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Proteomes 2018, 6(1), 6; doi:10.3390/proteomes6010006

Evaluation of Optimized Tube-Gel Methods of Sample Preparation for Large-Scale Plant Proteomics

PAPPSO, GQE-Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Paris-Saclay University, 91190 Gif-sur-Yvette, France
Author to whom correspondence should be addressed.
Received: 7 November 2017 / Revised: 24 January 2018 / Accepted: 29 January 2018 / Published: 30 January 2018
(This article belongs to the Special Issue Plant Proteomics 2017)
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The so-called tube-gel method is a sample preparation protocol allowing for management of SDS for protein solubilization through in-gel protein trapping. Because of its simplicity, we assumed that once miniaturized, this method could become a standard for large scale experiments. We evaluated the performances of two variants of the miniaturized version of the tube-gel method based on different solubilization buffers (Tris-SDS or urea-SDS). To this end, we compared them to two other digestion methods: (i) liquid digestion after protein solubilization in the absence of SDS (liquid method) and (ii) filter-aided sample preparation (FASP). As large-scale experiments may require long term gel storage, we also examined to which extent gel aging affected the results of the proteomics analysis. We showed that both tube-gel and FASP methods extracted membrane proteins better than the liquid method, while the latter allowed the identification and quantification of a greater number of proteins. All methods were equivalent regarding quantitative stability. However, important differences were observed regarding post-translational modifications. In particular, methionine oxidation was higher with the tube-gel method than with the other methods. Based on these results, and considering time, simplicity, and cost aspects, we conclude that the miniaturized tube-gel method is suitable for sample preparation in the context of large-scale experiments. View Full-Text
Keywords: plant proteomics; protein extraction; protein digestion; tube-gel; FASP; shotgun proteomics plant proteomics; protein extraction; protein digestion; tube-gel; FASP; shotgun proteomics

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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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Balliau, T.; Blein-Nicolas, M.; Zivy, M. Evaluation of Optimized Tube-Gel Methods of Sample Preparation for Large-Scale Plant Proteomics. Proteomes 2018, 6, 6.

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