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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

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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

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

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

Human_Testis_QE-HF

2019-06-17 | MSV000083983 | MassIVE

Chr16-HPP.Pilot experiment.JPR HPP Special issue

Project description:"The Chromosome 16 Consortium is integrated in the Human Proteome Project that aims to develop an entire map of the proteins encoded by the human genome following a gene-centric strategy (C-HPP) to make progress in the understanding of human biology in health and disease (B/D-HPP). To characterize the proteome of Chr16, three cell lines were selected, MCF7 breast cancer human epithelial cells, CCD18 human colon fibroblasts, and Jurkat human T lymphocytes. "

2013-01-11 | PXD000039 | 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

Human Testis LC-MS/MS - Multi-Protease Strategy Identifies Three PE2 Missing Proteins in Human Testis Tissue

Project description:Missing proteins(MPs) investigation is one of the critical missions of Chromosome-based Human Proteome Project(C-HPP). Through analyzing sequence of MPs from neXtProt database, we found that there are no detectable tryptic peptides for some MPs. Here, we attmept a multi-enzymes strategy to cover this problem. Lys-C, Glu-C and LysargiNase are used to produce more unique and detectable peptides of MPs.

2017-10-09 | PXD006465 | Pride

Chr16-HPP. Shotgun Analysis improvement. JPR HPP Special issue 2013. MCF7 Cell line.

Project description:The Chromosome 16 Consortium is integrated in the Human Proteome Project that aims to develop an entire map of the proteins encoded by the human genome following a gene-centric strategy (C-HPP) to make progress in the understanding of human biology in health and disease (B/D-HPP). To do this study four human cell lines were selected, MCF7 epithelial cells, CCD18 colon fibroblasts, Ramos and Jurkat B and T lymphocytes respectively. In particular, this subset includes all the data regarding the MCF7 cell line. 6 laboratories contributed to compile all the reported data.

2013-09-04 | PXD000442 | Pride

Chr16-HPP. Shotgun Analysis improvement. JPR HPP Special issue 2013. CCD18 Cell line.

Project description:The Chromosome 16 Consortium is integrated in the Human Proteome Project that aims to develop an entire map of the proteins encoded by the human genome following a gene-centric strategy (C-HPP) to make progress in the understanding of human biology in health and disease (B/D-HPP). To do this study four human cell lines were selected, MCF7 epithelial cells, CCD18 colon fibroblasts, Ramos and Jurkat B and T lymphocytes respectively. In particular, this subset includes all the data regarding the CCD18 cell line. 6 laboratories contributed to compile all the reported data.

2013-09-05 | PXD000449 | Pride

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