Structured Review

Thermo Fisher hplc ms
Selectivity and activity changes in selected variant enzymes as assessed using coupled assays Nucleoside production was measured via <t>HPLC/MS</t> analysis ( a ) from in situ generated sugar 1-phosphates in one step biocatalysis (PNP only), ( b ) from sugar 5-phosphates in the two-step tandem pathway (PPM and PNP) or ( c ) from ribose or <t>dideoxyribose</t> in the full biosynthetic pathway (RK, PPM and PNP) or the pathway without PPM. Enzyme variants used in each reaction are listed under bars (dashed line means no variant included). Direct phosphorylation of the sugar C1 position by wild-type RK in panel ( c , second from right) was tested in tandem with wild-type PNP for inosine production and PNP-46D6 for didanosine production to allow the best detection of activity. Turnover in panel ( a ) was normalized to PNP variant concentration and assay length. Production in panel ( b ) was normalized to incubation time. The full inosine pathway in ( c ) was incubated for 5 min, while didanosine production was for 10 h. Reactions in ( c ) without PPM were incubated for 10 h, however inosine production was normalized to 5 min to be directly comparable to production by the full pathway with PPM. Data are mean ± s.d. (n=2).
Hplc Ms, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 145 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Images

1) Product Images from "Bioretrosynthetic construction of a didanosine biosynthetic pathway"

Article Title: Bioretrosynthetic construction of a didanosine biosynthetic pathway

Journal: Nature chemical biology

doi: 10.1038/nchembio.1494

Selectivity and activity changes in selected variant enzymes as assessed using coupled assays Nucleoside production was measured via HPLC/MS analysis ( a ) from in situ generated sugar 1-phosphates in one step biocatalysis (PNP only), ( b ) from sugar 5-phosphates in the two-step tandem pathway (PPM and PNP) or ( c ) from ribose or dideoxyribose in the full biosynthetic pathway (RK, PPM and PNP) or the pathway without PPM. Enzyme variants used in each reaction are listed under bars (dashed line means no variant included). Direct phosphorylation of the sugar C1 position by wild-type RK in panel ( c , second from right) was tested in tandem with wild-type PNP for inosine production and PNP-46D6 for didanosine production to allow the best detection of activity. Turnover in panel ( a ) was normalized to PNP variant concentration and assay length. Production in panel ( b ) was normalized to incubation time. The full inosine pathway in ( c ) was incubated for 5 min, while didanosine production was for 10 h. Reactions in ( c ) without PPM were incubated for 10 h, however inosine production was normalized to 5 min to be directly comparable to production by the full pathway with PPM. Data are mean ± s.d. (n=2).
Figure Legend Snippet: Selectivity and activity changes in selected variant enzymes as assessed using coupled assays Nucleoside production was measured via HPLC/MS analysis ( a ) from in situ generated sugar 1-phosphates in one step biocatalysis (PNP only), ( b ) from sugar 5-phosphates in the two-step tandem pathway (PPM and PNP) or ( c ) from ribose or dideoxyribose in the full biosynthetic pathway (RK, PPM and PNP) or the pathway without PPM. Enzyme variants used in each reaction are listed under bars (dashed line means no variant included). Direct phosphorylation of the sugar C1 position by wild-type RK in panel ( c , second from right) was tested in tandem with wild-type PNP for inosine production and PNP-46D6 for didanosine production to allow the best detection of activity. Turnover in panel ( a ) was normalized to PNP variant concentration and assay length. Production in panel ( b ) was normalized to incubation time. The full inosine pathway in ( c ) was incubated for 5 min, while didanosine production was for 10 h. Reactions in ( c ) without PPM were incubated for 10 h, however inosine production was normalized to 5 min to be directly comparable to production by the full pathway with PPM. Data are mean ± s.d. (n=2).

Techniques Used: Activity Assay, Variant Assay, High Performance Liquid Chromatography, Mass Spectrometry, In Situ, Generated, Concentration Assay, Incubation

2) Product Images from "Ageing adversely affects the migration and function of marginal zone B cells"

Article Title: Ageing adversely affects the migration and function of marginal zone B cells

