Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Proteogenomics reanalysis of human testis data

ABSTRACT: Reanalysis of the human testis tissue dataset acquired for the Chromosome-centric Human Proteome Project (C-HPP; PRIDE project PXD002179), with a focus on identifying novel peptides for genome annotation.

INSTRUMENT(S): LTQ Orbitrap Velos

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Testis

SUBMITTER: Hendrik Weisser

LAB HEAD: Jyoti Sharma Choudhary

PROVIDER: PXD004785 | Pride | 2016-11-28

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	CHPP_SDS_3001.mzML	Mzml
	CHPP_SDS_3001.raw	Raw
	CHPP_SDS_3001_MSGFplus.mzid.gz	Mzid
	CHPP_SDS_3001_Mascot.mzid.gz	Mzid
	CHPP_SDS_3002.mzML	Mzml

Items per page:

1 - 5 of 601

Publications

Flexible Data Analysis Pipeline for High-Confidence Proteogenomics.

Weisser Hendrik H Wright James C JC Mudge Jonathan M JM Gutenbrunner Petra P Choudhary Jyoti S JS

Journal of proteome research 20161110 12

Proteogenomics leverages information derived from proteomic data to improve genome annotations. Of particular interest are "novel" peptides that provide direct evidence of protein expression for genomic regions not previously annotated as protein-coding. We present a modular, automated data analysis pipeline aimed at detecting such "novel" peptides in proteomic data sets. This pipeline implements criteria developed by proteomics and genome annotation experts for high-stringency peptide identific ...[more]

PMID: 27786492

Similar Datasets

Improving Human Genome Annotation Using a High-Stringency Proteogenomics Workflow

Project description:Reanalysis of three large human tissue proteomics datasets using a bespoke GENCODE database and multiOTHER algorithm high confidence pipeline.

2016-05-27 | PXD002967 | Pride

Identification of universally applicable and species-specific marker peptides for Bacillus anthracis

Project description:Anthrax is a zoonotic infection caused by the bacterium Bacillus anthracis (BA), a gram-positive, aerobic, spore-forming bacterium that can be misused as a biowarfare agent. The major patho-genicity factors of BA are encoded by genes located on two extrachromosomal plasmids, which are often targeted for specific identification of this pathogen. However, more recent findings show that these plasmids are not a unique feature of BA but can also occur in other Bacillus species. Furthermore, BA is a member of the Bacillus cereus group, a subgroup of closely related Bacilli. Due to the high genetic similarity within this group, it is a challenge to distinguish BA from other members of this group. In this study, we investigated if it is possible to identify species-specific and universally applicable marker peptides for BA. For this purpose, we applied a high-resolution mass spectrometry-based approach for 42 BA isolates. Together with the genomic sequencing data and by developing a bioinformatics data evaluation pipeline, which uses a database containing most of the publicly available protein sequences worldwide (UniParc), we were able to identify eleven universal marker peptides unique to BA, which are located on the chromosome and there-fore might overcome known problems like observable loss of plasmids in environmental species, plasmid loss during cultivation in the lab and that the virulence plasmids are not necessarily a unique feature of BA. The identified chromosomally encoded markers in this study could extend the small panel of already existing chromosomal targets and together with targets for the viru-lence plasmids may pave the way to an even more reliable identification of BA using genomics- as well as proteomics-based techniques.

2023-01-05 | PXD036243 | Pride

Low-Density Lipoprotein Receptor fuels the cellular cholesterol-mTORC1 axis required for CD8+ T cell activation

Project description:In this study, the contribution of cholesterol uptake by the low-density-lipoprotein receptor (LDLR) in the metabolic reprogramming of activated T cells was investigated at proteome level by mass-spectrometry-assisted shotgun proteomics.

2022-09-20 | PXD030365 | Pride

Comparison of the transcriptome, translatome and proteome response to diurnal oscillations in cyanobacteria

Project description:The aim of this study was to find the cause for the previously reported inconsistency between oscillating transcription and constant protein levels under day-night growth conditions in cyanobacteria. To determine whether translational regulation counteracts transcriptional changes, Synechocystis sp. PCC 6803 was cultivated in an artificial day-night setting and the level of transcription, translation and protein was measured across the genome at different time points using mRNA sequencing, ribosome profiling and quantitative proteomics. This proteomics data set represents one layer of a larger data set covering three 'omics' levels.

