Journal: bioRxiv

Article Title: Covalent Protein Painting Reveals Structural Changes in the Proteome in Alzheimer Disease

doi: 10.1101/2020.01.31.929117

Figure Lengend Snippet: Schematic of the CPP method. CPP includes in vivo chemical methylation of lysine residues at the surface of proteins and its detection with mass spectrometry. The flow chart shows each labeling step and the resultant relative measurement of surface accessibility for chemical modification based on mass spectrometric quantification of isotope labeled peptides. Proteins are labeled with isotope defined reagents at solvent exposed lysine residues (K) with two methyl moieties ( 13 CD 3 , heavy) in vivo . Protein are then digested in peptides with the endoproteinase Chymotrypsin, and all newly accessible primary amines labeled with two methyl moieties (CH 3 , light). Peptides are separated by liquid chromatography (LC) and transferred into gas phase by electrospray ionization (nano ESI). High mass resolution (Orbitrap) mass spectra (MS) and fragment ion mass spectra (MS/MS) are acquired. Peptides are identified with a database search using ProLuCID and quantified with Census. The “surfaces of all protein complexes” (SoPaX) algorithm within ProteinClusterQuant (PCQ) determines and compares the relative surface accessibility of lysine residues.

Article Snippet: Following chromatographic separation, peptides were transferred into an Orbitrap Lumos mass spectrometer by electrospray ionization (nanoEasy, Thermo Fisher Scientific).

Techniques: In Vivo, Methylation, Mass Spectrometry, Labeling, Modification, Liquid Chromatography, Tandem Mass Spectroscopy

Journal: Molecules : A Journal of Synthetic Chemistry and Natural Product Chemistry

Article Title: Hepatic Metabolism of Sakuranetin and Its Modulating Effects on Cytochrome P450s and UDP-Glucuronosyltransferases

doi: 10.3390/molecules23071542

Figure Lengend Snippet: HPLC-electrospray (ESI)-negative mass spectrum of metabolites of SKN dependent on NADPH, UDPGA, or both cofactors. Mass spectrum of SKN ( A ), mass spectrum of M1 ( B ), mass spectrum of M2 ( C ), mass spectrum of M3 ( D ), mass spectrum of M4 ( E ), mass spectrum of M5 ( F ), and mass spectrum of M6 ( G ) are shown. The metabolites are identified in Table 3 .

Article Snippet: LC-ESI-MS was performed with an LTQ linear ion trap mass spectrometer (Thermo Scientific, Waltham, MA, USA) with an ESI source, which was coupled with the Agilent HPLC system.

Techniques: High Performance Liquid Chromatography

Journal: Pharmacognosy Magazine

Article Title: Isolation and purification of schisandrol A from the stems of Schisandra chinensis and cytotoxicity against human hepatocarcinoma cell lines

doi: 10.4103/0973-1296.149726

Figure Lengend Snippet: Chemical structure and electrospray ionization-mass spectrometry spectra of schisandrol A

Article Snippet: Electrospray ionization-mass spectrometry was performed using Agilent 1100 Series LC-MS Trap SL (Agilent, USA).

Techniques: Mass Spectrometry

Journal: Chemical research in toxicology

Article Title: Exocyclic Deoxyadenosine Adducts of 1,2,3,4-Diepoxybutane: Synthesis, Structural Elucidation, and Mechanistic Studies

doi: 10.1021/tx900312e

Figure Lengend Snippet: Formation of exocyclic DEB-dA adducts in DNA in vitro and in vivo : capillary HPLC-ESI + MS/MS analysis of compounds 3 and 4 in enzymatic digests of calf thymus DNA treated with R,R DEB (A); S,S DEB (B); meso DEB (250 μM DEB, 24 h at 37 °C) (C); Concentration-dependent formation of exocyclic DEB-dA adducts 3 and 4 in calf thymus DNA treated with 0 – 1 mM DEB (24 h at 37 °C) (D); and capillary HPLC-ESI + MS/MS analysis of 3 and 4 in enzymatic digests of liver DNA from a B6C3F1 mouse exposed to 625 ppm butadiene for 2 weeks (E). No signals corresponding to 3 and 4 were observed in DNA digests from control animals.

Article Snippet: The majority of HPLC-ESI-MS experiments were performed with an Agilent 1100 capillary HPLC-ion trap mass spectrometer (Agilent Technologies, Inc.; Wilmington, DE).

