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Dramatic improvement of proteomic analysis of zebrafish liver tumor by effective protein extraction with sodium deoxycholate and heat denaturation.

Wang J, Lee YM, Li C, Li P, Li Z, Lim TK, Gong Z, Lin Q - Int J Anal Chem (2015)

Bottom Line: The laborious gel-based approach is slowly being replaced by the advancing in-solution digestion approach.However, there are still several difficulties such as difficult-to-solubilize proteins, poor proteomic analysis in complex tissue samples, and the presence of sample impurities.Henceforth, there is a great demand to formulate a highly efficient protein extraction buffer with high protein extraction efficiency from tissue samples, high compatibility with in-solution digestion, reduced number of sample handling steps to reduce sample loss, low time consumption, low cost, and ease of usage.

View Article: PubMed Central - PubMed

Affiliation: Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543.

ABSTRACT
Majority of the proteomic studies on tissue samples involve the use of gel-based approach for profiling and digestion. The laborious gel-based approach is slowly being replaced by the advancing in-solution digestion approach. However, there are still several difficulties such as difficult-to-solubilize proteins, poor proteomic analysis in complex tissue samples, and the presence of sample impurities. Henceforth, there is a great demand to formulate a highly efficient protein extraction buffer with high protein extraction efficiency from tissue samples, high compatibility with in-solution digestion, reduced number of sample handling steps to reduce sample loss, low time consumption, low cost, and ease of usage. Here, we evaluated various existing protein extraction buffers with zebrafish liver tumor samples and found that sodium deoxycholate- (DOC-) based extraction buffer with heat denaturation was the most effective approach for highly efficient extraction of proteins from complex tissues such as the zebrafish liver tumor. A total of 4,790 proteins have been identified using shotgun proteomics approach with 2D LC, which to our knowledge is the most comprehensive study for zebrafish liver tumor proteome.

No MeSH data available.


Related in: MedlinePlus

Distribution of proteins identified from the 2D shotgun dataset of DOC-extracted liver tumor samples based on (a) subcellular localization; (b) biological processes; (c) molecular functions. A total of 4,790 proteins were used in this GO analysis using STRAP. Percentages are rounded to the nearest whole number.
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fig4: Distribution of proteins identified from the 2D shotgun dataset of DOC-extracted liver tumor samples based on (a) subcellular localization; (b) biological processes; (c) molecular functions. A total of 4,790 proteins were used in this GO analysis using STRAP. Percentages are rounded to the nearest whole number.

Mentions: To the best of our knowledge, our study has by far the largest number of proteins reported to be identified from the zebrafish liver tissue. A full list of the proteins identified is presented in Supplementary Table  3. Using STRAP, the identified proteins were grouped according to their (1) subcellular locations, (2) biological processes, or (3) molecular functions. The data generated provide an overview of the proteins identified from xmrk oncogene induced zebrafish liver tumor (Figure 4).


Dramatic improvement of proteomic analysis of zebrafish liver tumor by effective protein extraction with sodium deoxycholate and heat denaturation.

Wang J, Lee YM, Li C, Li P, Li Z, Lim TK, Gong Z, Lin Q - Int J Anal Chem (2015)

Distribution of proteins identified from the 2D shotgun dataset of DOC-extracted liver tumor samples based on (a) subcellular localization; (b) biological processes; (c) molecular functions. A total of 4,790 proteins were used in this GO analysis using STRAP. Percentages are rounded to the nearest whole number.
© Copyright Policy - open-access
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC4383156&req=5

fig4: Distribution of proteins identified from the 2D shotgun dataset of DOC-extracted liver tumor samples based on (a) subcellular localization; (b) biological processes; (c) molecular functions. A total of 4,790 proteins were used in this GO analysis using STRAP. Percentages are rounded to the nearest whole number.
Mentions: To the best of our knowledge, our study has by far the largest number of proteins reported to be identified from the zebrafish liver tissue. A full list of the proteins identified is presented in Supplementary Table  3. Using STRAP, the identified proteins were grouped according to their (1) subcellular locations, (2) biological processes, or (3) molecular functions. The data generated provide an overview of the proteins identified from xmrk oncogene induced zebrafish liver tumor (Figure 4).

Bottom Line: The laborious gel-based approach is slowly being replaced by the advancing in-solution digestion approach.However, there are still several difficulties such as difficult-to-solubilize proteins, poor proteomic analysis in complex tissue samples, and the presence of sample impurities.Henceforth, there is a great demand to formulate a highly efficient protein extraction buffer with high protein extraction efficiency from tissue samples, high compatibility with in-solution digestion, reduced number of sample handling steps to reduce sample loss, low time consumption, low cost, and ease of usage.

View Article: PubMed Central - PubMed

Affiliation: Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543.

ABSTRACT
Majority of the proteomic studies on tissue samples involve the use of gel-based approach for profiling and digestion. The laborious gel-based approach is slowly being replaced by the advancing in-solution digestion approach. However, there are still several difficulties such as difficult-to-solubilize proteins, poor proteomic analysis in complex tissue samples, and the presence of sample impurities. Henceforth, there is a great demand to formulate a highly efficient protein extraction buffer with high protein extraction efficiency from tissue samples, high compatibility with in-solution digestion, reduced number of sample handling steps to reduce sample loss, low time consumption, low cost, and ease of usage. Here, we evaluated various existing protein extraction buffers with zebrafish liver tumor samples and found that sodium deoxycholate- (DOC-) based extraction buffer with heat denaturation was the most effective approach for highly efficient extraction of proteins from complex tissues such as the zebrafish liver tumor. A total of 4,790 proteins have been identified using shotgun proteomics approach with 2D LC, which to our knowledge is the most comprehensive study for zebrafish liver tumor proteome.

No MeSH data available.


Related in: MedlinePlus