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

Dataset's files

Source:

			Action	DRS
	190509_DL_OCIAML2_ACL_1.raw	Raw
	190509_DL_OCIAML2_ACL_1.tsv	Tabular
	190509_DL_OCIAML2_ACL_IAA_1.raw	Raw
	190509_DL_OCIAML2_ACL_IAA_1.tsv	Tabular
	190509_DL_OCIAML2_IAA_1.raw	Raw

Items per page:

1 - 5 of 7

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

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

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

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

Response Profiling Using Shotgun Proteomics Enables Establishing Global Metallodrug Mechanisms of Action - cytoplasmic proteins of KP1339-treated HCT 116 epithelial cells

Project description:Response profiling using shotgun proteomics for establishing global metallodrug mechanisms of action in two colon carcinoma cell lines, HCT116 and SW480, was applied and evaluated with the clinically approved arsenic trioxide. Surprisingly, the complete established mechanism of action of arsenic trioxide was observed by protein regulations in SW480, but not in HCT116 cells. Comparing the basal protein expression in the two cell lines revealed an 80% convergence of protein identifications, but with significant expression differences, which in turn seem affect the extent of protein regulation. For example, while a clear-cut redox response was observed in SW480 cells upon arsenic treatment, such an effect was lacking in HCT116 cells and the latter express drastically higher levels of the involved redox proteins. Response profiling was then used to investigate four anticancer metallodrugs (KP46, KP772, KP1339 and KP1537) by means of functional groups of proteins and mapped their effects according to DNA repair, endocytosis, protection from oxidative stress, protection from endoplasmatic reticulum (ER) stress, cell adhesion and mitochondrial function. We were able to characterize the global effects of these metallodrugs on the proteome and generate hypotheses on hitherto unrecognized mechanisms. Significant differences in the two colon cell lines strongly suggest that knowledge of mechanistic hallmarks of anticancer metallodrug action are imperative for the design of clinical studies and that outcome may be enhanced by means of patient stratification strategies according to these hallmarks.

2022-02-24 | PXD004767 | Pride

Targeting the Scaffold Protein Plectin by an Organometallic as a Strategy to Inhibit Tumour Invasiveness- cytoplasmic proteins of untreated HCT 116 epithelial cells, 3h

Project description:The inability of determining direct molecular targets of metal-based therapeutic agents beyond the platinum class is one of the major bottlenecks in their development. Here, we employ an integrated chemical proteomics and response profiling approach to identify and validate plestatins, based on an organometallic ruthenium(II) scaffold, as selective plectin-targeting agents. Plectin is a giant scaffold protein involved in controlling cytoarchitecture. Subcytotoxic concentrations of plestatins induce drastic morphological phenotypes on the microtubule (MT) network accompanied by a global down-regulation of translational activity. Plestatins possess anti-invasive properties in tumour spheroids and also display tumour-inhibiting effects in vivo after oral administration. The ability of plestatins to alter the MT network via plectin represents a unique mechanism to target MTs and shows promise as an anticancer strategy.

2022-03-01 | PXD005367 | Pride

Response Profiling Using Shotgun Proteomics Enables Establishing Global Metallodrug Mechanisms of Action - cytoplasmic proteins of KP1537-treated HCT 116 epithelial cells

2022-02-24 | PXD004768 | Pride

Targeting the Scaffold Protein Plectin by an Organometallic as a Strategy to Inhibit Tumour Invasiveness - cytoplasmic proteins of untreated HCT 116 epithelial cells, 24h

2022-03-01 | PXD005373 | Pride

Response Profiling Using Shotgun Proteomics Enables Establishing Global Metallodrug Mechanisms of Action - cytoplasmic proteins of KP772-treated HCT 116 epithelial cells

2022-02-24 | PXD004766 | Pride