In silico Proteome-wide Amino aCid and Elemental Composition （PACE） Analysis of Expression Proteomics Data Provides A Fingerprint of Dominant Metabolic Processes

Proteome-wide Amino aCid and Elemental composition （PACE） analysis is a novel and informative way of interrogating the proteome. The PACE approach consists of in silico decompo- sition of proteins detected and quantified in a proteomics experiment into 20 amino acids and five elements （C, H, N, O an...

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Published in:基因组蛋白质组与生物信息学报：英文版 2013, Vol.11 (4), p.219-229
Main Author: David M. Good Anwer Mamdoh Harshavardhan Budamgunta Roman A. Zubarev
Format: Article
Language:English
Subjects:
PACE
代谢过程
元素成分分析
定量蛋白质组学
指纹
数据分析
氨基酸
硅片
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Summary:Proteome-wide Amino aCid and Elemental composition （PACE） analysis is a novel and informative way of interrogating the proteome. The PACE approach consists of in silico decompo- sition of proteins detected and quantified in a proteomics experiment into 20 amino acids and five elements （C, H, N, O and S）, with protein abundances converted to relative abundances of amino acids and elements. The method is robust and very sensitive; it provides statistically reliable differ- entiation between very similar proteomes. In addition, PACE provides novel insights into prote- ome-wide metabolic processes, occurring, e.g., during cell starvation. For instance, both Escherichia coli and Synechocystis down-regulate sulfur-rich proteins upon sulfur deprivation, but E. coli preferentially down-regulates cysteine-rich proteins while Synechocystis mainly down- regulates methionine-rich proteins. Due to its relative simplicity, flexibility, generality and wide applicability, PACE analysis has the potential of becoming a standard analytical tool in proteomics.
ISSN:1672-0229