Relative quantitation of peptides in wild-type andCpefat/fat mouse pituitary using stable isotopic tags and mass spectrometry

2005 ◽  
Vol 40 (2) ◽  
pp. 227-237 ◽  
Author(s):  
Fa-Yun Che ◽  
Reeta Biswas ◽  
Lloyd D. Fricker
Keyword(s):  
Mass Spectrometry ◽  
Wild Type ◽  
Stable Isotopic ◽  
Relative Quantitation ◽  
Mouse Pituitary

Relative quantitation of glycans using stable isotopic labels 1-(d0/d5) phenyl-3-methyl-5-pyrazolone by mass spectrometry

2011 ◽  
Vol 418 (1) ◽  
pp. 1-9 ◽  
Author(s):  
Ping Zhang ◽  
Ying Zhang ◽  
Xiangdong Xue ◽  
Chenjian Wang ◽  
Zhongfu Wang ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Stable Isotopic ◽  
Relative Quantitation ◽  
Isotopic Labels

scholarly journals Imaging Sterols and Oxysterols in Mouse Brain Reveals Distinct Spatial Cholesterol Metabolism

2018 ◽  
Author(s):  
Eylan Yutuc ◽  
Roberto Angelini ◽  
Mark Baumert ◽  
Natalia Mast ◽  
Irina Pikuleva ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Mouse Brain ◽  
Brain Function ◽  
Mass Spectrometry Imaging ◽  
Cholesterol Metabolism ◽  
Biologically Active ◽  
Wild Type ◽  
Tissue Slices ◽  
The Brain

AbstractDysregulated cholesterol metabolism is implicated in a number of neurological disorders. Many sterols, including cholesterol and its precursors and metabolites, are biologically active and important for proper brain function. However, spatial cholesterol metabolism in brain and the resulting sterol distributions are poorly defined. To better understand cholesterol metabolism in situ across the complex functional regions of brain, we have developed on-tissue enzyme-assisted derivatisation in combination with micro-liquid-extraction for surface analysis and liquid chromatography - mass spectrometry to image sterols in tissue slices (10 µm) of mouse brain. The method provides sterolomic analysis at 400 µm spot diameter with a limit of quantification of 0.01 ng/mm2. It overcomes the limitations of previous mass spectrometry imaging techniques in analysis of low abundance and difficult to ionise sterol molecules, allowing isomer differentiation and structure identification. Here we demonstrate the spatial distribution and quantification of multiple sterols involved in cholesterol metabolic pathways in wild type and cholesterol 24S-hydroxylase knock-out mouse brain. The technology described provides a powerful tool for future studies of spatial cholesterol metabolism in healthy and diseased tissues.SignificanceThe brain is a remarkably complex organ and cholesterol homeostasis underpins brain function. It is known that cholesterol is not evenly distributed across different brain regions, however, the precise map of cholesterol metabolism in the brain remains unclear. If cholesterol metabolism is to be correlated with brain function it is essential to generate such a map. Here we describe an advanced mass spectrometry imaging platform to reveal spatial cholesterol metabolism in situ at 400 µm resolution on 10 µm tissue slices from mouse brain. We mapped, not only cholesterol, but also other biologically active sterols arising from cholesterol turnover in both wild type and mice lacking cholesterol 24-hydroxylase (Cyp46a1), the major cholesterol metabolising enzyme.

scholarly journals Alpha Carbonic Anhydrase 5 Mediates Stimulation of ATP Synthesis by Bicarbonate in Isolated Arabidopsis Thylakoids

2021 ◽  
Vol 12 ◽  
Author(s):  
Tatiana P. Fedorchuk ◽  
Inga A. Kireeva ◽  
Vera K. Opanasenko ◽  
Vasily V. Terentyev ◽  
Natalia N. Rudenko ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Arabidopsis Thaliana ◽  
Carbonic Anhydrase ◽  
Atp Synthesis ◽  
Thylakoid Membranes ◽  
Wild Type ◽  
Gene Encoding ◽  
Mutant Lines ◽  
Stimulation Of ◽  
Soluble Carbonic Anhydrase