Journal: Immunology

doi: 10.1111/imm.12737

Altered chemotaxis of aged B cells to CXCL 13 and sphingosine 1‐phosphate (S1P). (a) Chemotactic response of follicular (B220 + CD 93 − CD 21 mid CD 23 hi ), marginal zone (B220 + CD 93 − CD 21 hi CD 23 lo ) and CD 21/35 − CD 23 − (B220 + CD 93 − CD 21 lo CD 23 lo ) B‐cell populations to indicated concentration of CXCL 13 or S1P presented as the percentage of input of cells that have migrated through transwells into the lower chamber in a 4‐hr assay. Input cells were equal numbers of cells pooled from three young and three old mice and technical replicates are shown. Data are representative of two repeats and results were analysed via two‐way analysis of variance with Sidak's post‐test. Median fluorescence intensity of S1P 1 (b) or CXCR 5 (c) on follicular (B220 + CD 93 − CD 21 mid CD 23 hi ), marginal zone (B220 + CD 93 − CD 21 hi CD 23 lo ) and CD 21/35 − CD 23 − (B220 + CD 93 − CD 21 lo CD 23 lo ) B‐cell populations from young and aged mice. Results were analysed using t ‐test, n = 3 per group. (d) Concentration of S1P in the serum of young and aged mice, measured with HPLC . Results were analysed using Mann–Whitney U‐ test, there was no significant difference. n = 12 young mice and 22 old mice. (e) CXCL 13 area in the follicle of spleens from young and aged mice. Results were analysed via Mann–Whitney U ‐test, there was no significant difference, n = 3 to n = 6 mice per group. (f) Representative histological staining of CXCL 13 on young and aged spleens. Scale bars = 250 μ m . *** P
Figure Legend Snippet: Altered chemotaxis of aged B cells to CXCL 13 and sphingosine 1‐phosphate (S1P). (a) Chemotactic response of follicular (B220 + CD 93 − CD 21 mid CD 23 hi ), marginal zone (B220 + CD 93 − CD 21 hi CD 23 lo ) and CD 21/35 − CD 23 − (B220 + CD 93 − CD 21 lo CD 23 lo ) B‐cell populations to indicated concentration of CXCL 13 or S1P presented as the percentage of input of cells that have migrated through transwells into the lower chamber in a 4‐hr assay. Input cells were equal numbers of cells pooled from three young and three old mice and technical replicates are shown. Data are representative of two repeats and results were analysed via two‐way analysis of variance with Sidak's post‐test. Median fluorescence intensity of S1P 1 (b) or CXCR 5 (c) on follicular (B220 + CD 93 − CD 21 mid CD 23 hi ), marginal zone (B220 + CD 93 − CD 21 hi CD 23 lo ) and CD 21/35 − CD 23 − (B220 + CD 93 − CD 21 lo CD 23 lo ) B‐cell populations from young and aged mice. Results were analysed using t ‐test, n = 3 per group. (d) Concentration of S1P in the serum of young and aged mice, measured with HPLC . Results were analysed using Mann–Whitney U‐ test, there was no significant difference. n = 12 young mice and 22 old mice. (e) CXCL 13 area in the follicle of spleens from young and aged mice. Results were analysed via Mann–Whitney U ‐test, there was no significant difference, n = 3 to n = 6 mice per group. (f) Representative histological staining of CXCL 13 on young and aged spleens. Scale bars = 250 μ m . *** P

Techniques Used: Chemotaxis Assay, Concentration Assay, Mouse Assay, Fluorescence, High Performance Liquid Chromatography, MANN-WHITNEY, Staining

3) Product Images from "The Bulk of Autotaxin Activity Is Dispensable for Adult Mouse Life"

Article Title: The Bulk of Autotaxin Activity Is Dispensable for Adult Mouse Life

Journal: PLoS ONE

doi: 10.1371/journal.pone.0143083

Tmx-induced (180 mg/kg PO) R26Cre-ER T2 -mediated genetic ablation of ATX results in diminished ATX levels in tissues and plasma. (A) Real-Time RT-PCR analysis of relative ATX mRNA expression levels in different tissues normalized to the expression levels of B2M. (n = 5–10; exp = 2; with the exception of BAT/WAT n = 4, exp = 1). (B) Real-Time RT-PCR analysis of ATX mRNA expression levels, normalized to the expression levels of B2M, in different tissues following Tmx-induced genetic ablation of the Enpp2 gene. (n = 5–10; exp = 2; with the exception of BAT/WAT n = 4, exp = 1). (C) Section from a western blot for ATX (4F1 Ab) in the plasma of the indicated mice. The full images, together with a coomassie brilliant blue staining of the same samples as loading control, and an alternate blot with a commercial antibody can be found at S7 Fig (D) Plasma ATX activity in the plasma of the indicated mice as determined with the TOOS assay on natural LPC substrates (n = 13–27; exp = 3). (E) Plasma LPA levels of the indicated mice as determined by HPLC-MS/MS (n = 9–13; exp = 2). (D) Plasma lysophospholipid (LPLs) levels remain unchanged as measured with HPLC-MS/ MS (n = 9–13; exp = 2). All values in every panel are means (± SEM) and are presented (except A) normalised (%) to control values.
Figure Legend Snippet: Tmx-induced (180 mg/kg PO) R26Cre-ER T2 -mediated genetic ablation of ATX results in diminished ATX levels in tissues and plasma. (A) Real-Time RT-PCR analysis of relative ATX mRNA expression levels in different tissues normalized to the expression levels of B2M. (n = 5–10; exp = 2; with the exception of BAT/WAT n = 4, exp = 1). (B) Real-Time RT-PCR analysis of ATX mRNA expression levels, normalized to the expression levels of B2M, in different tissues following Tmx-induced genetic ablation of the Enpp2 gene. (n = 5–10; exp = 2; with the exception of BAT/WAT n = 4, exp = 1). (C) Section from a western blot for ATX (4F1 Ab) in the plasma of the indicated mice. The full images, together with a coomassie brilliant blue staining of the same samples as loading control, and an alternate blot with a commercial antibody can be found at S7 Fig (D) Plasma ATX activity in the plasma of the indicated mice as determined with the TOOS assay on natural LPC substrates (n = 13–27; exp = 3). (E) Plasma LPA levels of the indicated mice as determined by HPLC-MS/MS (n = 9–13; exp = 2). (D) Plasma lysophospholipid (LPLs) levels remain unchanged as measured with HPLC-MS/ MS (n = 9–13; exp = 2). All values in every panel are means (± SEM) and are presented (except A) normalised (%) to control values.

