Browse
Submit Data
Databases
API
Help

Dataset Information

330 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

CharmeRT - CharmeRT: Boosting peptide identifications by chimeric spectra identification and retention time prediction

ABSTRACT: Files include several HeLa tryptic digests with different isolation widths and different gradient times for chimeric spectra identification and validation, each of them as three technical replicates

INSTRUMENT(S): Q Exactive

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Hela Cell

SUBMITTER: Viktoria Dorfer

LAB HEAD: Karl Mechtler

PROVIDER: PXD007750 | Pride | 2018-06-12

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	HeLa_100ng_isow2_3hgradient_datasetI_rep1.msf	Msf
	HeLa_100ng_isow2_3hgradient_datasetI_rep1.raw	Raw
	HeLa_100ng_isow2_3hgradient_datasetI_rep2.msf	Msf
	HeLa_100ng_isow2_3hgradient_datasetI_rep2.raw	Raw
	HeLa_100ng_isow2_3hgradient_datasetI_rep3.msf	Msf

Items per page:

1 - 5 of 48

Publications

CharmeRT: Boosting Peptide Identifications by Chimeric Spectra Identification and Retention Time Prediction.

Dorfer Viktoria V Maltsev Sergey S Winkler Stephan S Mechtler Karl K

Journal of proteome research 20180628 8

Coeluting peptides are still a major challenge for the identification and validation of MS/MS spectra, but carry great potential. To tackle these problems, we have developed the here presented CharmeRT workflow, combining a chimeric spectra identification strategy implemented as part of the MS Amanda algorithm with the validation system Elutator, which incorporates a highly accurate retention time prediction algorithm. For high-resolution data sets this workflow identifies 38-64% chimeric spectr ...[more]

PMID: 29863353

Similar Datasets

Compensatory induction of MYC expression by sustained CDK9 inhibition via a BRD4-dependent mechanism: Pol II occupancy profiling by ChIP-Seq in HeLa cell line in the presence or absence of CDK9 inhibition

Project description:CDK9 is the kinase subunit of P-TEFb that enables RNA polymerase (Pol) II to transit from promoter-proximal pausing to productive elongation. Although considerable interest exists in CDK9 as a therapeutic target, little progress has been made due to the lack of highly selective inhibitors. Here, we describe the development of i-CDK9 as such an inhibitor that potently suppresses CDK9 phosphorylation of substrates and causes genome-wide Pol II pausing. While most genes experience reduced expression, MYC and other primary response genes increase expression upon sustained i-CDK9 treatment. Essential for this increase, the bromodomain protein BRD4 captures P-TEFb from 7SK snRNP to deliver to target genes and also enhances CDK9’s activity and resistance to inhibition. Because the i-CDK9-induced MYC expression and binding to P-TEFb compensate for P-TEFb’s loss of activity, only the simultaneous inhibition of CDK9 and MYC can efficiently induce growth arrest and apoptosis of cancer cells, suggesting the potential of a combinatorial treatment strategy. ChIP-seq of Pol II in HeLa cells before or after i-CDk9 treatment

2015-06-17 | E-GEOD-60953 | biostudies-arrayexpress

Pipelines and Systems for Threshold Avoiding Quantification of LC-MS/MS data

Project description:The accurate processing of complex LC-MS/MS data from biological samples is a major challenge for metabolomics, proteomics and related approaches. Here we present the Pipelines and Systems for Threshold Avoiding Quantification (PASTAQ) LC-MS/MS pre-processing toolset, which allows highly accurate quantification of data-dependent acquisition (DDA) LC-MS/MS datasets. PASTAQ performs compound quantification using single-stage (MS1) data and implements novel algorithms for high-performance and accurate quantification, retention time alignment, feature detection, and linking annotations frommultiple identification engines. PASTAQ offers straightforward parametrization and automatic generation of quality control plots for data and pre-processing assessment. This design results in smaller variance when analyzing replicates of proteomes mixed with known ratios, and allows the detection of peptides with a larger dynamic concentration range compared to widely used proteomics preprocessing tools. The performance of the pipeline is also demonstrated in a biological human serum dataset for the identification of gender related proteins.

2021-08-18 | PXD024584 | Pride

Expression data from HeLa cells after hnRNP L knockdown (versus luciferase control), including cycloheximide treatment

Project description:Transient siRNA-mediated knockdown of hnRNP L, followed by cycloheximide treatment to eliminate NMD. Supplementary files GSE37561_activated_exon.txt and GSE37561_repressed_exon.txt list exons predicted to be activated and repressed by hnRNPL, respectively. 3 biological replicates of hnRNP L (luciferase) knockdown samples

2014-02-13 | E-GEOD-37561 | biostudies-arrayexpress

HCD fragmentation of glycated peptides

Project description:Protein glycation is a highly disease-relevant concentration-dependent non-enzymatic reaction of reducing sugars with amine groups of proteins to form early as well as advanced glycation products (AGEs). To complement our blood proteomics studies in diabetics, we here established higher-energy collisional dissociation (HCD) fragmentation on Orbitrap mass spectrometers for analyzing protein glycation. We evaluated parameters to most efficiently fragment and identify early glycation products on in-vitro glycated model proteins. We then applied our optimized workflow for glycation analysis of the entire HeLa proteome as well as for single-run analysis of undepleted and unenriched blood plasma and whole blood. We conclude that HCD fragmentation is well suited for analyzing glycated peptides when integrating the dominant neutral loss into the analysis and that single-run plasma proteomics measurements have great potential to diagnosing the diabetic status of patients.

