Pm_labelled
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Unknown
ORGANISM(S): Halobacterium Nrc-1 (halobacterium)
SUBMITTER: Nitin Baliga
PROVIDER: PAe000184 | PeptideAtlas |
REPOSITORIES: PeptideAtlas
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Project description:Identification of targets of the protein disulfide reductase thioredoxin using liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) and thiol specific differential labeling with isotope-coded affinity tags (ICAT). Reduction of specific target disulfides is quantified by measuring ratios of cysteine residues labeled with the heavy (13C) and light (12C) ICAT reagents in peptides derived from tryptic digests of Trx-treated and non-treated samples. Keywords: protein, LC-MS/MS, ICAT
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Project description:Quantitative chemical proteomics was performed to profile the target proteins of ITCs.For the forward SILAC experiment, heavy-labeled cells were treated with the ITC probe (20 μM) for 30 min and light-labeled cells were pre-treated with the natural ITC (60 μM) for 30 min, followed by the ITC probe (20 μM) for another 30 min. For the reverse SILAC experiment, light-labeled cells were treated with the ITC probe (20 μM) for 30 min and heavy-labeled cells were treated with the natural ITC (60 μM) for 30 min, followed by the ITC probe (20 μM) for another 30 min.
2025-05-06 | PXD051941 | Pride
Project description:Using the covalent inhibitor SY-351 and quantitative SILAC phosphoproteomics, we identified CDK7 kinase substrates in human cells. We performed a double-label SILAC phosphoproteomics experiment, in which we metabolically labeled HL60 cells with light labeled (Lys0, Arg0) or heavy labeled (Lys8, Arg8) amino acids, which were treated with vehicle (DMSO) or 50 nM SY-351, followed by phosphopeptide enrichment and mass spectrometry analysis. The experimental design included two biological replicates of SY-351 treated heavy cells compared with DMSO treated light cells, a label-flip biological replicate of SY-351 light cells compared with DMSO treated heavy cells, and a null condition for which both heavy and light were treated with DMSO. The label-flip and null conditions control for systematic errors in phosphopeptide Heavy:Light SILAC ratios that are independent of the SY-351 treatment effect. We used a linear statistical model to capture these systematic errors, which improved our statistical power to detect phosphorylation sites that changed in abundance with SY-351 treatment.
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Project description:Halobacterium purple membrane experiment in which cells underexpressing phototrophy regulator (bat-) were labeled with heavy (d8) ICAT isotope, and cells overexpressing the phototrophy regulator (bat+) were labeled with light (d0) ICAT isotope.
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Project description:Halobacterium NRC-1 Diurnal experiment Light 2
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Project description:This SuperSeries is composed of the following subset Series: GSE7714: Halobacterium NRC-1 oxygen, light and phr1 perturbation GSE7715: Halobacterium NRC-1 oxygen, light and ura3 perturbation GSE7716: Halobacterium NRC-1 oxygen, light and phr1/phr2 perturbation GSE7717: Halobacterium NRC-1 oxygen, light and bop perturbation GSE7718: Halobacterium NRC-1 oxygen, light and phr2 perturbation GSE7719: Halobacterium NRC-1 oxygen, light and sop2 perturbation GSE7720: Halobacterium NRC-1 oxygen, light and afsQ2 perturbation GSE7721: Halobacterium NRC-1 oxygen, light and htlD perturbation GSE7722: Halobacterium NRC-1 oxygen, light and vng0750C perturbation GSE7723: Halobacterium NRC-1 oxygen, light and boa1 perturbation GSE7724: Halobacterium NRC-1 oxygen, light and ark perturbation GSE7725: Halobacterium NRC-1 oxygen, light and boa4 perturbation GSE7726: Halobacterium NRC-1 oxygen, light and htr1 perturbation GSE7727: Halobacterium NRC-1 oxygen, light and kinA2 perturbation GSE7728: Halobacterium NRC-1 oxygen, light and htr8 perturbation GSE7729: Halobacterium NRC-1 oxygen and light perturbation GSE7730: Halobacterium NRC-1 oxygen, light and phoR perturbation GSE7731: Halobacterium NRC-1 oxygen, light and htr2 perturbation GSE7732: Halobacterium NRC-1 oxygen, light and vng1296C perturbation GSE7733: Halobacterium NRC-1 oxygen, light and vng2334C perturbation GSE7734: Halobacterium NRC-1 oxygen, light and zim perturbation GSE7735: Halobacterium NRC-1 oxygen, light and kinA2 perturbation, experiment 2 GSE7736: Halobacterium NRC-1 oxygen, light and sop2 perturbation, experiment 2 GSE7737: Halobacterium NRC-1 oxygen, light and vng0019h perturbation GSE7738: Halobacterium NRC-1 oxygen, light and gap perturbation Refer to individual Series