We studied bicarbonate-induced stimulation of photophosphorylation in thylakoids isolated from leaves of Arabidopsis thaliana plants. This stimulation was not observed in thylakoids of wild-type in the presence of mafenide, a soluble carbonic anhydrase inhibitor, and was absent in thylakoids of two mutant lines lacking the gene encoding alpha carbonic anhydrase 5 (αCA5). Using mass spectrometry, we revealed the presence of αCA5 in stromal thylakoid membranes of wild-type plants. A possible mechanism of the photophosphorylation stimulation by bicarbonate that involves αCA5 is proposed.

scholarly journals The ubiquitin-dependent ATPase p97 removes cytotoxic trapped PARP1 from chromatin

2022 ◽  
Author(s):  
Dragomir B. Krastev ◽  
Shudong Li ◽  
Yilun Sun ◽  
Andrew J. Wicks ◽  
Gwendoline Hoslett ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Homologous Recombination ◽  
Ubiquitin Ligase ◽  
Antitumour Activity ◽  
Parp Inhibitor ◽  
Bound State ◽  
Parp Inhibitors ◽  
Tumour Cells ◽  
Wild Type ◽  
Endogenous Proteins

AbstractPoly (ADP-ribose) polymerase (PARP) inhibitors elicit antitumour activity in homologous recombination-defective cancers by trapping PARP1 in a chromatin-bound state. How cells process trapped PARP1 remains unclear. Using wild-type and a trapping-deficient PARP1 mutant combined with rapid immunoprecipitation mass spectrometry of endogenous proteins and Apex2 proximity labelling, we delineated mass spectrometry-based interactomes of trapped and non-trapped PARP1. These analyses identified an interaction between trapped PARP1 and the ubiquitin-regulated p97 ATPase/segregase. We found that following trapping, PARP1 is SUMOylated by PIAS4 and subsequently ubiquitylated by the SUMO-targeted E3 ubiquitin ligase RNF4, events that promote recruitment of p97 and removal of trapped PARP1 from chromatin. Small-molecule p97-complex inhibitors, including a metabolite of the clinically used drug disulfiram (CuET), prolonged PARP1 trapping and enhanced PARP inhibitor-induced cytotoxicity in homologous recombination-defective tumour cells and patient-derived tumour organoids. Together, these results suggest that p97 ATPase plays a key role in the processing of trapped PARP1 and the response of tumour cells to PARP inhibitors.

scholarly journals The histone chaperone Spt6 is required for normal recruitment of the capping enzyme Abd1 to transcribed regions

2021 ◽  
Author(s):  
Rajaraman Gopalakrishnan ◽  
Fred Winston
Keyword(s):  
Mass Spectrometry ◽  
Rna Polymerase Ii ◽  
Transcription Elongation ◽  
Histone Chaperone ◽  
Mrna Processing ◽  
Wild Type ◽  
Elongation Complex ◽  
Protein Levels ◽  
Genome Wide ◽  
Capping Enzyme

The histone chaperone Spt6 is involved in promoting elongation of RNA polymerase II (RNAPII), maintaining chromatin structure, regulating co-transcriptional histone modifications, and controlling mRNA processing. These diverse functions of Spt6 are partly mediated through its interactions with RNAPII and other factors in the transcription elongation complex. In this study, we used mass spectrometry to characterize the differences in RNAPII interacting factors between wild-type cells and those depleted for Spt6, leading to the identification of proteins that depend on Spt6 for their interaction with RNAPII. The altered association of some of these factors could be attributed to changes in steady-state protein levels. However, Abd1, the mRNA cap methyltransferase, had decreased association with RNAPII after Spt6 depletion despite unchanged Abd1 protein levels, showing a requirement for Spt6 in mediating the Abd1-RNAPII interaction. Genome-wide studies showed that Spt6 is required for maintaining the level of Abd1 over transcribed regions, as well as the level of Spt5, another protein known to recruit Abd1 to chromatin. Abd1 levels were particularly decreased at the 5 ends of genes after Spt6 depletion, suggesting a greater need for Spt6 in Abd1 recruitment over these regions. Together, our results show that Spt6 is important in regulating the composition of the transcription elongation complex and reveal a previously unknown function for Spt6 in the recruitment of Abd1.

scholarly journals Characterization of Plasmodium falciparum NEDD8 and identification of cullins as its substrates