Techniques Used: Quantitative RT-PCR, Expressing, Western Blot, Mouse Assay, Staining, Activity Assay, High Performance Liquid Chromatography, Mass Spectrometry

4) Product Images from "Tissue Distribution of 5-Hydroxymethylcytosine and Search for Active Demethylation Intermediates"

Article Title: Tissue Distribution of 5-Hydroxymethylcytosine and Search for Active Demethylation Intermediates

Journal: PLoS ONE

doi: 10.1371/journal.pone.0015367

Detection of potential demethylation intermediates caC, hmU, and fC. A) HPLC-chromatogram of the synthesized cytosine and uracil modifications caC, hmC, hmU, mC, and fC as 2′-deoxynucleosides showing excellent separation of the compounds. B) Detected values of the potential intermediates as example in olfactory bulb. The red line indicates the detection limits of the modified nucleosides in enzymatically digested DNA samples.
Figure Legend Snippet: Detection of potential demethylation intermediates caC, hmU, and fC. A) HPLC-chromatogram of the synthesized cytosine and uracil modifications caC, hmC, hmU, mC, and fC as 2′-deoxynucleosides showing excellent separation of the compounds. B) Detected values of the potential intermediates as example in olfactory bulb. The red line indicates the detection limits of the modified nucleosides in enzymatically digested DNA samples.

Techniques Used: High Performance Liquid Chromatography, Synthesized, Modification

5) Product Images from "Obesity is associated with changes in oxysterol metabolism and levels in mice liver, hypothalamus, adipose tissue and plasma"

Article Title: Obesity is associated with changes in oxysterol metabolism and levels in mice liver, hypothalamus, adipose tissue and plasma

Journal: Scientific Reports

doi: 10.1038/srep19694

Plasmatic oxysterol levels during the development of diet-induced obesity. Oxysterol levels were quantified by HPLC-MS in mouse plasma of the diet-induced obesity model. At each time-point (i.e. 1; 2; 4; 6; 8 and 16 weeks) a control and a high-fat group were sacrificed. The data are reported as percentage of each respective control group (shown as a dotted line). Data are mean ± s.e.m. Student’s t-test between HFD group and the respective CTL group. *P
Figure Legend Snippet: Plasmatic oxysterol levels during the development of diet-induced obesity. Oxysterol levels were quantified by HPLC-MS in mouse plasma of the diet-induced obesity model. At each time-point (i.e. 1; 2; 4; 6; 8 and 16 weeks) a control and a high-fat group were sacrificed. The data are reported as percentage of each respective control group (shown as a dotted line). Data are mean ± s.e.m. Student’s t-test between HFD group and the respective CTL group. *P

Techniques Used: High Performance Liquid Chromatography, Mass Spectrometry, CTL Assay

Hepatic oxysterol levels and expression of their metabolic enzymes during the development of diet-induced obesity. Schematic representation of the main metabolic steps involved in the synthesis and degradation of the oxysterols measured throughout the HFD study in the liver. The figure shows the variations in oxysterol levels and mRNA expression of their metabolic enzymes, compared to the respective control mice, at the different time-points throughout the study. At each time-point (i.e. 1; 2; 4; 6; 8 and 16 weeks) a control and a high-fat group were sacrificed. Oxysterol levels were quantified by HPLC-MS and mRNA enzyme expression was measured by qRT-PCR. Red color indicates an increase and blue color indicates a decrease of the HFD group compared to control group. Data (mean ± s.e.m) are reported in Table S2 . Student’s t-test between HFD group and the respective CTL group. *P
Figure Legend Snippet: Hepatic oxysterol levels and expression of their metabolic enzymes during the development of diet-induced obesity. Schematic representation of the main metabolic steps involved in the synthesis and degradation of the oxysterols measured throughout the HFD study in the liver. The figure shows the variations in oxysterol levels and mRNA expression of their metabolic enzymes, compared to the respective control mice, at the different time-points throughout the study. At each time-point (i.e. 1; 2; 4; 6; 8 and 16 weeks) a control and a high-fat group were sacrificed. Oxysterol levels were quantified by HPLC-MS and mRNA enzyme expression was measured by qRT-PCR. Red color indicates an increase and blue color indicates a decrease of the HFD group compared to control group. Data (mean ± s.e.m) are reported in Table S2 . Student’s t-test between HFD group and the respective CTL group. *P