2008-01-02 | E-GEOD-7740 | biostudies-arrayexpress
Project description:To globally profile the fatty-acylation substrate proteins of RID, we utilized the bioorthogonal chemical reporter Alk-16, an alkynyl-functionalized fatty acid analogue, to metabolically label fatty-acylated proteins in living cells. To identify the substrate proteins of RID, we sought to perform quantitative chemical proteomics experiments by combining the Alk-16 metabolic labeling and stable isotope labeling by amino acids in cell culture (SILAC) . In order to eliminate potential false positives due to isotope labeling and to increase identification reliability, we designed a dual SILAC workflow. In the “Forward” SILAC experiment, cells were cultured in standard SILAC heavy and light media before transfection to express RID-WT and RID-CA, respectively. In the “Reverse” SILAC experiment, the isotope labeling was switched and the heavy- and light-labeled cells were transfected with RID-CA and RID-WT, respectively. Cells were labeled with Alk-16 and the lysates were then mixed equally. The combined lysates were treated with NH2OH, followed by click reaction with azido-biotin, streptavidin enrichment, and trypsin digestion. The resulting peptide samples were analyzed by mass spectrometry for protein identification. The heavy-to-light (H/L) SILAC ratios of identified proteins were quantified to evaluate the extent of enrichment.
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Project description:RKO cells were cultured in SILAC (stable isotope labeling by amino acids in cell culture) DMEM medium. TRIP6 knockdown cells were labeled with heavy lysine (Lys8) and arginine (Arg10), while wild-type TRIP6 cells were cultured with light isotopes. Total proteins were then extracted and analyzed by mass spectrometry. Each experiment consists of 12 fractions and was performed in three independent replicates.
2026-02-04 | PXD073555 | Pride
Project description:Array data detailing the progression of DNA replication in the yeast Lachancea waltii. L. waltii cells were pregrown in heavy isotope medium and synchronized at early S phase. They were then released into normal medium, wherein DNA replication proceeds. Replicated DNA molecules are thus of heavy-light (HL) composition as compared to unreplicated molecules, which are heavy-heavy (HH). 4 time points were taken and the percent of heavy-light DNA was determined at each time point. The heavy-heavy and heavy-light DNA molecules were separated by ultracentrifugation, differentially labeled, and hybridized to a genomic array for L. waltii. The array thus shows the progression of DNA replication.
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Project description:The presence of a protein at the cell surface is regulated by the exocytic and endocytic membrane trafficking pathways. We have recently discovered that the nutrient, or amino acids, plays a substantial role in promoting the endocytic membrane trafficking. Here we ask if the nutrient can regulate the cell surface presentation of proteins, which has not been addressed in the literature according to our knowledge. To that end, HeLa cells are labeled with heavy and light isotopes. In the forward labeling experiment, heavy and light cells are treated with DMEM and HBSS for 2 hours respectively. Cells are surface-biotinylated and are subsequently mixed, lysed and subjected to affinity purification by Streptavidin beads. Reverse labeling experiment is identically performed except that heavy and light cells are treated with HBSS and DMEM respectively. Our proteomics data demonstrate that many cell surface exposed proteins, such as signaling receptors, ligands, extracellular matrix proteins, trans-Golgi network cargo adaptor proteins and Golgi enzymes, can be regulated by the nutrient. Our study implies that the nutrient might play essential roles in intracellular membrane trafficking and in shaping a cell’s interactions with its environment.
2019-04-03 | PXD011136 | Pride