2021-09-10 | PXD023812 | Pride

Bottom-up proteomics of EZH2 mutants in isogenic cells

Project description:The Enhancer of Zeste 2 Polycomb Repressive Complex 2 Subunit (EZH2) is an essential epigenetic modifier able to methylate lysine 27 on histone H3 (H3K27) to induce chromatin compaction, protein complex recruitment and ultimately transcriptional repression. Hematologic malignancies, including Diffuse Large B cell lymphoma (DLBCL) and Acute myeloid leukemia (AML) have shown a high EZH2-mutation frequency (>20%) associated with poor clinical outcomes. Particularly, two distinct oncogenic mutations, so-called gain-of-function (Y641F and A677G) and loss-of-function (H689A and F667I) are found in the catalytic domain of EZH2. In this study, a comprehensive multi-omics approach was employed to characterize downstream effects of H3K27me3 deposition driven by EZH2 mutations. Human embryonic kidney cells (HEK293T) were transfected to generate three stable EZH2 mutants: EZH2(Y641F), EZH2(A677G), and EZH2(H689A/F667I), which were validated via immunoblotting and DIA-MS-based histone profiling assay. Subsequently, constructs were analyzed under a comprehensive multi-omics approach including label-free whole-cell proteomics, acquired with a Bruker timsTOF Pro HPLC-MS/MS with Ion Mobility. Important protein interactors at nuclear level were dysregulated, such as SMYD3 (SET and MYND domain containing 3), NSD2 (nuclear receptor binding SET domain protein 2) and CHD7 (chromodomain helicase DNA binding protein 7), suggesting a cooperative network of chromatin remodelers for gene expression reprogramming.

2023-10-24 | PXD042875 | Pride

Identification of regulatory networks and crosstalk factors in brown adipose tissue and liver of a cold-exposed cardiometabolic mouse model

Project description:oActivationf brown adipose tissue (BAT) has gained central attention due to its known ability to dissipate energy and counteract cardiometabolic diseases (CMDs). The cold exposure on BAT activation and the induction of thermogenesis have been extensively studied, but reports on the effects at the proteomic level in metabolic tissues of animal models mimicking CMD in humans are lacking.

2024-08-16 | PXD051640 | Pride

Investigation of protein allocation and utilization in the versatile chemolithoautotroph Cupriavidus necator

Project description:The aim of this study was to understand how autotrophic (CO2-fixing) bacteria balance the different needs for substrate assimilation, growth functions, and resilience in order to thrive in their environment.To this end, the proteome of the model chemolithoautotroph Ralstonia eutropha a.k.a. Cupriavidus necator was studied in different environmental conditions (four limiting substrates, and five different growth rates). Cupriavidus was cultivated in substrate-limited chemostats with fructose, formate, succinate and ammonium limitation to obtain steady state cell samples. The dilution rate/growth rate was increased step-wise from 0.05 to 0.25 1/h in 0.05 steps. Protein quantity was determined by LC-MS, and enzyme utilization was investigated by resource balance analysis modeling.

2022-02-17 | PXD024819 | Pride

PeptideShaker - A complex standard for protein identification, designed by evolution

Project description:Mass spectrometry-based proteomics data, obtained experimentally or via public repositories, remains challenging to analyze. This challenge is particularly felt when re-analysing or re-purposing public data sets, endeavours that otherwise hold great potential. PeptideShaker is an open source system that greatly simplifies the interpretation and dissemination of proteomics data, and that automates the re-analysis of public data, thus completing the proteomics data cycle (http://peptide-shaker.googlecode.com).

2014-06-24 | PXD001077 | Pride

MHCquant: Automated and reproducible data analysis for immunopeptidomics

Project description:Personalized multi-peptide vaccines are currently being discussed intensively for tumor immunotherapy. In order to find epitopes - short, immunogenic peptides - suitable to elicit an immune response, human leukocyte antigen-presented peptides from cancer tissue samples are purified using immunoaffinity purification and analyzed by high performance liquid chromatography coupled to mass spectrometry. Here we report on a novel computational pipeline to identify peptides from large-scale immunopeptidomics raw data sets. In the conducted experiments we benchmarked our workflow to other existing mass spectrometry analysis software and achieved higher sensitivity. A dataset of 38 HLA immunopeptidomics raw files of peripheral blood mononuclear cells (PBMCs) from 10 healthy volunteers and 4 JY cell lines was used to assess the performance of the pipeline at each processing step. In addition, 66 isotope labeled known HLA-presented peptides were spiked into the JY cell extracts decreasing in concentration by log10 steps from 100 fmol to 0.1 fmol.

2019-10-14 | PXD011628 | Pride

Generation of ENSEMBL-based proteogenomics databases boost the identification of novel peptides

Project description:A novel bioinformatics tool pypgatk and the pgdb workflow is presented in study to create proteogenomics databases based on ENSEMBL resources. The tools allow the generation of protein sequences from novel protein-coding transcripts by performing a three-frame translation of pseudogenes, lncRNAs, and other non-canonical transcripts, such as those produced by alternative splicing events. It also includes exonic out-of-frame translation from otherwise canonical protein-coding mRNAs. Moreover, the tool enables the generation of variant protein sequences from multiple sources of genomic variants including COSMIC, cBioportal, gnomAD, and mutations detected from sequencing of patient samples. pypgatk and pgdb provide multiple functionalities for database handling, notably optimized target/decoy generation by the algorithm DecoyPyrat. Finally, we perform a reanalysis of four public datasets in PRIDE by generating cell-type specific databases for 65 cell lines using the pypgatk and pgdb workflow, revealing a wealth of non-canonical or cryptic peptides amounting to more than 10% of the total number of peptides identified (43,501 out of 402,512).

2021-10-26 | PXD029360 | 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