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15N metabolic labeling quantification workflow in Arabidopsis using Protein Prospector [article]

Ruben Shrestha, Andres V. Reyes, Peter R. Baker, Zhi-Yong Wang, Robert J. Chalkley, Shou-Ling Xu
2021 bioRxiv   pre-print

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Metabolic labeling using stable isotopes is widely used for the relative quantification of proteins in proteomic studies. In plants, metabolic labeling using 15N has great potential, but the associated complexity of data analysis has limited its usage. Here, we present the 15N stable-isotope labeled protein quantification workflow utilizing open-access web-based software Protein Prospector (PP). Further, we discuss several important features of 15N labeling required to make reliable and precise
more » ... protein quantification. These features include ratio adjustment based on labeling efficiency, median and interquartile range for protein ratios, isotope cluster pattern matching to flag incorrect monoisotopic peak assignment, and caching of quantification results for fast retrieval.
doi:10.1101/2021.11.30.470624 fatcat:l2emkiamkvhifgbe4ony7oml6a
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Ruben Shrestha, Andres V. Reyes, Peter R. Baker, Zhi-Yong Wang, Robert J. Chalkley, Shou-Ling Xu. "15N metabolic labeling quantification workflow in Arabidopsis using Protein Prospector." bioRxiv (2021)