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TSAAT030c

ABSTRACT: TSAA time 30 experiment cleavable ICAT

INSTRUMENT(S): LTQ

ORGANISM(S): Saccharomyces Cerevisiae (yeast)

SUBMITTER: Mark Flory, Ruedi Aebersold et al. (ISB)

PROVIDER: PAe000086 | PeptideAtlas | 2006-12-31

REPOSITORIES: PeptideAtlas

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			Action	DRS
	PAe000086_404_search.params.tar.gz	Other
	PAe000086_404_searchdatabase_spectrast.splib	Other
	PAe000086_404_searchdatabase_tandem.fasta	Fasta
	PAe000086_404_spectrast.params	Other
	PAe000086_404_tandem.params	Other

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1 - 5 of 13

Publications

Quantitative proteomic analysis of the budding yeast cell cycle using acid-cleavable isotope-coded affinity tag reagents.

Flory Mark R MR Lee Hookeun H Bonneau Richard R Mallick Parag P Serikawa Kyle K Morris David R DR Aebersold Ruedi R

Proteomics 20061201 23

Quantitative profiling of proteins, the direct effectors of nearly all biological functions, will undoubtedly complement technologies for the measurement of mRNA. Systematic proteomic measurement of the cell cycle is now possible by using stable isotopic labeling with isotope-coded affinity tag reagents and software tools for high-throughput analysis of LC-MS/MS data. We provide here the first such study achieving quantitative, global proteomic measurement of a time-course gene expression experi ...[more]

PMID: 17133367

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Identification of targets of the protein disulfide reductase thioredoxin

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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ABA GC - ICAT EXPERIMENT OF UNTREATED AND ABA TREATED GUARD CELLS HILIC REPLICATE 1

Project description:ICAT EXPERIMENT OF UNTREATED AND ABA TREATED GUARD CELLS HILIC REPLICATE 1

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Translation State Array Analysis of Thrombin Stimulated Human Endothelial Cells

Project description:Confluent human umbilical vein endothelial cells (HUVECs) were exposed to Thrombin (2 U/mL) for 2 hours. Ribosomal profiling via gradient centrifugation and fractionation was used to separate monosome, or under-translated, and polysome, or actively translated, mRNA species that were then used to probe cDNA arrays, a process known as Translation State Array Analysis (TSAA). Four samples were obtained from these experiments, Control Monosome, Control Polysome, Thrombin Monosome, and Thrombin Polysome. Using the normalized signal intensities from the GeneFilters, we calculated a translation index, or measure of movement of an mRNA molecule from the monosome to the polysome fraction upon stimulation. This calculation was made as follows: (thrombin polysome/thrombin monosome)/(control polysome/control monosome). Translational indices greater than 2.5 (upregulated) or lower than 0.4 (downregulated) were chosen for further study. TSAA data suggests that JunB is translationally regulated by thrombin stimulation. Immunocytochemistry, western blotting and RT-PCR were used to verify the results of TSAA. Keywords: Translation State Array Analysis

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Eliminating genome-wide and transcriptome-wide off-target mutations by base editor [tBE_target_genomic_seq]

Project description:Conjugation of CRISPR-Cas9 with cytidine deaminases leads to base editors (BEs) for programmable C-to-T editing, which holds potentials in clinical applications, but suffers from off-target (OT) mutations. By taking advantage of a cleavable deoxycytidine deaminase inhibitor (dCDI) domain, a transformer BE (tBE) system is developed to induce efficient editing with only background levels of genome-wide and transcriptome-wide OT mutations. After being produced, tBE remains inactive at OT sites with the fusion of a cleavable dCDI, thus eliminating unintended mutations. Only when binding at on-target sites, tBE is transformed to cleave off the dCDI domain and catalyzes targeted deamination for precise base changes. After delivery into mice via a dual-AAV system, tBE created a premature stop codon in Pcsk9 and significantly reduced serum PCSK9 level, which resulted in ~30-40% decrease of total cholesterol. Together, the development of tBE establishes a highly-precise base editing system and its in vivo efficacy envisions potential therapeutic applications.

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Eliminating genome-wide and transcriptome-wide off-target mutations by base editor

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