Techniques: In Vitro, In Vivo, High Performance Liquid Chromatography, Mass Spectrometry, Concentration Assay

Journal: Nucleic Acids Research

Article Title: Quantitative analysis of the oxidative DNA lesion, 2,2-diamino-4-(2-deoxy-?-d-erythro-pentofuranosyl)amino]-5(2H)-oxazolone (oxazolone), in vitro and in vivo by isotope dilution-capillary HPLC-ESI-MS/MS

doi: 10.1093/nar/gkl596

Figure Lengend Snippet: Experimental scheme for HPLC-ESI-MS/MS analysis of 8-oxo-dG and oxazolone in DNA.

Article Snippet: Our HPLC-ESI-MS/MS method for 8-oxo-dG employed selected reaction monitoring of the transitions 284.2 [M + H]+ →168.2 [M + 2H − dR]+ (8-oxo-dG) and 289.2 [M + H]+ →173.2 [M + 2H − dR]+ (15 N5 –8-oxo-dG) on an Agilent 1100 capillary HPLC- Ion Trap MS system.

Techniques: High Performance Liquid Chromatography, Mass Spectrometry

Journal: Nucleic Acids Research

Article Title: Quantitative analysis of the oxidative DNA lesion, 2,2-diamino-4-(2-deoxy-?-d-erythro-pentofuranosyl)amino]-5(2H)-oxazolone (oxazolone), in vitro and in vivo by isotope dilution-capillary HPLC-ESI-MS/MS

doi: 10.1093/nar/gkl596

Figure Lengend Snippet: HPLC-ESI + -MS/MS analysis of oxazolone in enzymatic hydrolysates of rat liver DNA (300 μg) following off-line HPLC purification ( Scheme 2 ). An Agilent 1100 series capillary HPLC was interfaced to a Thermo-Finnigan TSQ Quantum Ultra mass spectrometer. A Thermo Hypersil-Keystone Hypercarb column (0.5 × 100 mm, 5 μm) was eluted at a flow rate of 12 μl/min with a gradient of isopropanol/acetonitrile (3:1) (solvent B) in 0.05% acetic acid (solvent A). The spray voltage was set to 3.1 kV, the source temperature was 250°C, and the sheath gas pressure was 30 psi. Quantitative analyses were performed in selected reaction monitoring mode using the transitions m/z 247.1→87.1 [M + 2H − dR − CO 2 ] + , and m/z 251.1→91.1 for oxazolone and 15 N 4 -oxazolone, respectively.

Article Snippet: Our HPLC-ESI-MS/MS method for 8-oxo-dG employed selected reaction monitoring of the transitions 284.2 [M + H]+ →168.2 [M + 2H − dR]+ (8-oxo-dG) and 289.2 [M + H]+ →173.2 [M + 2H − dR]+ (15 N5 –8-oxo-dG) on an Agilent 1100 capillary HPLC- Ion Trap MS system.

Techniques: High Performance Liquid Chromatography, Mass Spectrometry, Purification, Flow Cytometry

Journal: Nucleic Acids Research

Article Title: Quantitative analysis of the oxidative DNA lesion, 2,2-diamino-4-(2-deoxy-?-d-erythro-pentofuranosyl)amino]-5(2H)-oxazolone (oxazolone), in vitro and in vivo by isotope dilution-capillary HPLC-ESI-MS/MS

doi: 10.1093/nar/gkl596

Figure Lengend Snippet: HPLC-ESI + -MS/MS analysis of 8-oxo-dG in an enzymatic hydrolysate of rat liver DNA (80 μg). An Agilent 1100 series capillary HPLC-ion trap MS system was used. A Zorbax SB C18 column (0.5 × 150 mm, 5 (m) was maintained at 10°C and eluted at a flow rate of 12 (l/min with a gradient of methanol (solvent B) in 15 mM ammonium acetate (solvent A). The mass spectrometer was operated in the positive ion MS/MS mode. Quantitative analyses were performed in selected reaction monitoring mode using the transitions m/z 284.1→168.0 (M + 2H − dR) + for 8-oxo-dG and the corresponding transition m/z 289.1→173 for [ 15 N 5 ]-8-oxo-dG.

Article Snippet: Our HPLC-ESI-MS/MS method for 8-oxo-dG employed selected reaction monitoring of the transitions 284.2 [M + H]+ →168.2 [M + 2H − dR]+ (8-oxo-dG) and 289.2 [M + H]+ →173.2 [M + 2H − dR]+ (15 N5 –8-oxo-dG) on an Agilent 1100 capillary HPLC- Ion Trap MS system.

