THE USE OF TOOLS DENSITOMETRY IN THE QUANTITATIVE COMPUTATIONS OF PROTEIN FRACTIONS
https://doi.org/10.21323/2414-438X-2017-2-3-49-65
Abstract
In the study of proteomic profiles of proteins, many scientists stop at the stage of obtaining the final data of the experiment in the form of gels. They have got no information on the possibilities and prospects concerning the application of modern computer and bioinformatics resources that allow to convert the result from qualitative to quantitative form. The use of computer technology allowed to save the recorded images and carry out the calculations with chromatograms using digital video images.
Densitometry with the use of video technology is characterized by high calculation speed and low cost of consumables. Digitally archived chromatograms may be used at any time for a number of applications including calculation.
Thus, the “manual” bioinformatics analysis allows not only to use different densitometer software for conversion and storage of gels in digital form, but also to quantitatively interpret the results obtained.
This paper presents the methods for practical application of bioinformatics tools in the interpretation of protein profiles obtained by one-dimensional and two-dimensional electrophoresis and converted into digital image. The aspects of the quantitative interpretation of electrophoretograms from one-dimensional electrophoresis (1DE) and two-dimensional electrophoresis (2DE) resulting from the studies of muscle tissue of farm animals are reviewed. Examples of various calculation software usage are given. The work in this direction will allow to considerably expand approaches for identification and quantification of protein markers related to quality, functionality and safety of food raw materials and finished products and to carry out metrological examination of the results for confirmation of product compliance.
About the Author
Natalia L. Vostrikova
V.M. Gorbatov Federal Research Center for Food Systems of Russian Academy of Sciences
Russian Federation
candidate of technical sciences, head of «Scientific and methodical work, biological and analytical research»laboratory, V.M. Gorbatov Federal Research Center for Food Systems of Russian Academy of Sciences. 109316, Moscow, Talalikhina str., 26 Tel.: +7–495–676–79–81
Russian Federation
candidate of technical sciences, head of «Scientific and methodical work, biological and analytical research»laboratory, V.M. Gorbatov Federal Research Center for Food Systems of Russian Academy of Sciences. 109316, Moscow, Talalikhina str., 26 Tel.: +7–495–676–79–81
References
1. Westermeier, R. Proteomics in Practice: A Guide to Successful Experimental Design/ R. Westermeier, T. Naven, H.R. Hopker// Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.—2008. — p. 1–8.
2. Westermeier, R. Proteomics in Practice: A Guide to Successful Experimental Design/ R. Westermeier, T. Naven, H.R. Hopker // Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim. — 2008. — P. 15–19.
3. Zheng, С.Y. Native PAGE eliminates the problem of PEG–SDS interaction in SDS–PAGE and provides an alternative to HPLC in characterization of protein PEGylation / C.Y. Zheng, G. Ma, Z. Su // Electrophoresis. — 2007. — № 28. — Р. 2801–2807.
4. Xu, С. Software for computational peptide identification from MS-MS data / C. Xu, B. Ma.// Drug Discovery Today. — 2006. — Vol. 11. — № 13/14. — Р. 595–600.
5. Righetti, P.G. The Proteome Revisited Theory and Practice of all Relevant Electrophoretic Steps / P.G. Righetti, A. Stoyanov, M.Y. Zhukov // Journal of Chromatography Library. — 2001. — Volume 63. — Pages V–VII.
6. The collection of methodical instructions for students on practical training in “Medical Informatics” for the 060101-Medical case (full-time education) / comp. E. I. Kichigina, [and others]. — Krasnoyarsk: KrasGMUprintshop, 2012.— 385 P.
7. Shishkin, S.S. Proteomic Approaches for the Study of Transgelins as Tumor-associated Proteins and Potential Biomarkers / S.S. Shishkin, M.A. Kovaleva, L.S. Eryomina, K.V. Lisitskaya, L.I. Kovalev // Current Proteomics.— 2013. — Vol. 10.— № 2. — Р. 165–178.
