Mining the Wheat Grain Proteome
Abstract
:1. Introduction
2. Results and Discussion
2.1. Testing Flour Weights
2.2. Testing Extraction Buffers
2.3. Testing Proteases
2.4. Testing LC Separation
2.5. Validating the Shotgun Proteomics Method
2.6. Data Mining of Protein Identification
3. Materials and Methods
3.1. Materials
3.1.1. Wheat Cultivation and Sampling
3.1.2. Wheat Grain Processing
3.2. Methods
3.2.1. Flour Weighing, Protein Extraction, and Protein Assay
3.2.2. Protein Digestion, Digest SPE Clean-Up, and Peptide Reconstitution
3.2.3. LC–MS and LC–MS/MS
LC Separation Columns
LC Methods
ESI–MS
ESI–MS/MS
LC–MS Validation Run
3.2.4. Data Processing, Database Search, and Statistical Analyses
Data File Processing
Protein Identification
Data Normalisation and Statistical Analyses
Data Mining
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Items Quantified | Quantities |
---|---|
Number of LC–MS peaks | 60,473 |
Number of LC–MS clusters | 20,254 |
Cluster size range | 2–11 |
Cluster charge range | 2–10 |
Cluster m/z range | 300.17–1996.52 |
Cluster mass range | 598.34–8989.81 |
Base peak range | 9–137,721 |
Number of clusters with peptide identity | 13,165 |
Number of identified unique peptides | 12,404 |
Number of identified accessions | 8738 |
Number of identified annotated proteins | 1390 |
Range of peptides/accession | 1–65 |
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Vincent, D.; Bui, A.; Ram, D.; Ezernieks, V.; Bedon, F.; Panozzo, J.; Maharjan, P.; Rochfort, S.; Daetwyler, H.; Hayden, M. Mining the Wheat Grain Proteome. Int. J. Mol. Sci. 2022, 23, 713. https://doi.org/10.3390/ijms23020713
Vincent D, Bui A, Ram D, Ezernieks V, Bedon F, Panozzo J, Maharjan P, Rochfort S, Daetwyler H, Hayden M. Mining the Wheat Grain Proteome. International Journal of Molecular Sciences. 2022; 23(2):713. https://doi.org/10.3390/ijms23020713
Chicago/Turabian StyleVincent, Delphine, AnhDuyen Bui, Doris Ram, Vilnis Ezernieks, Frank Bedon, Joe Panozzo, Pankaj Maharjan, Simone Rochfort, Hans Daetwyler, and Matthew Hayden. 2022. "Mining the Wheat Grain Proteome" International Journal of Molecular Sciences 23, no. 2: 713. https://doi.org/10.3390/ijms23020713
APA StyleVincent, D., Bui, A., Ram, D., Ezernieks, V., Bedon, F., Panozzo, J., Maharjan, P., Rochfort, S., Daetwyler, H., & Hayden, M. (2022). Mining the Wheat Grain Proteome. International Journal of Molecular Sciences, 23(2), 713. https://doi.org/10.3390/ijms23020713