Techniques: High Performance Liquid Chromatography, Mass Spectrometry, Flow Cytometry

Journal: Chemical research in toxicology

Article Title: CROSS-LINKING OF THE HUMAN DNA REPAIR PROTEIN O6-ALKYLGUANINE DNA ALKYLTRANSFERASE TO DNA IN THE PRESENCE OF 1,2,3,4-DIEPOXYBUTANE

doi: 10.1021/tx0600088

Figure Lengend Snippet: HPLC-ESI + -MS analysis of C145A hAGT protein following treatment with dG monoepoxide. (A) HPLC-ESI + -MS of untreated C145A hAGT. Top : Total ion chromatogram; Bottom : ESI + mass spectrum of the 16.2 min protein peak; Inset : Deconvoluted mass spectrum of the 16.2 min peak (observed M = 23 015 Da, calculated M = 23 012 Da). (B) HPLC-ESI + -MS of C145A hAGT mutant following incubation dG monoepoxide. Top : Total ion chromatogram; Bottom : ESI + mass spectrum of the 16.1 min protein peak; Inset : Deconvoluted mass spectrum of the 16.1 min peak: A = C145A hAGT containing a single cross-link to dG (observed M = 23 367 Da, calculated M = 23 365 Da); B = unmodified protein (observed M = 23 014 Da, calculated M = 23 012 Da).

Article Snippet: HPLC-ESI+ -MS/MS analysis of hAGT and C145A hAGT tryptic peptides was performed using the same Agilent 1100 capillary HPLC-ion trap MS system.

Techniques: High Performance Liquid Chromatography, Mass Spectrometry, Mutagenesis, Incubation

Journal: Chemical research in toxicology

Article Title: CROSS-LINKING OF THE HUMAN DNA REPAIR PROTEIN O6-ALKYLGUANINE DNA ALKYLTRANSFERASE TO DNA IN THE PRESENCE OF 1,2,3,4-DIEPOXYBUTANE

doi: 10.1021/tx0600088

Figure Lengend Snippet: HPLC-ESI + -MS/MS analysis of 1-( S -cysteinyl)-4-(guan-7-yl)-2,3-butanediol (Cys-Gua-BD) in total digests of AGT protein treated with dG monoepoxide. (A) Extracted ion chromatogram of Cys-Gua-BD ( m/z 359.7 [M + H] + ) resulting from the total digestion of dG monoepoxide-treated hAGT; Inset : MS/MS fragmentation of Cys-Gua-BD. (B) Extracted ion chromatogram of Cys-Gua-BD ( m/z 359.4 [M + H] + ) resulting from the total digestion of dG monoepoxide-treated C145A hAGT; Inset : MS/MS fragmentation of Cys-Gua-BD.

Article Snippet: HPLC-ESI+ -MS/MS analysis of hAGT and C145A hAGT tryptic peptides was performed using the same Agilent 1100 capillary HPLC-ion trap MS system.

Techniques: High Performance Liquid Chromatography, Mass Spectrometry

Journal: Chemical research in toxicology

Article Title: CROSS-LINKING OF THE HUMAN DNA REPAIR PROTEIN O6-ALKYLGUANINE DNA ALKYLTRANSFERASE TO DNA IN THE PRESENCE OF 1,2,3,4-DIEPOXYBUTANE

doi: 10.1021/tx0600088

Figure Lengend Snippet: HPLC-ESI + -MS/MS analysis of hAGT tryptic peptides G 136 NPVPILIPCHR 147 and V 148 VCSSGGAVGNYSGGLAVK 165 containing DEB-induced 2′,3′,4′-trihydroxybut-1′-yl adducts to active site cysteine residues Cys 145 (A) and Cys 150 (B). Top: Extracted ion chromatograms; Bottom : MS/MS spectra. Modified fragment ions are indicated by “*”.

Article Snippet: HPLC-ESI+ -MS/MS analysis of hAGT and C145A hAGT tryptic peptides was performed using the same Agilent 1100 capillary HPLC-ion trap MS system.

Techniques: High Performance Liquid Chromatography, Mass Spectrometry, Modification

Journal: Chemical research in toxicology

Article Title: CROSS-LINKING OF THE HUMAN DNA REPAIR PROTEIN O6-ALKYLGUANINE DNA ALKYLTRANSFERASE TO DNA IN THE PRESENCE OF 1,2,3,4-DIEPOXYBUTANE

doi: 10.1021/tx0600088

Figure Lengend Snippet: HPLC-ESI + -MS/MS analysis of hAGT tryptic peptide V 148 VCSSGGAVGNYSG GLAVK 165 containing dG monoepoxide-induced butanediol cross-link between Cys 150 and guanine. Top: Extracted ion chromatogram of m/z 953.6 [M + 2H] 2+ ; Bottom : MS/MS spectrum. Modified fragment ions are indicated by “*”.

