Dataset Information

A draft map of rhesus monkey tissue proteome for biomedical research.

ABSTRACT: Data from ProteomeXchange, PXD ID: PXD001972. Experiment: male, file: MALE_PROSTATE_MID.msf.mgf. Published as part of PLoS One. 2015 May 14;10(5):e0126243 . From the Abstract: {{i}} Though the rhesus monkey is one of the most valuable non-human primate animal models for various human diseases because of its manageable size and genetic and proteomic similarities with humans, proteomic research using rhesus monkeys still remains challenging due to the lack of a complete protein sequence database and effective strategy. To investigate the most effective and high-throughput proteomic strategy, comparative data analysis was performed employing various protein databases and search engines ... {{/i}}

INSTRUMENT(S): Instrument

ORGANISM(S): Homo_sapiens_viruses, Rhesus_monkey_papillomavirus_1_uid14025, Rhesus

DISEASE(S): Not Available

SUBMITTER: Jin-Gyun Lee, et al.

PROVIDER: GPM32310019946 | GPMDB |

REPOSITORIES: GPMDB

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A draft map of rhesus monkey tissue proteome for biomedical research.

Lee Jin-Gyun JG McKinney Kimberly Q KQ Lee Yong-Yook YY Chung Hae-Na HN Pavlopoulos Antonis J AJ Jung Kook Y KY Kim Woong-Ki WK Kuroda Marcelo J MJ Han David K DK Hwang Sunil S

PloS one 20150514 5

Though the rhesus monkey is one of the most valuable non-human primate animal models for various human diseases because of its manageable size and genetic and proteomic similarities with humans, proteomic research using rhesus monkeys still remains challenging due to the lack of a complete protein sequence database and effective strategy. To investigate the most effective and high-throughput proteomic strategy, comparative data analysis was performed employing various protein databases and searc ...[more]

PMID: 25974132

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Project description:Molecular profiling of human primary cell types is essential for holistic understanding of human biology. Here we present a map of 28 human primary cell types with comprehensive measurements of expressed transcripts and proteins. Three major clusters of epithelial, endothelial, and mesenchymal cell types were observed both at transcriptome and proteome level along with discovery of several cell type specific proteins. Among them, we characterized the novel epithelial specific protein C1orf116 which was further validated with immunohistochemistry across various human tissues. Comprehensive proteome profiling across cell types allowed characterization of ten orphan proteins including TMEM252 and TM4SF18 which lacked protein level evidence. Exhaustive protein database search considering 27 biologically relevant post-translational modifications and 12 chemical modifications was performed, thanks to the increased performance of cloud-based search engine. This, for the first time, provided the catalog of post-translational modifications across cell types, which serve as a resource of PTMs for future studies. We characterized proteins such as protein EEF1A1with various types of PTMs and understudied PTMs including histidine methylation, and O-acetylation of serine. Interestingly, the unexpected higher frequency of dioxidation on tryptophan than that of methionine led us to characterize oxidative mitochondria complex subunit proteins modified through oxidative phosphorylation in mitochondria, which was mostly considered as chemical artifact so far. Overall, these indicated that considering various PTMs during protein database search from non-enriched samples could be routinely used in proteomics experiments. Further, protein database search strategy considering alternative translational start sites, splice junctions, and translational readthrough provided a unique opportunity to refine genome annotation with their proteomic evidence. We believe that our data with the large catalog of transcriptome and proteome of normal human primary cells provide a cornerstone for holistic understanding of cell biology.

Dataset Information

A draft map of rhesus monkey tissue proteome for biomedical research.

Publications

A draft map of rhesus monkey tissue proteome for biomedical research.

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