2020 ◽  
Author(s):  
Manish Bhattacharjee ◽  
Navin Adhikari ◽  
Renu Sudhakar ◽  
Zeba Rizvi ◽  
Divya Das ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Plasmodium Falciparum ◽  
Western Blot ◽  
Wild Type ◽  
Malaria Parasites ◽  
Post Translational Modifications ◽  
Functional Conservation ◽  
Cellular Processes ◽  
Physiological Substrates

ABSTRACTA variety of post-translational modifications of Plasmodium falciparum proteins, including phosphorylation and ubiquitination, are shown to have key regulatory roles. The neural precursor cell expressed developmentally downregulated protein 8 (NEDD8) is a ubiquitin-like modifier of cullin-RING E3 ubiquitin ligases, which regulate diverse cellular processes, including the cell-cycle. Although neddylation pathway is conserved in eukaryotes, it is yet to be characterized in Plasmodium and related apicomplexan parasites. Towards studying the neddylation pathway in malaria parasites, we characterized P. falciparum NEDD8 (PfNEDD8) and identified cullins as its physiological substrates. PfNEDD8 is a 76 amino acid residue protein without the C-terminal tail, indicating that it can be readily conjugated. The wild type and mutant (Gly75Gly76 mutated to Ala75Ala76) PfNEDD8 were expressed in P. falciparum. Western blot of wild type PfNEDD8-expressing parasites indicated multiple high molecular weight conjugates, which were absent in the parasites expressing the mutant, indicating conjugation of NEDD8 to proteins through Gly76. Immunoprecipitation followed by mass spectrometry of wild type PfNEDD8-expressing parasites identified several proteins, including two putative cullins. Furthermore, we expressed PfNEDD8 in mutant S. cerevisiae strains that lacked endogenous NEDD8 (Δrub1) or NEDD8 conjugating E2 enzyme (ΔUbc12). The western blot of complemented strains and mass spectrometry of PfNEDD8 immunoprecipitate showed conjugation of PfNEDD8 to S. cerevisiae cullin cdc53, demonstrating functional conservation and cullins as the physiological substrates of PfNEDD8. The characterization of PfNEDD8 and identification of cullins as its substrates make ground for investigation of specific roles and drug target potential of neddylation pathway in malaria parasites.

scholarly journals New Methodologies for Qualitative and Semi-Quantitative Determination of Carbon-Centered Free Radicals in Cigarette Smoke Using Liquid ChromatographyTandem Mass Spectrometry and Gas Chromatography-Mass Selective Detection

2010 ◽  
Vol 24 (2) ◽  
pp. 58-71 ◽  
Author(s):  
AR Gerardi ◽  
WM Coleman
Keyword(s):  
Mass Spectrometry ◽  
Gas Chromatography ◽  
Free Radicals ◽  
Cigarette Smoke ◽  
Selective Detection ◽  
Selected Ion Monitoring ◽  
Relative Quantitation ◽  
Liquid Chromatography Tandem Mass ◽  
New Methodologies

AbstractSeveral approaches were explored to develop a high throughput procedure for relative determination of 14 different carbon-centered free radicals, both acyl and alkylaminocarbonyl type, in cigarette smoke. Two trapping procedures using 3-cyano-2,2,5,5-tetramethyl-1-pyrrolidinyloxy, or 3-cyanoproxyl radical (3-CNP) were designed for this study: a) trapping in solution and b) trapping on a solid support which was a Cambridge filter pad. Fresh whole smoke and vapor phase smoke from mainstream cigarette smoke from Kentucky Reference Cigarettes 2R4F, as partitioned via an unadulterated Cambridge filter pad, were transferred into each trapping system in separate experiments. The 3-CNP coated Cambridge filter pad approach was shown to be superior to the impinger procedure as described in this study. Gas chromatography coupled with mass selective detection (GC-MS) was employed for the first time as an alternate means of detecting several relatively highly concentrated radical adducts. Liquid chromatography tandem mass spectrometry (LC-MS/MS) with precursor ion monitoring and selected ion monitoring (SIM) was used for detecting the large array of radicals, including several not previously reported: formyl, crotonyl, acrolein, aminocarbonyl, and anilinocarbonyl radicals. Relative quantitation was achieved using as external calibration standards of 4-(1-pyrrolidino)benzaldehyde and nicotine. It was determined that the yield of carbon-centered free radicals by reference cigarette 2R4F was approximately 265 nmoles/cigarette at 35 mL puff/60 sec interval/2 sec duration smoking conditions.

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