Article Snippet: HPLC-ESI+ -MS/MS analysis of hAGT and C145A hAGT tryptic peptides was performed using the same Agilent 1100 capillary HPLC-ion trap MS system.

Techniques: High Performance Liquid Chromatography, Mass Spectrometry, Modification

Journal: Chemical research in toxicology

Article Title: CROSS-LINKING OF THE HUMAN DNA REPAIR PROTEIN O6-ALKYLGUANINE DNA ALKYLTRANSFERASE TO DNA IN THE PRESENCE OF 1,2,3,4-DIEPOXYBUTANE

doi: 10.1021/tx0600088

Figure Lengend Snippet: HPLC-ESI + -MS/MS analysis of hAGT tryptic peptide G 136 NPVPILIPCHR 147 containing a dG monoepoxide-induced butanediol cross-link between Cys 145 and guanine. Top: Extracted ion chromatogram of m/z 777.0 [M + 2H] 2+ ; Bottom: MS/MS spectrum. Modified fragment ions are indicated by “*”.

Article Snippet: HPLC-ESI+ -MS/MS analysis of hAGT and C145A hAGT tryptic peptides was performed using the same Agilent 1100 capillary HPLC-ion trap MS system.

Techniques: High Performance Liquid Chromatography, Mass Spectrometry, Modification

Journal: Chemical research in toxicology

Article Title: CROSS-LINKING OF THE HUMAN DNA REPAIR PROTEIN O6-ALKYLGUANINE DNA ALKYLTRANSFERASE TO DNA IN THE PRESENCE OF 1,2,3,4-DIEPOXYBUTANE

doi: 10.1021/tx0600088

Figure Lengend Snippet: HPLC-ESI + -MS/MS analysis of hAGT tryptic peptides containing DEB-induced butanediol cross-links to guanine. (A) Top: Extracted ion chromatogram of hAGT tryptic peptide G 136 NPVPILIPCHR 147 cross-linked to guanine ( m/z 776.9 [M + 2H] 2+ ); Bottom: MS/MS spectrum of tryptic peptide G 136 NPVPILIPCHR 147 mapping the cross-link to Cys 145 . (B) Top: Extracted ion chromatogram of hAGT tryptic peptide V 148 VCSSGGAVGNYSGGLAVK 165 cross-linked to guanine ( m/z 952.9 [M + 2H] 2+ ); Bottom: MS/MS spectrum of tryptic peptide V 148 VCSSGGAVGNYSGGLAVK 165 mapping the cross-link to Cys 150 . Modified fragment ions are indicated by “*”.

Article Snippet: HPLC-ESI+ -MS/MS analysis of hAGT and C145A hAGT tryptic peptides was performed using the same Agilent 1100 capillary HPLC-ion trap MS system.

Techniques: High Performance Liquid Chromatography, Mass Spectrometry, Modification

Journal: Infection and Immunity

Article Title: A Subset of Protective γ9δ2 T Cells Is Activated by Novel Mycobacterial Glycolipid Components

doi: 10.1128/IAI.01322-15

Figure Lengend Snippet: 6- O -Methylglucose lipopolysaccharide (mGLP), a derivative or similar product thereof, is responsible for expansion of mycobacterium inhibition-specific γ 9 δ 2 T cells. The 100% MeOH fraction eluted from silica was further analyzed by 1 H NMR and MALDI-TOF. (A) 1 H NMR analysis of the 100% MeOH eluate was performed on 4.0 mg of material. NMR spectra revealed a significant presence of O -methyl groups and α-anomeric protons corresponding to hexosyl residues. A representative 100% MeOH fraction (1 μl) from a silica gel column loaded with H37Rv total lipid from the chloroform-methanol-water (10:10:3) extraction and eluted with an increasing methanol gradient was mixed with DHB matrix (1 μl) and analyzed in negative electrospray mode. Spectra revealed a high-molecular-mass product in the m/z range of 3,600 to 4,000 (B), with peaks separated by 14 amu (C). (D) GC-MS profile of silica gel column fractions from the chloroform-methanol-water (10:10:3) extract: (1) neutral monosaccharide standard, (2) 100% MeOH, (3) 80% MeOH-CHCl 3 , (4) 60% MeOH-CHCl 3 , and (5) 40% MeOH-CHCl 3 .