Techniques Used: Expressing, Mouse Assay, High Performance Liquid Chromatography, Mass Spectrometry, Quantitative RT-PCR, CTL Assay

Oxysterol levels in the liver, plasma and adipose tissue of the ob/ob genetic model of obesity. Oxysterol levels were quantified by HPLC-MS in ( a ) the liver, ( b ) the plasma and ( c ) the adipose tissue in the ob/ob model. The data are reported as percentage of the control group (ob/lean) (shown as a dotted line). Data are mean ± s.e.m.; student’s t-test between ob/ob group and the ob/lean group *P
Figure Legend Snippet: Oxysterol levels in the liver, plasma and adipose tissue of the ob/ob genetic model of obesity. Oxysterol levels were quantified by HPLC-MS in ( a ) the liver, ( b ) the plasma and ( c ) the adipose tissue in the ob/ob model. The data are reported as percentage of the control group (ob/lean) (shown as a dotted line). Data are mean ± s.e.m.; student’s t-test between ob/ob group and the ob/lean group *P

Techniques Used: High Performance Liquid Chromatography, Mass Spectrometry

Adipose tissue oxysterol levels during the development of diet-induced obesity. Oxysterol levels were quantified by HPLC-MS in mouse subcutaneous adipose tissue of the diet-induced obesity model. At each time-point (i.e. 1; 2; 4; 6; 8 and 16 weeks) a control and a high-fat group were sacrificed. The data are reported as percentage of each respective control group (shown as a dotted line). Data are mean ± s.e.m. Student’s t-test between HFD group and the respective CTL group. *P
Figure Legend Snippet: Adipose tissue oxysterol levels during the development of diet-induced obesity. Oxysterol levels were quantified by HPLC-MS in mouse subcutaneous adipose tissue of the diet-induced obesity model. At each time-point (i.e. 1; 2; 4; 6; 8 and 16 weeks) a control and a high-fat group were sacrificed. The data are reported as percentage of each respective control group (shown as a dotted line). Data are mean ± s.e.m. Student’s t-test between HFD group and the respective CTL group. *P

Techniques Used: High Performance Liquid Chromatography, Mass Spectrometry, CTL Assay

Hypothalamic oxysterol levels and expression of their metabolic enzymes during the development of diet-induced obesity. Schematic representation of the main metabolic steps involved in the synthesis and degradation of the oxysterols measured throughout the HFD study in the hypothalamus. The figure shows the variations in oxysterol levels and mRNA expression of their metabolic enzymes, compared to the respective control mice, at the different time-points throughout the study. At each time-point (i.e. 1; 2; 4; 6; 8 and 16 weeks) a normal diet (control) and a high-fat group were sacrificed. Oxysterol levels were quantified by HPLC-MS and mRNA enzyme expression was measured by qRT-PCR. Red color indicates an increase and blue color indicates a decrease of the HFD group compared to control group. Data (mean ± s.e.m) are reported in Table S1 . Student’s t-test between HFD group and the respective CTL group. *P
Figure Legend Snippet: Hypothalamic oxysterol levels and expression of their metabolic enzymes during the development of diet-induced obesity. Schematic representation of the main metabolic steps involved in the synthesis and degradation of the oxysterols measured throughout the HFD study in the hypothalamus. The figure shows the variations in oxysterol levels and mRNA expression of their metabolic enzymes, compared to the respective control mice, at the different time-points throughout the study. At each time-point (i.e. 1; 2; 4; 6; 8 and 16 weeks) a normal diet (control) and a high-fat group were sacrificed. Oxysterol levels were quantified by HPLC-MS and mRNA enzyme expression was measured by qRT-PCR. Red color indicates an increase and blue color indicates a decrease of the HFD group compared to control group. Data (mean ± s.e.m) are reported in Table S1 . Student’s t-test between HFD group and the respective CTL group. *P

Techniques Used: Expressing, Mouse Assay, High Performance Liquid Chromatography, Mass Spectrometry, Quantitative RT-PCR, CTL Assay

Related Articles

Fluorescence:

Article Title: Glucose-6-Phosphate Dehydrogenase Protects Escherichia coli from Tellurite-Mediated Oxidative Stress
Article Snippet: .. Fluorescence intensity was determined using an Applied Biosystems equipment CytoFluor 4000 Fluorescence Multi-well Plate Reader (excitation 490 nm, emission 519 nm) and normalized to protein concentration as described earlier , . .. Assessing intracellular ROS by flow cytometry was performed in the same way with minor modifications.