2017-01-02 | PXD004182 | Pride

Genome-wide profiling of H3K27ac, H3K4me1, H3K27me3 and H3K9me3 (ChIP-seq) in U2OS-GR and U2OS-AR cells

Project description:We performed ChIP-seq targeting the H3K27ac, H3K4me1, H3K27me3 and H3K9me3 in the U2OS-GR and U2OS-AR cell lines. The cell lines are derived from U2OS ATTC:HTB-96 and stably transfected with an expression construct for either rat GR or human AR, respectively. The U2OS-GR cells were treated with dexamethasone (1 µM) or vehicle (ethanol) for 90 minutes. The U2OS-AR cells were treated with R1881 (5 nM) or vehicle (DMSO) for 4 hours.

2021-03-09 | E-MTAB-9617 | biostudies-arrayexpress

Elimination of mitochondrial DNA variants by nuclear genome transfer in human oocytes.

Project description:Nuclear genome exchange between different oocytes results in efficient development and stem cell derivation. No differences in homozgyous CNVs were found between swaPS and pES lines. No differences in total copy number variations were found between the swaPS and pES lines. DNA was isolated from cultured cells. Affymetrix SNP arrays were used in accordance with the manufacturer's instructions. Copy number analysis was performed using NEXUS 6.0.

2013-01-01 | E-GEOD-42271 | biostudies-arrayexpress

Transcriptional regulation of FAM134B by TFEB/TFE3 controls ER-phagy in response to starvation and chondrocyte differentiation

Project description:Lysosomal degradation of the endoplasmic reticulum (ER) via autophagy (ER-phagy) is emerging as a critical regulator of cell homeostasis and function1. The recent identification of ER-phagy receptors has shed light on the molecular mechanism underlining this process; however, the signaling pathways regulating ER-phagy in response to cellular needs are still largely unknown. We found that the nutrient responsive transcription factors TFEB and TFE3 - master regulators of lysosomal biogenesis and autophagy2- control ER-phagy by inducing the expression of the ER-phagy receptor FAM134B. The TFEB/TFE3-FAM134B axis promotes ER-phagy activation upon prolonged starvation. In addition, we discovered that this pathway is activated in chondrocytes by FGF signaling, a critical regulator of cell differentiation 3. FGF signaling induces a JNK-dependent proteasomal degradation of the insulin receptor substrate 1, which inhibits the insulin-PI3K-PKB/Akt-mTORC1 pathway and promotes TFEB/TFE3 nuclear translocation and FAM134B induction. Consistent with a role of the TFEB/TFE3-FAM134B axis in chondrocytes, FAM134B knock-down impairs cartilage growth and mineralization in medaka fish. This study identifies a new signaling pathway that allows ER-phagy to respond to both metabolic and developmental cues.

2020-07-15 | PXD015326 | Pride

Picky – a simple online method designer for targeted proteomics

Project description:The accuracy of the retention time prediction build into picky was tested on a digested HeLa sample analyzed with a standard data-dependend acquisition method (top20).

2017-12-13 | PXD008212 | Pride

Activation of autophagy by starvation and mTOR inhibition in three human cell lines

Project description:The aim of the project was to characterize changes in gene expression that are associated with induced autophagic flux. We engineered HeLa, HEK 293 and SH-SY5Y cell lines to express tandem-fluorecent LC3 (tf-LC3). The ratio of the red and green fluorophores indicated how much of the LC3 is in the acidic interior of lysosomes, which was a proxy measure for autophagic flux. RNA sequencing was performed for the cell lines at baseline and 1h, 15h and 30h after treatments. Additional untreated samples were also sequenced at some but not all time points. Autophagy was induced by amino acid starvation or mTOR inhibition (AZD8055).

2022-08-25 | E-MTAB-12020 | biostudies-arrayexpress

Transcriptional regulation of ER-phagy by MiT/TFE factors controls chondrocyte differentiation and bone formation

Project description:Lysosomal-autophagic degradation of Endoplasmic Reticulum via autophagy (ER-phagy) is emerging as critical regulator of ER homeostasis and function. However, the molecular mechanisms governing ER-phagy are still unknown. Working in chondrocytes, we found that ER-phagy and lysosome biogenesis are co-activated by FGF signaling during hypertrophic differentiation, a mandatory step for bone formation. FGF induced ER-phagy trough IRS1-dependent inhibition of the insulin signaling and activation of MiT/TFE transcription factors, master regulators of lysosome biogenesis. MiT/TFE promoted ER-phagy through the induction of the ER-phagy receptor FAM134B. Notably, the activation of ER-phagy promotes chondrocytes differentiation and secretion of factors required for cartilage replacement by bone. Consistently, medaka fish knock-down for FAM134B have impaired ossification of cranial bones. Thus, ER-phagy is a transcriptionally regulated process that participates to cell differentiation during development.

2020-07-15 | PXD015331 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data