Article Snippet: A single-reaction monitoring (SRM) assay was developed for detection and quantification of HMBPP using a Waters Xevo TQ-S triple quadrapole mass spectrometer (MS) with electrospray ionization coupled to a Waters Acquity ultraperformance liquid chromatography instrument (UPLC).

Techniques: Inhibition, Nuclear Magnetic Resonance, Gas Chromatography-Mass Spectrometry

Journal: Chemical research in toxicology

Article Title: Bioactive 4-Oxoheptanedioic Monoamide Derivatives of Proteins and Ethanolaminephospholipids: Products of Docosahexaenoate Oxidation

doi: 10.1021/acs.chemrestox.6b00218

Figure Lengend Snippet: HPLC/ESI/MS/MS analysis of OHdiA adduct production in the reaction of KOHA-PC with Ac-Gly-Lys-OMe dipeptide. (A) Authentic 4-oxoheptanedioic acid ( 1 ) standard. (B) Reaction product mixture after 48 h incubation at room temperature.

Article Snippet: LC-ESI/MS/MS analysis of OHdiA adducts was performed on a Quattro Ultima triple-quadrupole mass spectrometer (Micromass, Wythenshawe, UK) equipped with a Waters Alliance 2690 HPLC system with an auto-injector (Waters, Milford, MA).

Techniques: High Performance Liquid Chromatography, Mass Spectrometry, Incubation

Journal: Chemical research in toxicology

Article Title: Bioactive 4-Oxoheptanedioic Monoamide Derivatives of Proteins and Ethanolaminephospholipids: Products of Docosahexaenoate Oxidation

doi: 10.1021/acs.chemrestox.6b00218

Figure Lengend Snippet: LC/ESI/MS/MS evidence for OHdiA derivatives in human plasma. OHdiA-diPFB was detected after acid hydrolysis followed by PFB esterification. (A) MRM for synthetic authentic standard OHdiA-diPFB. (B) MRM for PFB derivative of 4-oxoheptanedioic acid from

Article Snippet: LC-ESI/MS/MS analysis of OHdiA adducts was performed on a Quattro Ultima triple-quadrupole mass spectrometer (Micromass, Wythenshawe, UK) equipped with a Waters Alliance 2690 HPLC system with an auto-injector (Waters, Milford, MA).

Techniques: Mass Spectrometry

Journal: Chemical research in toxicology

Article Title: Bioactive 4-Oxoheptanedioic Monoamide Derivatives of Proteins and Ethanolaminephospholipids: Products of Docosahexaenoate Oxidation

doi: 10.1021/acs.chemrestox.6b00218

Figure Lengend Snippet: HPLC/ESI/MS/MS analysis after acid hydrolysis and pentafluorobenzyl esterification of the OHdiA monoamide produced by the reaction of KOHA-PC with Ac-Gly-Lys-OMe dipeptide. (A) Authentic OHdiA-diPFB standard. (B) Reaction product mixture from incubation

Article Snippet: LC-ESI/MS/MS analysis of OHdiA adducts was performed on a Quattro Ultima triple-quadrupole mass spectrometer (Micromass, Wythenshawe, UK) equipped with a Waters Alliance 2690 HPLC system with an auto-injector (Waters, Milford, MA).

Techniques: High Performance Liquid Chromatography, Mass Spectrometry, Produced, Incubation

Journal: Chemical research in toxicology

Article Title: Bioactive 4-Oxoheptanedioic Monoamide Derivatives of Proteins and Ethanolaminephospholipids: Products of Docosahexaenoate Oxidation

doi: 10.1021/acs.chemrestox.6b00218

Figure Lengend Snippet: HPLC/ESI/MS/MS analysis of OHdiA produced by copper-catalyzed oxidation of DHA-PC for 48 h (A) without DPPE or (B) with DPPE after 0 h incubation or (C) with DPPE after 48 h incubation followed by hydrolysis with 6 N HCl at 100 °C for 5 h.

Article Snippet: LC-ESI/MS/MS analysis of OHdiA adducts was performed on a Quattro Ultima triple-quadrupole mass spectrometer (Micromass, Wythenshawe, UK) equipped with a Waters Alliance 2690 HPLC system with an auto-injector (Waters, Milford, MA).

Techniques: High Performance Liquid Chromatography, Mass Spectrometry, Produced, Incubation