Blocking Assay:

Article Title: Neonatal Hyperoxic Exposure Persistently Alters Lung Secretoglobins and Annexin A1
Article Snippet: .. Following blocking with 10% dry milk in tris-buffered saline with Tween 20 (TBS-T), membranes were probed for CCSP or ANXA1 using polyclonal rabbit anti-human CCSP (1 : 5000 in TBS-T; Seven Hills Bioreagents, Cincinnati, OH) or rabbit anti-human ANXA1 (1 : 4000 in TBS-T; Invitrogen) primary antibodies which cross-react with murine CCSP and ANXA1, respectively. .. Peroxidase-conjugated goat anti-rabbit IgG secondary antibodies (1 : 12,000 in TBS-T; BioRad) were then used.

other:

Article Title: Spns2, a transporter of phosphorylated sphingoid bases, regulates their blood and lymph levels, and the lymphatic network
Article Snippet: Internal standards (0.5 nmol each; Avanti Polar Lipids, Alabaster, AL, USA) were added to samples, lipids were extracted, and sphingolipids were quantified by LC-ESI-MS/MS (ABI 4000 QTrap system; Applied Biosystems, Foster City, CA, USA) as described previously ( ).

Mass Spectrometry:

Article Title: Quantitative analysis of sphingolipids for lipidomics using triple quadrupole and quadrupole linear ion trap mass spectrometers [S]
Article Snippet: .. Two systems were used for these analyses: a Perkin Elmer Series 200 MicroPump system coupled to a PE Sciex API 3000 triple quadrupole (QQQ) mass spectrometer (Applied Biosystems, Foster City, CA), and a Shimadzu LC-10 AD VP binary pump system coupled to a Perkin Elmer Series 200 autoinjector coupled to a 4000 quadrupole linear-ion trap (QTrap) (Applied Biosystems, Foster City, CA) operating in a triple quadrupole mode. .. For both instruments, Q1 and Q3 were set to pass molecularly distinctive precursor and product ions (or a scan across multiple m/z in Q1 or Q3), using N2 to collisionally induce dissociations in Q2 (which was offset from Q1 by 30–120 eV); the ion source temperature varied between 300 and 500°C depending on solvent composition and mass spectrometer.

Protein Concentration:

Article Title: Glucose-6-Phosphate Dehydrogenase Protects Escherichia coli from Tellurite-Mediated Oxidative Stress
Article Snippet: .. Fluorescence intensity was determined using an Applied Biosystems equipment CytoFluor 4000 Fluorescence Multi-well Plate Reader (excitation 490 nm, emission 519 nm) and normalized to protein concentration as described earlier , . .. Assessing intracellular ROS by flow cytometry was performed in the same way with minor modifications.

Western Blot:

Article Title: POTENTIAL ROLE OF H-FERRITIN IN MITIGATING VALVULAR MINERALIZATION
Article Snippet: .. Western blot analysis for ENPP2 was performed using anti-human ENPP2 (Thermo Fisher Scientific; PA5–12478; 4000 ng/mL). .. Sox9 Western blot was performed with rabbit anti-human Sox9 (Abcam; ab26414; 2000 ng/mL).

Staining:

Article Title: Effects of connexin-mimetic peptides on gap junction functionality and connexin expression in cultured vascular cells
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    Thermo Fisher hplc ms ms
    Genotoxicity of PhIP in Apc +/+ and Apc Min/+ cell lines. Apc +/+ and Apc Min/+ cells were treated with the indicated concentrations of PhIP for 24 h. (A) Genotoxicity was evaluated by <t>HPLC-MS/MS</t> quantification of <t>dG-C8-PhIP</t> in DNA. (B) Genotoxicity was evaluated with γHAX ICW assay. Bars represent the average of at least three independent experiments with SEM. Statistically significant increase in H2AX phosphorylation compared with DMSO control using Student’s test; *, p
    Hplc Ms Ms, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 94/100, based on 114 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher high performance liquid chromatography mass spectrometry hplc ms hplc programs
    Category of <t>HPLC-MS-identified</t> <t>glycylglycerins.</t> In human iPSCs, the glycylation of glycerin forms three different kinds of glycylglycerins, including monoglycylglycerins (MGG), diglycylglycerins (DGG) and triglycylglycerin (TGG). All these glycylglycerins carry positive charges in their amino groups at ≤pH 7.0 and can form isoforms as shown in the right bottom corner box.
    High Performance Liquid Chromatography Mass Spectrometry Hplc Ms Hplc Programs, 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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    Thermo Fisher hplc esi ms ms analysis
    Summary of primer extension products formed by hpol κ as identified by capillary <t>HPLC-ESI-MS/MS.</t>
    Hplc Esi Ms Ms Analysis, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 89/100, based on 17 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Genotoxicity of PhIP in Apc +/+ and Apc Min/+ cell lines. Apc +/+ and Apc Min/+ cells were treated with the indicated concentrations of PhIP for 24 h. (A) Genotoxicity was evaluated by HPLC-MS/MS quantification of dG-C8-PhIP in DNA. (B) Genotoxicity was evaluated with γHAX ICW assay. Bars represent the average of at least three independent experiments with SEM. Statistically significant increase in H2AX phosphorylation compared with DMSO control using Student’s test; *, p

