow. ( A ) Glucose, acetate, fatty acids, and amino acids produce acetyl-CoA for use in acetylating cytoplasmic and nuclear proteins. The thicker arrows indicate that glucose contributes more to the production of acetyl-coA that subsequently acetylates proteins, compared to acetate. ( B ) The workflow consisted of growing HeLa cells in heavy-labeled media, collecting samples at eight time points, lysing the cells, digesting the proteins, enriching for acetylated peptides, and analyzing the peptides by mass spectrometry. The <t>Orbitrap</t> image is adapted from Thermo Fisher Scientific 56 . The cartoon cell matter and lab equipment were slightly modified from Servier Medical Art 57 .
    Tribrid Mass Spectrometer, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 79 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/tribrid mass spectrometer/product/Thermo Fisher
    Average 99 stars, based on 79 article reviews
    Price from $9.99 to $1999.99
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    85
    JEOL auto mass mass spectrometer
    Metabolic Labeling and Workflow. ( A ) Glucose, acetate, fatty acids, and amino acids produce acetyl-CoA for use in acetylating cytoplasmic and nuclear proteins. The thicker arrows indicate that glucose contributes more to the production of acetyl-coA that subsequently acetylates proteins, compared to acetate. ( B ) The workflow consisted of growing HeLa cells in heavy-labeled media, collecting samples at eight time points, lysing the cells, digesting the proteins, enriching for acetylated peptides, and analyzing the peptides by mass spectrometry. The <t>Orbitrap</t> image is adapted from Thermo Fisher Scientific 56 . The cartoon cell matter and lab equipment were slightly modified from Servier Medical Art 57 .
    Auto Mass Mass Spectrometer, supplied by JEOL, used in various techniques. Bioz Stars score: 85/100, based on 8 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/auto mass mass spectrometer/product/JEOL
    Average 85 stars, based on 8 article reviews
    Price from $9.99 to $1999.99
    auto mass mass spectrometer - by Bioz Stars, 2020-08
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    92
    Bruker Corporation mass spectrometers
    Metabolic Labeling and Workflow. ( A ) Glucose, acetate, fatty acids, and amino acids produce acetyl-CoA for use in acetylating cytoplasmic and nuclear proteins. The thicker arrows indicate that glucose contributes more to the production of acetyl-coA that subsequently acetylates proteins, compared to acetate. ( B ) The workflow consisted of growing HeLa cells in heavy-labeled media, collecting samples at eight time points, lysing the cells, digesting the proteins, enriching for acetylated peptides, and analyzing the peptides by mass spectrometry. The <t>Orbitrap</t> image is adapted from Thermo Fisher Scientific 56 . The cartoon cell matter and lab equipment were slightly modified from Servier Medical Art 57 .
    Mass Spectrometers, supplied by Bruker Corporation, used in various techniques. Bioz Stars score: 92/100, based on 80 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/mass spectrometers/product/Bruker Corporation
    Average 92 stars, based on 80 article reviews
    Price from $9.99 to $1999.99
    mass spectrometers - by Bioz Stars, 2020-08
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    92
    Thermo Fisher q exactive mass spectrometer
    Metabolic Labeling and Workflow. ( A ) Glucose, acetate, fatty acids, and amino acids produce acetyl-CoA for use in acetylating cytoplasmic and nuclear proteins. The thicker arrows indicate that glucose contributes more to the production of acetyl-coA that subsequently acetylates proteins, compared to acetate. ( B ) The workflow consisted of growing HeLa cells in heavy-labeled media, collecting samples at eight time points, lysing the cells, digesting the proteins, enriching for acetylated peptides, and analyzing the peptides by mass spectrometry. The <t>Orbitrap</t> image is adapted from Thermo Fisher Scientific 56 . The cartoon cell matter and lab equipment were slightly modified from Servier Medical Art 57 .
    Q Exactive Mass Spectrometer, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 92/100, based on 11445 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/q exactive mass spectrometer/product/Thermo Fisher
    Average 92 stars, based on 11445 article reviews
    Price from $9.99 to $1999.99
    q exactive mass spectrometer - by Bioz Stars, 2020-08
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    99
    Thermo Fisher mass spectrometric
    Metabolic Labeling and Workflow. ( A ) Glucose, acetate, fatty acids, and amino acids produce acetyl-CoA for use in acetylating cytoplasmic and nuclear proteins. The thicker arrows indicate that glucose contributes more to the production of acetyl-coA that subsequently acetylates proteins, compared to acetate. ( B ) The workflow consisted of growing HeLa cells in heavy-labeled media, collecting samples at eight time points, lysing the cells, digesting the proteins, enriching for acetylated peptides, and analyzing the peptides by mass spectrometry. The <t>Orbitrap</t> image is adapted from Thermo Fisher Scientific 56 . The cartoon cell matter and lab equipment were slightly modified from Servier Medical Art 57 .
    Mass Spectrometric, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 100 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/mass spectrometric/product/Thermo Fisher
    Average 99 stars, based on 100 article reviews
    Price from $9.99 to $1999.99
    mass spectrometric - by Bioz Stars, 2020-08
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    Image Search Results


