AUTHOR=Shrestha Ruben , Reyes Andres V. , Baker Peter R. , Wang Zhi-Yong , Chalkley Robert J. , Xu Shou-Ling 

TITLE=15N Metabolic Labeling Quantification Workflow in Arabidopsis Using Protein Prospector

JOURNAL=Frontiers in Plant Science

VOLUME=13

YEAR=2022

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2022.832562

DOI=10.3389/fpls.2022.832562

ISSN=1664-462X

ABSTRACT=<p>Metabolic labeling using stable isotopes is widely used for the relative quantification of proteins in proteomic studies. In plants, metabolic labeling using <sup>15</sup>N has great potential, but the associated complexity of data analysis has limited its usage. Here, we present the <sup>15</sup>N stable-isotope labeled protein quantification workflow utilizing open-access web-based software Protein Prospector. Further, we discuss several important features of <sup>15</sup>N labeling required to make reliable and precise 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.</p>