    Journal: PLoS ONE

    Article Title: Combined Genotoxic Effects of a Polycyclic Aromatic Hydrocarbon (B(a)P) and an Heterocyclic Amine (PhIP) in Relation to Colorectal Carcinogenesis

    doi: 10.1371/journal.pone.0058591

    Figure Lengend Snippet: Genotoxicity of PhIP in Apc +/+ and Apc Min/+ cell lines. Apc +/+ and Apc Min/+ cells were treated with the indicated concentrations of PhIP for 24 h. (A) Genotoxicity was evaluated by HPLC-MS/MS quantification of dG-C8-PhIP in DNA. (B) Genotoxicity was evaluated with γHAX ICW assay. Bars represent the average of at least three independent experiments with SEM. Statistically significant increase in H2AX phosphorylation compared with DMSO control using Student’s test; *, p

    Article Snippet: The dG-C8-PhIP adducts were quantified by HPLC-MS/MS using of a Surveyor HPLC pump (Thermo Scientific, Les Ullis, France) associated with a TSQ Quantum Discovery Max triple quadrupole (Thermo Scientific, Les Ullis, France).

    Techniques: High Performance Liquid Chromatography, Mass Spectrometry

    Synergic genotoxicity of B( a )P and PhIP in Apc +/+ and Apc Min/+ cell lines. Apc +/+ and Apc Min/+ cells were treated with the indicated concentrations of BaP and PhIP for 24 h. (A) Genotoxicity was evaluated by quantification by HPLC-MS/MS quantification of B( a )P- and PhIP-derived DNA adducts. (B) Genotoxicity was evaluated with γHAX ICW assay. Bars represent the average of at least three independent experiments with SEM. Statistically significant increase in H2AX phosphorylation compared with DMSO control using Student’s test; **, p

    Journal: PLoS ONE

    Article Title: Combined Genotoxic Effects of a Polycyclic Aromatic Hydrocarbon (B(a)P) and an Heterocyclic Amine (PhIP) in Relation to Colorectal Carcinogenesis

    doi: 10.1371/journal.pone.0058591

    Figure Lengend Snippet: Synergic genotoxicity of B( a )P and PhIP in Apc +/+ and Apc Min/+ cell lines. Apc +/+ and Apc Min/+ cells were treated with the indicated concentrations of BaP and PhIP for 24 h. (A) Genotoxicity was evaluated by quantification by HPLC-MS/MS quantification of B( a )P- and PhIP-derived DNA adducts. (B) Genotoxicity was evaluated with γHAX ICW assay. Bars represent the average of at least three independent experiments with SEM. Statistically significant increase in H2AX phosphorylation compared with DMSO control using Student’s test; **, p

    Article Snippet: The dG-C8-PhIP adducts were quantified by HPLC-MS/MS using of a Surveyor HPLC pump (Thermo Scientific, Les Ullis, France) associated with a TSQ Quantum Discovery Max triple quadrupole (Thermo Scientific, Les Ullis, France).

    Techniques: High Performance Liquid Chromatography, Mass Spectrometry, Derivative Assay

    Detection of Ppc-1 in cells and tissues. (A) RPE cells were treated with 10 μM Ppc-1 for 12 h, and then lipid fraction was prepared from cells, and analyzed on HPLC-MS/MS system B. The positions of Ppc-1 ([M+H] + = 356.19 m/z ) and its derivatives are indicated. (B) Sera and tissues were collected from mice at the time points indicated after a single shot of Ppc-1 (0.8 mg/kg), and the lipid fraction was prepared and analyzed similarly. The peak areas were calculated, and the results are expressed as mean and SD.

    Journal: PLoS ONE

    Article Title: Weight Loss by Ppc-1, a Novel Small Molecule Mitochondrial Uncoupler Derived from Slime Mold

    doi: 10.1371/journal.pone.0117088

    Figure Lengend Snippet: Detection of Ppc-1 in cells and tissues. (A) RPE cells were treated with 10 μM Ppc-1 for 12 h, and then lipid fraction was prepared from cells, and analyzed on HPLC-MS/MS system B. The positions of Ppc-1 ([M+H] + = 356.19 m/z ) and its derivatives are indicated. (B) Sera and tissues were collected from mice at the time points indicated after a single shot of Ppc-1 (0.8 mg/kg), and the lipid fraction was prepared and analyzed similarly. The peak areas were calculated, and the results are expressed as mean and SD.