    Development of a quantitative high-resolution mass spectrometry to directly measure intracellular 5-AZA-CdR and AZA. ( a ) Chemical structures of cytidine, deoxycytidine, AZA and 5-AZA-CdR. ( b ) Schematic depicting intracellular metabolism of AZA. Following cellular uptake and phosphorylation, ~80% of AZA gets incorporated into RNA by RNA polymerases. The remaining fraction is converted into 5-AZA-CdR by ribonucleotide reductase and incorporated into DNA by DNA polymerases. ( c ) Representative high-resolution Orbitrap mass spectra at RT of 0.98 min, showing clear baseline separation between 5-AZA-CdR, 15N-dC and 13C-dC (left, with respective m/z values) despite their identical chromatographic retention times (right). ( d ) Schematic depicting the optimised method incorporating steps to improve sensitivity of detection of intracellular 5-AZA-CdR and AZA by LC–MS.

    Journal: Leukemia

    Article Title: AZA-MS: a novel multiparameter mass spectrometry method to determine the intracellular dynamics of azacitidine therapy in vivo

    doi: 10.1038/leu.2017.340

    Figure Lengend Snippet: Development of a quantitative high-resolution mass spectrometry to directly measure intracellular 5-AZA-CdR and AZA. ( a ) Chemical structures of cytidine, deoxycytidine, AZA and 5-AZA-CdR. ( b ) Schematic depicting intracellular metabolism of AZA. Following cellular uptake and phosphorylation, ~80% of AZA gets incorporated into RNA by RNA polymerases. The remaining fraction is converted into 5-AZA-CdR by ribonucleotide reductase and incorporated into DNA by DNA polymerases. ( c ) Representative high-resolution Orbitrap mass spectra at RT of 0.98 min, showing clear baseline separation between 5-AZA-CdR, 15N-dC and 13C-dC (left, with respective m/z values) despite their identical chromatographic retention times (right). ( d ) Schematic depicting the optimised method incorporating steps to improve sensitivity of detection of intracellular 5-AZA-CdR and AZA by LC–MS.

    Article Snippet: Mass spectrometry and data analysis LC–MS analysis was performed utilising an ultra-high-performance liquid chromatography system (Dionex u3000 system, Thermo Fisher Scientific) interfaced to an Orbitrap mass spectrometer (Q Exactive Plus, Thermo Fisher Scientific) using a heated electrospray interface operated in the positive ion mode.

    Techniques: Mass Spectrometry, Liquid Chromatography with Mass Spectroscopy

    MS spectra (mass range: m/z 200–1000) by Orbitrap and MS/MS spectra (parent ion: m/z 316.1, mass range: 297.0–299.0 and 240.0–242.0) by TSQ for blank paper substrates subject to different treatments. (a) untreated 31 ET paper,

    Journal: The Analyst

    Article Title: Quantitative Paper Spray Mass Spectrometry Analysis of Drugs of Abuse

    doi: 10.1039/c3an00934c

    Figure Lengend Snippet: MS spectra (mass range: m/z 200–1000) by Orbitrap and MS/MS spectra (parent ion: m/z 316.1, mass range: 297.0–299.0 and 240.0–242.0) by TSQ for blank paper substrates subject to different treatments. (a) untreated 31 ET paper,

    Article Snippet: The MS spectra were recorded using an Exactive Orbitrap mass spectrometer (Exactive, Thermo Scientific, CA).