8. Interview with A.Y. Lyanguzov, State Research Institute of Extremely Clean Biopreparations, Lecturer of Biochemistry Department of Biology and Soil Faculty of St. Petersburg State University[Electronic source: URL: http://old.ci.ru/inform23_02/p_22.htm/. Access date: 26.09.2017]
9. Vostrikova N.L., Chernukha I.M. Bioinformatics as a tool forinterpretation of proteomic profiles of meat protein. // Theory and practice of meat processing. 2017; — V 2. — No. 1. — P 4. DOI:10.21323/2414–438X‑2017–2–1–4–17
10. Shishkin, S.S. The application of proteomic technologies for the analysis of muscle proteins of farm animals used in the meat industry (Review)/S.S. Shishkin, L.I. Kovalev, M.A. Kovaleva, A.V. Ivanov, L.S. Eremina, E.G. Sadykhov// Applied Biochemistry and Microbiology.—2014. — Vol. 50.—№ 5. — P. 421–432.
11. Afanasiev D.A., Akhremko A.G., Chernukha I.M., Mashentseva N.G. Determination of the beef protein profile during autolysis//International scientific-practical conference dedicated to the memory of Vasily Matveevich Gorbatov. M.: VNIIMP.— 2016. — РР. 39.
12. Kovalev, L.I. Proteomic research of proteins in the samples of pork andpork products/L.I. Kovalev, S.S. Shishkin, M.A. Kovaleva, A.V. Ivanov, N.L.Vostrikova, I.M.Chernukha// Vseomyase.— 2013. — No. 3. — РР. 32–34.
13. Chernukha I.M., Fedulova L.V., Kotenkova E.A. et al.The Influence of autolysis on the protein-peptide profile of Bos taurus and Sus scrofa heart and aorta tissues // Theory and practice of meat processing. 2016;1(2):4–9. (In Russ.) DOI:10.21323/2414–438X‑2016–1–2–4–9
14. Picard, B. Recent advances in omic technologies for meat quality management / B. Picard, B. Lebret, I. Cassar-Malek, L. Liaubet, C. Berri, B. Le Bihan-Duval, J.F. Hocquette, G. Renand // Meat Science. — 2015. — Vol. 109. — P. 18–26.
15. Zhang, R. Polymorphisms and expression analysis of SOX‑6 in relation to porcine growth, carcass, and meat quality traits. / R. Zhang, C. Gross-Brinkhaus, H. Heidt, M.J. Uddin, M.U. Cinar, D. Tesfaye, E. Tholen, C. Looft, K. Schellander, C. Neuhoff // Meat Science –2015. — Vol.107. — P. 26–32.
16. Lametsch, R. Proteomics in Muscle-to-Meat Conversion // Proceedings of the American Meat Science Association 64th Reciprocal Meat Conference (June 19–222011, Kansas State University Manhattan, Kansas).— 2012. — P. 19–23.
17. UniProtKB/Swiss-Prot/SIB Swiss Institute of Bioinformatics [Electronic source: URL: http://web.expasy.org/docs/swissprot_guideline.html. Access date: 18.07.2017]
18. Sun, H. Proteomic and bioinformatic analysis of differentially expressed proteins in denervated skeletal muscle / H. Sun, J. Qiu, Y. Chen, M.Yu, F. Ding, X. Gu, // International journal of molecular medicine.— 2014. — Vol. 33.— № 6. — P. 1586–1596.
19. Manyukhin, Y.S. The study of horsemeat proteins by the use proteomic technologies/Y.S.Manyukhin , I.M. Chernukha, L.I. Kovalev, A.V. Ivanov, M.A. Kovaleva, S.S. Shishkin // Vse o myase. — 2014. — No. 3. — P. 20–25.
20. Moczkowska, М. The effect of the packaging system and storage time on myofibrillar protein degradation and oxidation process in relation to beef tenderness./ M. Moczkowska, A. Półtorak, M. Montowska, E. Pospiech, A. Wierzbicka // Meat Science.— 2017. — Vol. 130. — P. 7–15.
Review
For citations:
Vostrikova N.L. THE USE OF TOOLS DENSITOMETRY IN THE QUANTITATIVE COMPUTATIONS OF PROTEIN FRACTIONS. Theory and practice of meat processing. 2017;2(3):49-65. https://doi.org/10.21323/2414-438X-2017-2-3-49-65
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