    Article Snippet: For the detection of Ppc-1, the extracts were analyzed on HPLC-MS/MS system B (HPLC, UltiMate 3000; MS, Orbitrap, Thermo Scientific) controlled by XCALIBUR.

    Techniques: High Performance Liquid Chromatography, Mass Spectrometry, Mouse Assay

    Category of HPLC-MS-identified glycylglycerins. In human iPSCs, the glycylation of glycerin forms three different kinds of glycylglycerins, including monoglycylglycerins (MGG), diglycylglycerins (DGG) and triglycylglycerin (TGG). All these glycylglycerins carry positive charges in their amino groups at ≤pH 7.0 and can form isoforms as shown in the right bottom corner box.

    Journal: Nucleic Acids Research

    Article Title: Novel glycylated sugar alcohols protect ESC-specific microRNAs from degradation in iPS cells

    doi: 10.1093/nar/gkw186

    Figure Lengend Snippet: Category of HPLC-MS-identified glycylglycerins. In human iPSCs, the glycylation of glycerin forms three different kinds of glycylglycerins, including monoglycylglycerins (MGG), diglycylglycerins (DGG) and triglycylglycerin (TGG). All these glycylglycerins carry positive charges in their amino groups at ≤pH 7.0 and can form isoforms as shown in the right bottom corner box.

    Article Snippet: Analyses of glycylglycerins using high performance liquid chromatography—mass spectrometry (HPLC-MS) HPLC programs were run by an Ultimate 3000 HPLC machine (Thermo Scientific, Waltham, MA, USA) with a DNAPac PA-100 column (BioLC Semi-Prep 9 × 250 mm) at a flow rate of 3.6 ml/min.

    Techniques: High Performance Liquid Chromatography, Mass Spectrometry

    HPLC detection of glycylglycerin production and glycylglycerin-bound pre-miRNA. ( A ) HPLC analyses showed that production of glycylglycerins can naturally occur in a pure chemical reaction between glycine and glycerin at pH 6.8 in the presence of L-ascorbic acid (vit.C), but not in the same reaction at pH 7.3. ( B ) HPLC peak of DGG/TGG-mixed pre-miR-302a was shifted from 12.23 min at pH 7.3 (unbound) to 1.76 min at pH 6.8 (DGG/TGG-bound), indicating a marked loss of pre-miRNA negative charges after binding with DGG/TGG. After HPLC separation at pH 6.8, the DGG/TGG-bound pre-miR-302a was collected from the 1.7–1.8 min section of HPLC fragments and further used for MS analyses, as shown in Figure 7A . ( C ) Chemical 3D modeling of electro-binding between DGG/TGG and pre-miRNA/siRNA suggested that the long strand structures of 1,3-diglycylglycerin and 1,2,3-triglycylglycerin may fit into the minor grooves of the pre-miRNA/siRNA double helix structures and hence bind to the negatively charged phosphodiester-linkage backbones (green shadow) located in the minor grooves of pre-miRNA/siRNA via the positively charged amino groups of DGG/TGG, so as to form a layer of protective coating for preserving pre-miRNA/siRNA integrity.

    Journal: Nucleic Acids Research

    Article Title: Novel glycylated sugar alcohols protect ESC-specific microRNAs from degradation in iPS cells

    doi: 10.1093/nar/gkw186

    Figure Lengend Snippet: HPLC detection of glycylglycerin production and glycylglycerin-bound pre-miRNA. ( A ) HPLC analyses showed that production of glycylglycerins can naturally occur in a pure chemical reaction between glycine and glycerin at pH 6.8 in the presence of L-ascorbic acid (vit.C), but not in the same reaction at pH 7.3. ( B ) HPLC peak of DGG/TGG-mixed pre-miR-302a was shifted from 12.23 min at pH 7.3 (unbound) to 1.76 min at pH 6.8 (DGG/TGG-bound), indicating a marked loss of pre-miRNA negative charges after binding with DGG/TGG. After HPLC separation at pH 6.8, the DGG/TGG-bound pre-miR-302a was collected from the 1.7–1.8 min section of HPLC fragments and further used for MS analyses, as shown in Figure 7A . ( C ) Chemical 3D modeling of electro-binding between DGG/TGG and pre-miRNA/siRNA suggested that the long strand structures of 1,3-diglycylglycerin and 1,2,3-triglycylglycerin may fit into the minor grooves of the pre-miRNA/siRNA double helix structures and hence bind to the negatively charged phosphodiester-linkage backbones (green shadow) located in the minor grooves of pre-miRNA/siRNA via the positively charged amino groups of DGG/TGG, so as to form a layer of protective coating for preserving pre-miRNA/siRNA integrity.