    Techniques: Mass Spectrometry

    Example of study design for iTRAQ ® protocol in the experimental rat model of invasive aspergillosis. Upper right panel , the iTRAQ ® reagent is designed as an isobaric stable tag consisting in a charged reporter group that retains charge (N,N-dimethylpiperazine), a peptide reactive group (N-hydoxy-succinimide) that is amide-linked to the N-terminus and the ε-amino side chains of all the peptides got from prior tryptic digestion, and a neutral balance portion (carbonyl) to maintain an overall mass of 305 kDa by the means of differential isotopic enrichment with 13 C, 15 N and 18 O atoms [ 33 ]. The selection of the reporter region in the low mass area enables keeping the additive mass to the fragments as negligible as possible in order to minimize any side effect during chromatographic separation and to avoid any interference with other fragment ions during mass spectrometry analysis, thus allowing for the highest degree of confidence; Main panel , after intra-tracheal challenge with bacterial lipopolysaccharides (LPS) or Aspergillus fumigatus conidia, rat samples were pooled according to their clinical status: healthy controls at baseline before intra-tracheal challenge in blood, non- Aspergillus inflammatory controls and Aspergillus -diseased cases, both in blood and in lung parenchyma for the last two groups [ 19 , 20 ]. Overabundant proteins, like albumin and immunoglobulins, were removed through a commercial kit before mass spectrometry analysis [ 23 , 56 ], and specific labelling with individuals tags, ranging from 113-iTRAQ ® to 117-iTRAQ ® reagents, was then applied to each pooled aliquot [ 16 ]. The reporter-balance peptides remained intact, so that for one given common protein, the five multiplexed rat samples had an identical m/z : the peptide fragments were equal, only the reporter ions were different. Indeed, the precursor ions, and all the internal fragment ions, i . e . type b- and y-ions respectively, contain all five members of the tag set, but remain isobaric, i . e . the five species have the same atomic mass but different arrangements. After collision in the QExactive ® Orbitrap mass spectrometry (MS) instrument, the five reporter group ions appeared as distinct masses ranging between m/z 113–117, while the remainder of the sequence-informative b- and–y ions remain isobaric and their individual current signal intensities were additive. The relative concentration of the peptides in every samples pool was then deduced from the relative signal intensities of the corresponding reporter ions. Protein identification was achieved by comparison of the peptide sequences with Specific SwissProt ® reviewed non-redundant database ( http://www.uniprot.org/uniprot/ ) of Rattus norvegicus (rat) proteome using the Sequest ® HT search engine (Washington DC, U.S.A.). Abbreviations : b-ion, Precursor ion; C, Carbon; Da, Dalton; MS, Mass spectrometry; m/z , Mass-to-charge ratio; O, Oxygen; N, Azote; y-ion, Internal ion; U.S.A., United States of America.

    Journal: PLoS ONE

    Article Title: Translational proteomic study to address host protein changes during aspergillosis

