Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Human proteome derivatized with iodoacetamide and acrylamide

ABSTRACT: This dataset was generated to parametrize and benchmark software for unbiased discovery of post-translationally modified peptides.

INSTRUMENT(S): Orbitrap Fusion

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Cell Suspension Culture

DISEASE(S): Acute Leukemia

SUBMITTER: Alex Kentsis

LAB HEAD: Alex Kentsis

PROVIDER: PXD019793 | Pride | 2021-07-22

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Publications

Discovery of Protein Modifications Using Differential Tandem Mass Spectrometry Proteomics.

Cifani Paolo P Li Zhi Z Luo Danmeng D Grivainis Mark M Intlekofer Andrew M AM Fenyö David D Kentsis Alex A

Journal of proteome research 20210322 4

Recent studies have revealed diverse amino acid, post-translational, and noncanonical modifications of proteins in diverse organisms and tissues. However, their unbiased detection and analysis remain hindered by technical limitations. Here, we present a spectral alignment method for the identification of protein modifications using high-resolution mass spectrometry proteomics. Termed SAMPEI for spectral alignment-based modified peptide identification, this open-source algorithm is designed for t ...[more]

PMID: 33749263

Similar Datasets

Mitotic post-translational modifications of histones promote chromatin compaction in vitro

Project description:As histones undergo major changes in their post-translational modifications during mitotic entry, we speculated that the spectrum of cell cycle-specific histone modifications might contribute to chromosome compaction during mitosis. To test this hypothesis, we isolated core histones from interphase and mitotic cells and reconstituted chromatin with them. We used mass spectrometry to show that key post-translational modifications remained intact during our isolation procedure.

2018-10-24 | PXD007116 | Pride

Mitochondrial respiratory chain is essential for hematopoietic stem cell function

Project description:Adult and fetal hematopoietic stem cells (HSCs) display a glycolytic phenotype, which is required for maintenance of stemness; however, whether mitochondrial respiration is required to maintain HSC function is not known. Here we report that loss of the mitochondrial complex III subunit Rieske iron sulfur protein (RISP) in fetal mouse HSCs allows them to proliferate but impairs their differentiation, resulting in anemia and prenatal death. RISP null fetal HSCs displayed impaired respiration resulting in a decreased NAD+/NADH ratio. RISP null fetal HSCs and progenitors exhibited an increase in both DNA and histone methylation concomitant with increases in 2-hydroxyglutarate (2-HG), a metabolite known to inhibit DNA and histone demethylases. RISP inactivation in adult HSCs also impaired respiration resulting in loss of quiescence resulting in severe pancytopenia and lethality. Thus, respiration is dispensable for adult or fetal HSC proliferation, but essential for fetal HSC differentiation and maintenance of adult HSC quiescence.

2017-09-13 | PXD006054 | Pride

Composition analysis of Strongyloides venezuelensis Larvae proteome

Project description:This project is a compositional analysis of L3 larvae stage of Strongyloides Venezuelensis.

2020-01-09 | PXD013703 | Pride

Shotgun analysis of serum proteome on Schistosoma mansoni infection

Project description:This project is a Shotgun analysis of serum proteome on Schistosoma mansoni infection

2022-08-18 | PXD031974 | Pride

Histone post translational modification mass sprectrometry SUZ12 exon 4 cell lines

Project description:We investigate the contribution of each SUZ12 isoform on PRC2 activity on chromatin using our different ESC lines. As an additional comparison for ∆ex4 cells (SUZ12-S), we included an ESC clone in which an unsuccessful CRISPR editing event resulted in a mutant allele with nearly constitutive splicing of exon 4 (herein, CSex4) and normal Suz12 expression levels (expressing only SUZ12-L). First, we profiled H3K27 bulk PTMs by WB and observed that, while CSex4 cells showed no major differences to control cells, ∆ex4 cells displayed lower levels of H3K27me2 and -me3, with higher levels of mono-methylation and acetylation. Similar results were obtained when comparing SUZ12-L and SUZ12-S ESC rescue lines. To validate these findings with an antibody-independent technique, and to additionally profile other histone PTMs, we analysed these cells with histone-MS. In line with the previous estimates26, WT cells displayed approximately 85% of H3K27 methylation. This proportion was largely similar in CSex4 cells, while it dropped to ~50% in ∆ex4 cells, with H3K27me2 and -me3 being the most affected modifications. Notably, H3K27me2/3 loss in ∆ex4 cells occurred at histone peptides regardless of their H3K36 methylation status. Moreover, the global H3K36 methylation rates were not affected in either CSex4 or ∆ex4 cells (Figure S4C), and no major changes in methylation or acetylation levels were observed at other residues. Importantly, reintroduction of SUZ12-L in KO cells rescued a higher degree of methylation compared to SUZ12-S. Overall, these results indicate that SUZ12-S alone is unable to maintain global physiological levels of H3K27 methylation; rather SUZ12-L is also necessary for this task.

2024-03-18 | PXD046640 | Pride

Assessment of cytotoxicity of (N-isopropyl acrylamide) and poly(N-isopropyl acrylamide)-coated surfaces.

Project description: Not available

| S-EPMC3979476 | biostudies-literature

Peptidomics of circular cysteine-rich plant peptides – Analysis of the diversity of cyclotides from Viola tricolor by transcriptome- and proteome-mining

Project description:circular peptides, cystine-knot, transcriptome, peptidomics, Violaceae, ribosomally synthesized and post-translationally modified peptides natural products, mass spectrometry, 1kp

2015-10-02 | PXD002867 | Pride

A genetically encoded acrylamide functionality.

Project description: Not available

| S-EPMC3746000 | biostudies-other

Cord blood acrylamide levels and birth size, and interactions with genetic variants in acrylamide-metabolising genes.

Project description: Not available

| S-EPMC8015021 | biostudies-literature

Acrylamide acute neurotoxicity in adult zebrafish.

Project description: Not available

| S-EPMC5962567 | biostudies-literature