    Article Snippet: Analyses of glycylglycerins using high performance liquid chromatography—mass spectrometry (HPLC-MS) HPLC programs were run by an Ultimate 3000 HPLC machine (Thermo Scientific, Waltham, MA, USA) with a DNAPac PA-100 column (BioLC Semi-Prep 9 × 250 mm) at a flow rate of 3.6 ml/min.

    Techniques: High Performance Liquid Chromatography, Binding Assay, Mass Spectrometry, Preserving

    Summary of primer extension products formed by hpol κ as identified by capillary HPLC-ESI-MS/MS.

    Journal: The Journal of Biological Chemistry

    Article Title: Translesion Synthesis across 1,N6-(2-Hydroxy-3-hydroxymethylpropan-1,3-diyl)-2?-deoxyadenosine (1,N6-?-HMHP-dA) Adducts by Human and Archebacterial DNA Polymerases *

    doi: 10.1074/jbc.M112.396788

    Figure Lengend Snippet: Summary of primer extension products formed by hpol κ as identified by capillary HPLC-ESI-MS/MS.

    Article Snippet: HPLC-ESI− -MS/MS analysis was conducted on an Eksigent HPLC system (Eksigent, Dublin, CA) interfaced to a Thermo LTQ Orbitrap Velos mass spectrometer (Thermo Fisher Scientific, Waltham, MA).

    Techniques: High Performance Liquid Chromatography, Mass Spectrometry

    HPLC-ESI − -MS/MS analysis of hpol κ in vitro replication products on 1, N 6 - γ - HMHP-dA-adduct containing template. Primer-template complexes (100 pmol) were incubated at 37 °C for 4 h in the presence of hpol κ (40 pmol)

    Journal: The Journal of Biological Chemistry

    Article Title: Translesion Synthesis across 1,N6-(2-Hydroxy-3-hydroxymethylpropan-1,3-diyl)-2?-deoxyadenosine (1,N6-?-HMHP-dA) Adducts by Human and Archebacterial DNA Polymerases *

    doi: 10.1074/jbc.M112.396788

    Figure Lengend Snippet: HPLC-ESI − -MS/MS analysis of hpol κ in vitro replication products on 1, N 6 - γ - HMHP-dA-adduct containing template. Primer-template complexes (100 pmol) were incubated at 37 °C for 4 h in the presence of hpol κ (40 pmol)

    Article Snippet: HPLC-ESI− -MS/MS analysis was conducted on an Eksigent HPLC system (Eksigent, Dublin, CA) interfaced to a Thermo LTQ Orbitrap Velos mass spectrometer (Thermo Fisher Scientific, Waltham, MA).

    Techniques: High Performance Liquid Chromatography, Mass Spectrometry, In Vitro, Incubation

    Summary of primer extension products formed by Dpo4 as identified by capillary HPLC-ESI-MS/MS.

    Journal: The Journal of Biological Chemistry

    Article Title: Translesion Synthesis across 1,N6-(2-Hydroxy-3-hydroxymethylpropan-1,3-diyl)-2?-deoxyadenosine (1,N6-?-HMHP-dA) Adducts by Human and Archebacterial DNA Polymerases *

    doi: 10.1074/jbc.M112.396788

    Figure Lengend Snippet: Summary of primer extension products formed by Dpo4 as identified by capillary HPLC-ESI-MS/MS.

    Article Snippet: HPLC-ESI− -MS/MS analysis was conducted on an Eksigent HPLC system (Eksigent, Dublin, CA) interfaced to a Thermo LTQ Orbitrap Velos mass spectrometer (Thermo Fisher Scientific, Waltham, MA).

    Techniques: High Performance Liquid Chromatography, Mass Spectrometry

    Summary of primer extension products formed by hpol η as identified by capillary HPLC-ESI-MS/MS.

    Journal: The Journal of Biological Chemistry

    Article Title: Translesion Synthesis across 1,N6-(2-Hydroxy-3-hydroxymethylpropan-1,3-diyl)-2?-deoxyadenosine (1,N6-?-HMHP-dA) Adducts by Human and Archebacterial DNA Polymerases *

    doi: 10.1074/jbc.M112.396788

    Figure Lengend Snippet: Summary of primer extension products formed by hpol η as identified by capillary HPLC-ESI-MS/MS.

    Article Snippet: HPLC-ESI− -MS/MS analysis was conducted on an Eksigent HPLC system (Eksigent, Dublin, CA) interfaced to a Thermo LTQ Orbitrap Velos mass spectrometer (Thermo Fisher Scientific, Waltham, MA).

    Techniques: High Performance Liquid Chromatography, Mass Spectrometry