Dataset Information

Zebra fish fin proteome - Proteome profile of zebrafish caudal fin based on one-dimensional gel electrophoresis LCMS/MS and two-dimensional gel electrophoresis MALDI MS/MS analysis

ABSTRACT: Fin

INSTRUMENT(S): LTQ FT, instrument model

ORGANISM(S): Danio Rerio (zebrafish) (brachydanio Rerio)

SUBMITTER: Mohammed Idris

PROVIDER: PRD000300 | Pride | 2011-05-05

REPOSITORIES: Pride

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Dataset's files

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			Action	DRS
	PRIDE_Exp_Complete_Ac_13681.pride.mgf.gz	Mgf
	PRIDE_Exp_Complete_Ac_13681.xml.gz	Xml
	PRIDE_Exp_Complete_Ac_13682.pride.mgf.gz	Mgf
	PRIDE_Exp_Complete_Ac_13682.xml.gz	Xml
	PRIDE_Exp_Complete_Ac_13683.pride.mgf.gz	Mgf

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Publications

Proteome profile of zebrafish caudal fin based on one-dimensional gel electrophoresis LCMS/MS and two-dimensional gel electrophoresis MALDI MS/MS analysis.

Singh Sachin K SK Lakshmi Mula G Meena MG Saxena Sandeep S Swamy Cherukuvada V Brahmendra CV Idris Mohammed M MM

Journal of separation science 20101202 2

Zebrafish (Danio rerio) is the widely used vertebrate model animal for understanding the complexity of development and disease process. Zebrafish has been also extensively used in understanding the mechanism of regeneration for its extensive capability of regenerating fins and other tissues. We have analyzed the proteome profile of zebrafish caudal fin in its native state based on one-dimensional gel electrophoresis LCMS/MS and two-dimensional gel electrophoresis MS/MS analyses. A total of 417 p ...[more]

PMID: 21246729

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Project description:BackgroundProteome analysis is frequently applied in identifying the proteins or biomarkers in knee synovial fluids (SF) that are associated with osteoarthritis and other arthritic disorders. The 2-dimensional gel electrophoresis (2-DE) is the technique of choice in these studies. Disease biomarkers usually appear in low concentrations and may be masked by high abundant proteins. Therefore, the main aim of this study was to find the most suitable sample preparation method that can optimize the expression of proteins on 2-DE gels that can be used to develop a reference proteome picture for non-osteoarthritic knee synovial fluid samples. Proteome pictures obtained from osteoarthritic knee synovial fluids can then be compared with the reference proteome pictures obtained in this study to assist us in identifying the disease biomarkers more correctly.ResultsThe proteomic tool of 2-DE with immobilized pH gradients was applied in this study. A total of 12 2-DE gel images were constructed from SF samples that were free of osteoarthritis. In these samples, 3 were not treated with any sample preparation methods, 3 were treated with acetone, 3 were treated with 2-DE Clean-Up Kit, and 3 were treated with the combination of acetone and 2-D Clean-Up Kit prior to 2-DE analysis. Gel images were analyzed using the PDQuest Basic 8.0.1 Analytical software. Protein spots that were of interest were excised from the gels and sent for identification by mass spectrometry. Total SF total protein concentration was calculated to be 21.98 ± 0.86 mg/mL. The untreated SF samples were detected to have 456 ± 33 protein spots on 2-DE gel images. Acetone treated SF samples were detected to have 320 ± 28 protein spots, 2-D Clean-Up Kit treated SF samples were detected to have 413 ± 31 protein spots, and the combined treatment method of acetone and 2-D Clean-Up Kit was detected to have 278 ± 26 protein spots 2-DE gel images. SF samples treated with 2-D Clean-Up Kit revealed clearer presentation of the isoforms and increased intensities of the less abundant proteins of haptoglobin, apolipoprotein A-IV, prostaglandin-D synthase, alpha-1B-glycoprotein, and alpha-2-HS-glycoprotein on 2-DE gel images as compared with untreated SF samples and SF samples treated with acetone.ConclusionsThe acetone precipitation method and the combined treatment effect of acetone and 2-DE Clean-Up Kit are not preferred in preparing SF samples for 2-DE analysis as both protein intensities and numbers decrease significantly. On the other hand, 2-D Clean-Up Kit treated SF samples revealed clearer isoforms and higher intensities for the less abundant proteins of haptoglobin, apolipoprotein A-IV, prostaglandin-D synthase, alpha-1B-glycoprotein, and alpha-2-HS-glycoprotein on 2-DE gels. As a result, it is recommended that SF samples should be treated with protein clean up products such as 2-D Clean-Up Kit first before conducting proteomic research in searching for the relevant biomarkers associated with knee osteoarthritis.