Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

1 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 (ncbitaxon:9606)

SUBMITTER: Jyoti Sharma Choudhary

PROVIDER: MSV000083973 | MassIVE | Thu Jun 13 09:49:00 BST 2019

SECONDARY ACCESSION(S): PXD004785

REPOSITORIES: MassIVE

ACCESS DATA

Json Xml

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

Proteogenomics reanalysis of human testis data

Project description: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.

2016-11-28 | PXD004785 | Pride

Human_Testis_QE-HF - Deep Coverage Proteomics Identifies More Low-Abundance Missing Proteins in Human Testis Tissue with Q-Exactive HF Mass Spectrometer

Project description:The Chromosome-Centric Human Proteome Project (C-HPP) aims at finding existence evidence of missing proteins (MPs) at the early stage. Based on previous research, it has been proved that human testis tissue is suitable for further research of MPs because of its high gene expression level and high transcriptome complexity. However, the limits of dynamic range in mass spectrometric analysis and the deficiency in sensitivity and resolution will seriously affect the detection efficiency. In this study, we used Q-Exactive HF to detect three individual testis tissues dealted with two separation methods (tricine-SDS-PAGE and SDS-PAGE).

2016-09-30 | PXD004092 | Pride

CN-CHPP 2015 Testis Project - Tissue-Based Proteogenomics Reveals that Human Testis Endows Plentiful Missing Proteins

Project description:The testis tissue-based trans-omics was a feasible approach to find more missing proteins (MPs) because it was reported higher gene expression found in testis tissues. Three testis tissues and two protein separation strategies were selected to quantitatively evaluate gene expression abundance at the proteomic and transcriptomic levels. The project have been jointly supervised by Ping Xu and Siqi Liu.

2015-11-03 | PXD002179 | Pride

2018CHPP - Digging for Missing Proteins Using Low-Molecular-Weight Protein Enrichment and a "Mirror Protease" Strategy

Project description:ABSTRACT Since 2012, Chromosome-Centric Human Proteome Project (C-HPP) launched the journey of missing proteins (MPs) investigation for completing human proteome project (HPP). We found the majority of MPs were distributed in low molecular weight (LMW) ranges, especially in 0-40 kDa. The identification of LMW proteins is challenging owing to their low length, low abundancy, and hydrophobicity. Even worse, many sequences from Trypsin digestion are unlikely to yield detectable peptides or composed less number of observable peptides in MS detection. Therefore, we focused on small MPs by combining LMW protein enrichment and mirror-protease strategy on human testis samples. The in-depth testis LMW protein profiling documented 4,063 proteins from which 2,565 proteins were belong to LMW proteins and 1,130 proteins had mirror peptides. This provided mass spectral evidence for small MPs further verification, and two MPs were verified in seven identified MPs. For Q8N688, confident peptides were verified from Trypsin and LysargiNase digestions, and continuous b/y-ion peptide was obtained by mirror-spectrum matching. Two verified peptides of Q86WR6 were from gel-separation and gel-elution dataset, respectively. And the other 5 MPs cannot be distinguished sufficiently as PE1, but need more verification information.

2018-10-04 | PXD010093 | Pride

CN-CHPP 2015 Testis Project

2018-06-26 | MSV000082510 | MassIVE

Analysis of transcription in the Drosophila melanogaster testis

Project description:Identification and annotation of all the genes in the sequenced Drosophila genome is a work in progress. Wild-type testis function requires many genes and is thus of potentially high value for the identification of transcription units. We therefore undertook a survey of the repertoire of genes expressed in the Drosophila testis by computational and microarray analysis. We generated 3141 high-quality testis expressed sequence tags (ESTs). Testis ESTs computationally collapsed into 1560 cDNA set used for further analysis. Of those, 11% correspond to named genes, and 33% provide biological evidence for a predicted gene. A surprising 47% fail to align with existing ESTs and 16% with predicted genes in the current genome release. EST frequency and microarray expression profiles indicate that the testis mRNA population is highly complex and shows an extended range of transcript abundance. Furthermore, >80% of the genes expressed in the testis showed onefold overexpression relative to ovaries, or gonadectomized flies. Additionally, >3% showed more than threefold overexpression at p <0.05. Surprisingly, 22% of the genes most highly overexpressed in testis match Drosophila genomic sequence, but not predicted genes. These data strongly support the idea that sequencing additional cDNA libraries from defined tissues, such as testis, will be important tools for refined annotation of the Drosophila genome. Additionally, these data suggest that the number of genes in Drosophila will significantly exceed the conservative estimate of 13,601. Keywords: other

2003-07-16 | GSE462 | GEO

Enrichment strategy for searching missing protein

Project description:Enrichment strategy for searching missing protein is a project under the guidance of Chromosome-Centric Human Proteome Project (C-HPP). We developed systematical enrichment strategies for revealing the existence of MPs including low molecular weight (LMW), membrane proteins, post-translational modification (PTM), and nucleic acid associated.

2015-07-14 | PXD002255 | Pride

Human_Testis_QE-HF

2019-06-17 | MSV000083983 | MassIVE

Reanalysis of dataset PXD005780: “Relating human gut metagenome and metaproteome”

Project description:This project contains raw data, intermediate files and results is a re-analysis of the publicly available dataset from the PRIDE dataset PXD005780. The RAW files were processed using ThermoRawFileParser, SearchGUI and PeptideShaker through standard settings (see ‘Data Processing Protocol’). This reanalysis work is part of the MetaPUF (MetaProteomics with Unknown Function) project, which is a collaboration between EMBL-EBI and the University of Luxembourg. The dataset was selected with the following conditions: 1. It has been made publicly available in PRIDE and focuses on metaproteomics of the human gut; 2. The corresponding metagenomics assemblies were also available from ENA (European Nucleotide Archive) or MGnify. The processed peptide reports for each sample are available to view at the contig level on the MGnify website. In total, the reanalysis identified 15,417 unique proteins from 15 samples.

2022-05-04 | PXD032303 | Pride

Reanalysis of dataset PXD003791: “MuSt multiomics - Integrated multi-omics of the human gut microbiome in a case study of familial type 1 diabetes”

Project description:This project contains raw data, intermediate files and results is a re-analysis of the publicly available dataset from the PRIDE dataset PXD003791. The RAW files were processed using ThermoRawFileParser, SearchGUI and PeptideShaker through standard settings (see ‘Data Processing Protocol’). This reanalysis work is part of the MetaPUF (MetaProteomics with Unknown Function) project, which is a collaboration between EMBL-EBI and the University of Luxembourg. The dataset was selected with the following conditions: 1. It has been made publicly available in PRIDE and focuses on metaproteomics of the human gut; 2. The corresponding metagenomics assemblies were also available from ENA (European Nucleotide Archive) or MGnify. The processed peptide reports for each sample are available to view at the contig level on the MGnify website. In total, the reanalysis identified 59,613 unique proteins from 36 samples.

2022-06-17 | PXD034617 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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