    doi: 10.1371/journal.pone.0200843

    Figure Lengend Snippet: Example of study design for iTRAQ ® protocol in the experimental rat model of invasive aspergillosis. Upper right panel , the iTRAQ ® reagent is designed as an isobaric stable tag consisting in a charged reporter group that retains charge (N,N-dimethylpiperazine), a peptide reactive group (N-hydoxy-succinimide) that is amide-linked to the N-terminus and the ε-amino side chains of all the peptides got from prior tryptic digestion, and a neutral balance portion (carbonyl) to maintain an overall mass of 305 kDa by the means of differential isotopic enrichment with 13 C, 15 N and 18 O atoms [ 33 ]. The selection of the reporter region in the low mass area enables keeping the additive mass to the fragments as negligible as possible in order to minimize any side effect during chromatographic separation and to avoid any interference with other fragment ions during mass spectrometry analysis, thus allowing for the highest degree of confidence; Main panel , after intra-tracheal challenge with bacterial lipopolysaccharides (LPS) or Aspergillus fumigatus conidia, rat samples were pooled according to their clinical status: healthy controls at baseline before intra-tracheal challenge in blood, non- Aspergillus inflammatory controls and Aspergillus -diseased cases, both in blood and in lung parenchyma for the last two groups [ 19 , 20 ]. Overabundant proteins, like albumin and immunoglobulins, were removed through a commercial kit before mass spectrometry analysis [ 23 , 56 ], and specific labelling with individuals tags, ranging from 113-iTRAQ ® to 117-iTRAQ ® reagents, was then applied to each pooled aliquot [ 16 ]. The reporter-balance peptides remained intact, so that for one given common protein, the five multiplexed rat samples had an identical m/z : the peptide fragments were equal, only the reporter ions were different. Indeed, the precursor ions, and all the internal fragment ions, i . e . type b- and y-ions respectively, contain all five members of the tag set, but remain isobaric, i . e . the five species have the same atomic mass but different arrangements. After collision in the QExactive ® Orbitrap mass spectrometry (MS) instrument, the five reporter group ions appeared as distinct masses ranging between m/z 113–117, while the remainder of the sequence-informative b- and–y ions remain isobaric and their individual current signal intensities were additive. The relative concentration of the peptides in every samples pool was then deduced from the relative signal intensities of the corresponding reporter ions. Protein identification was achieved by comparison of the peptide sequences with Specific SwissProt ® reviewed non-redundant database ( http://www.uniprot.org/uniprot/ ) of Rattus norvegicus (rat) proteome using the Sequest ® HT search engine (Washington DC, U.S.A.). Abbreviations : b-ion, Precursor ion; C, Carbon; Da, Dalton; MS, Mass spectrometry; m/z , Mass-to-charge ratio; O, Oxygen; N, Azote; y-ion, Internal ion; U.S.A., United States of America.

    Article Snippet: Then, the eluates were individually run in a QExactive® Orbitrap mass spectrometer (ThermoFisher Scientific, Pittsburg, PA, U.S.A.) in a data-dependent mode, with an automatic gain control target of 1.0x106 for full MS at 70,000 resolution, and of 2.0x105 for dd-MS2 at 17,500 resolution in positive mode.

    Techniques: Selection, Mass Spectrometry, Sequencing, Concentration Assay

    Metabolic Labeling and Workflow. ( A ) Glucose, acetate, fatty acids, and amino acids produce acetyl-CoA for use in acetylating cytoplasmic and nuclear proteins. The thicker arrows indicate that glucose contributes more to the production of acetyl-coA that subsequently acetylates proteins, compared to acetate. ( B ) The workflow consisted of growing HeLa cells in heavy-labeled media, collecting samples at eight time points, lysing the cells, digesting the proteins, enriching for acetylated peptides, and analyzing the peptides by mass spectrometry. The Orbitrap image is adapted from Thermo Fisher Scientific 56 . The cartoon cell matter and lab equipment were slightly modified from Servier Medical Art 57 .

    Journal: Scientific Reports

    Article Title: Proteome-wide acetylation dynamics in human cells

    doi: 10.1038/s41598-017-09918-3

    Figure Lengend Snippet: Metabolic Labeling and Workflow. ( A ) Glucose, acetate, fatty acids, and amino acids produce acetyl-CoA for use in acetylating cytoplasmic and nuclear proteins. The thicker arrows indicate that glucose contributes more to the production of acetyl-coA that subsequently acetylates proteins, compared to acetate. ( B ) The workflow consisted of growing HeLa cells in heavy-labeled media, collecting samples at eight time points, lysing the cells, digesting the proteins, enriching for acetylated peptides, and analyzing the peptides by mass spectrometry. The Orbitrap image is adapted from Thermo Fisher Scientific 56 . The cartoon cell matter and lab equipment were slightly modified from Servier Medical Art 57 .

    Article Snippet: Acetylated peptides were then enriched using anti-acetyl-lysine antibodies and run on nano liquid chromatography coupled online with tandem mass spectrometry (nanoLC-MS/MS) on an Orbitrap Fusion mass spectrometer (Thermo Fisher Scientific), which allows for detection of isotope incorporation into acetylated proteins.

    Techniques: Labeling, Mass Spectrometry, Modification