ArticleFrontiers in plant science2016
Shotgun Proteomics of Tomato Fruits: Evaluation, Optimization and Validation of Sample Preparation Methods and Mass Spectrometric Parameters.
Article in Frontiers in plant science, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- Acerola and Its By-Products as Sources of Bioactive Compounds: Phytochemical Profile and Biological Effects in Experimental and Clinical Studies.Molecules (Basel, Switzerland) · 2026Review
- Multi-omics analysis of non-pungent (Physiology and molecular biology of plants : an international journal of functional plant biology · 2025Article
- Proteomic insights into fruit-pathogen interactions: managing biotic stress in fruit.Plant cell reports · 2025Review
- The variegatedComputational and structural biotechnology journal · 2024Article
- Getting Ready for Large-Scale Proteomics in Crop Plants.Nutrients · 2023Article
- Reduced γ-glutamyl hydrolase activity likely contributes to high folate levels in Periyakulam-1 tomato.Horticulture research · 2023Article
- Translating theFrontiers in cell and developmental biology · 2022Review
- Changes in the microsomal proteome of tomato fruit during ripening.Scientific reports · 2019Article
- Assessment and Refinement of Sample Preparation Methods for Deep and Quantitative Plant Proteome Profiling.Proteomics · 2018Article
- Green-fruited Solanum habrochaites lacks fruit-specific carotenogenesis due to metabolic and structural blocks.Journal of experimental botany · 2017Article
- Enhanced production of berberine in In vitro regenerated cell of Tinospora cordifolia and its analysis through LCMS QToF.3 Biotech · 2017Article
Corrections and comments
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Authors and funding
6 authors.
Funding
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Abstract
An optimized protocol was developed for shotgun proteomics of tomato fruit, which is a recalcitrant tissue due to a high percentage of sugars and secondary metabolites. A number of protein extraction and fractionation techniques were examined for optimal protein extraction from tomato fruits followed by peptide separation on nanoLCMS. Of all evaluated extraction agents, buffer saturated phenol was the most efficient. In-gel digestion [SDS-PAGE followed by separation on LCMS (GeLCMS)] of phenol-extracted sample yielded a maximal number of proteins. For in-solution digested samples, fractionation by strong anion exchange chromatography (SAX) also gave similar high proteome coverage. For shotgun proteomic profiling, optimization of mass spectrometry parameters such as automatic gain control targets (5E+05 for MS, 1E+04 for MS/MS); ion injection times (500 ms for MS, 100 ms for MS/MS); resolution of 30,000; signal threshold of 500; top N-value of 20 and fragmentation by collision-induced dissociation yielded the highest number of proteins. Validation of the above protocol in two tomato cultivars demonstrated its reproducibility, consistency, and robustness with a CV of < 10%. The protocol facilitated the detection of five-fold higher number of proteins compared to published reports in tomato fruits. The protocol outlined would be useful for high-throughput proteome analysis from tomato fruits and can be applied to other recalcitrant tissues.
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