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Quantitative proteomic analysis of heat shock response using tandem mass tags

ABSTRACT: Analysis of precision of TMT quantitation at the peptide level using multinotch MS3

INSTRUMENT(S): Orbitrap Fusion Lumos, Orbitrap Fusion

ORGANISM(S): Saccharomyces Cerevisiae (baker's Yeast)

SUBMITTER: Aaron Storey

LAB HEAD: Jeffrey Lewis

PROVIDER: PXD014552 | Pride | 2020-02-17

REPOSITORIES: Pride

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			Action	DRS
	2nd_lewis_SF1.mzML	Mzml
	2nd_lewis_SF1.raw	Raw
	2nd_lewis_SF1.raw (F052725).pride.mztab.gz	Mztab
	2nd_lewis_SF1.rawF052725.mzid.gz	Mzid
	2nd_lewis_SF1.rawF052725.mzid_2nd_lewis_SF1.raw_F052725.MGF	Mzid

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Publications

Accurate and Sensitive Quantitation of the Dynamic Heat Shock Proteome Using Tandem Mass Tags.

Storey Aaron J AJ Hardman Rebecca E RE Byrum Stephanie D SD Mackintosh Samuel G SG Edmondson Rick D RD Wahls Wayne P WP Tackett Alan J AJ Lewis Jeffrey A JA

Journal of proteome research 20200219 3

Cells respond to environmental perturbations and insults through modulating protein abundance and function. However, the majority of studies have focused on changes in RNA abundance because quantitative transcriptomics has historically been more facile than quantitative proteomics. Modern Orbitrap mass spectrometers now provide sensitive and deep proteome coverage, allowing direct, global quantification of not only protein abundance but also post-translational modifications (PTMs) that regulate ...[more]

PMID: 32027144

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Quantitative proteomic analysis of heat shock response using tandem mass tags

Project description:Analysis of precision of TMT quantitation at the peptide level using multinotch MS3

2020-02-18 | PXD012973 | Pride

Dysregulation of circulating protease activity in COVID-19-associated superinfection

Project description:Infection by SARS-CoV-2 and subsequent COVID-19 can cause viral sepsis and septic shock. Our past studies demonstrated that dysregulated systemic proteolysis is associated with the pathological mechanism in bacterial septic shock. Thus, here we perform shotgun proteomics and peptidomics analysis by LC-MS/MS to identify and quantify the circulating protein and peptide profile of COVID-19 patient plasma. Plasma samples from four COVID-19 patients were collected at different time points of their ICU stay, including samples from a patient with COVID-19-induced sepsis and bacterial superinfection. By combining mass spectrometry analysis with enzymatic activity assays, our study elucidates the possible pathological involvement of proteolysis in COVID-19-induced sepsis, with particular insight into the dyregulation of protease-mediated systems, such as the coagulation cascade.

2023-03-10 | PXD029181 | Pride

Reanalysis of Pandey lab's draft of the human proteome

Project description:The availability of human genome sequence has transformed biomedical research over the past decade. However, an equivalent map for the human proteome with direct measurements of proteins and peptides was lacking. To this end, Akhilesh Pandey's lab reported a draft map of the human proteome based on high resolution Fourier transform mass spectrometry-based proteomics technology, which included an in-depth proteomic profiling of 30 histologically normal human samples including 17 adult tissues, 7 fetal tissues and 6 purified primary hematopoietic cells ( http://dx.doi.org/10.1038/nature13302 ). The profiling resulted in identification of proteins encoded by greater than 17,000 genes accounting for ~84% of the total annotated protein-coding genes in humans. This large human proteome catalog (available as an interactive web-based resource at http://www.humanproteomemap.org) complements available human genome and transcriptome data to accelerate biomedical research in health and disease. Pandey's lab and collaborators request that those considering use of this primary dataset for commercial purposes contact pandey@jhmi.edu. The full details of this study can be found in the PRIDE database: www.ebi.ac.uk/pride/archive/projects/PXD000561/. This ArrayExpress entry represents a top level summary of the metadata only which formed the basis of the reanalysis performed by Joyti Choudhary's team ( jc4@sanger.ac.uk ), results of which are presented in the Expression Atlas at EMBL-EBI : http://www.ebi.ac.uk/gxa/experiments/E-PROT-1.

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DNA-PKcs kinase activity stabilizes the transcription factor Egr1 in activated immune cells

Project description:To gain insight into the function of DNA-PKcs within immune cells, we performed a quantitative phosphoproteomic screen in T cells to identify first order phosphorylation targets of DNA-PKcs. Results indicate that DNA-PKcs phosphorylates the transcription factor Egr1 (early growth response protein 1) at S301. Expression of Egr1 is induced early upon T cell activation and dictates T cell response by modulating expression of cytokines and key costimulatory molecules. Mutation of serine 301 to alanine via CRISPR-Cas9 resulted in increased proteasomal degradation of Egr1 and a decrease in Egr1-dependent transcription of IL2 (interleukin-2) in activated T cells. Our findings identify DNA-PKcs as a critical intermediary link between T cell activation and T cell fate and a novel phosphosite involved in regulating Egr1 activity.

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2010-05-26 | E-GEOD-10762 | biostudies-arrayexpress

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Project description:We have developed a multi-analyte fluid-phase protein array technology termed high-throughput immunophenotyping using transcription (HIT). This method employs a panel of monoclonal antibodies, each tagged with a unique oligonucleotide sequence that serves as a molecular barcode. After staining a sample, T7 polymerase amplifies the tags which are then hybridized to a DNA microarray for indirect measurement of each analyte. Here we screened 90 antibodies directed against a panel of cell surface markers as well as 4 isotype controls to compare resting human naive CD4+ T cells versus CD4+ T cells activated for 48 h with anti-CD3/anti-CD28 coated beads. Keywords: protein profiling, response to stimulus Two-condition experiment, activated versus resting cells. Biological replicates: 3 normal human donors, each donor served as an internal control. One replicate per array. One of the biological replicates was performed as a dye-swap to monitor dye-bias. We also performed a self-self comparison between activated cells from two different donors.

2010-05-26 | E-GEOD-10665 | biostudies-arrayexpress

ProteoViz: A toolset for interactive analysis of phosphoproteomics data

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