Dataset Information

Towards defining the nuclear proteome.

ABSTRACT: BACKGROUND: The nucleus is a complex cellular organelle and accurately defining its protein content is essential before any systematic characterization can be considered. RESULTS: We report direct evidence for 2,568 mammalian proteins within the nuclear proteome: the nuclear subcellular localization of 1,529 proteins based on a high-throughput subcellular localization protocol of full-length proteins and an additional 1,039 proteins for which clear experimental evidence is documented in published literature. This is direct evidence that the nuclear proteome consists of at least 14% of the entire proteome. This dataset was used to evaluate computational approaches designed to identify additional nuclear proteins. CONCLUSION: This represents direct experimental evidence that the nuclear proteome consists of at least 14% of the entire proteome. This high-quality nuclear proteome dataset was used to evaluate computational approaches designed to identify additional nuclear proteins. Based on this analysis, researchers can determine the stringency and types of lines of evidence they consider to infer the size and complement of the nuclear proteome.

SUBMITTER: Fink JL

PROVIDER: S-EPMC2395251 | biostudies-literature | 2008

REPOSITORIES: biostudies-literature

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Towards defining the nuclear proteome.

Fink J Lynn JL Karunaratne Seetha S Mittal Amit A Gardiner Donald M DM Hamilton Nicholas N Mahony Donna D Kai Chikatoshi C Suzuki Harukazu H Hayashizaki Yosihide Y Teasdale Rohan D RD

Genome biology 20080123 1

<h4>Background</h4>The nucleus is a complex cellular organelle and accurately defining its protein content is essential before any systematic characterization can be considered.<h4>Results</h4>We report direct evidence for 2,568 mammalian proteins within the nuclear proteome: the nuclear subcellular localization of 1,529 proteins based on a high-throughput subcellular localization protocol of full-length proteins and an additional 1,039 proteins for which clear experimental evidence is documente ...[more]

PMID: 18211718

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Project description:BACKGROUND:Knowledge of the mouse salivary proteome is not well documented and as a result, very limited. Currently, several salivary proteins remain unidentified and for some others, their function yet to be determined. The goal of the present study is to utilize mass spectrometry analysis to widen our knowledge of mouse salivary proteins, and through extensive database searches, provide further insight into the array of proteins that can be found in saliva. A comprehensive mouse salivary proteome will also facilitate the development of mouse models to study specific biomarkers of many human diseases. RESULTS:Individual saliva samples were collected from male and female mice, and later pooled according to sex. Two pools of saliva from female mice (2 samples/pool) and 2 pools of saliva from male mice were used for analysis utilizing high performance liquid chromatograph mass spectrometry (nano-RPLC-MS/MS). The resulting datasets identified 345 proteins: 174 proteins were represented in saliva obtained from both sexes, as well as 82 others that were more female specific and 89 that were more male specific. Of these sex linked proteins, twelve were identified as exclusively sex-limited; 10 unique to males and 2 unique to females. Functional analysis of the 345 proteins identified 128 proteins with catalytic activity characteristics; indicative of proteins involved in digestion, and 35 proteins associated with stress response, host defense, and wound healing functions. Submission of the list of 345 proteins to the BioMart data mining tool in the Ensembl database further allowed us to identify a total of 283 orthologous human genes, of which, 131 proteins were recently reported to be present in the human salivary proteome. CONCLUSIONS:The present study is the most comprehensive list to date of the proteins that constitute the mouse salivary proteome. The data presented can serve as a useful resource for identifying potentially useful biomarkers of human health and disease.

Dataset Information

Towards defining the nuclear proteome.

Publications

Towards defining the nuclear proteome.

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