Abstract
Both the phosphorylation and dephosphorylation of plant proteins is involved in multiple biological processes, especially in regard to signal transduction. The identification of phosphopeptides from MS (mass spectrometry)-based methods and their subsequent quantification play an important role in plant phosphoproteomics analysis. Phosphopeptide(s) identification and label-free quantification can determine dynamic changes of phosphorylation events in plants. Both MaxQuant and Proteome Discoverer are professional software tools used to identify and quantify large-scale MS-based phosphoproteomic data. This chapter gives a detailed workflow of MaxQuant and Proteome Discoverer software to analyze large amounts of phosphoproteomic-related MS data for the identification and quantification of label-free plant phosphopeptides.
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Change history
08 December 2021
In the original version of this book, the title of chapter 13 was published with a typographical error. It has now been rectified in the revised version of this book.
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Li, S., Zan, H., Zhu, Z., Lu, D., Krall, L. (2021). Plant Phosphopeptide Identification and Label-Free Quantification by MaxQuant and Proteome Discoverer Software. In: Wu, X.N. (eds) Plant Phosphoproteomics. Methods in Molecular Biology, vol 2358. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1625-3_13
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DOI: https://doi.org/10.1007/978-1-0716-1625-3_13
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