In silico Proteome-wide Amino aCid and Elemental Composition (PACE) Analysis of Expression Proteomics Data Provides A Fingerprint of Dominant Metabolic Processes |
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Authors: | David MGood Anwer Mamdoh Harshavardhan Budamgunta Roman AZubarev |
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Institution: | 1. Division of Physiological Chemistry I,Department of Medical Biochemistry and Biophysics,Karolinska Institute,SE 171 77 Stockholm,Sweden 2. Division of Physiological Chemistry I,Department of Medical Biochemistry and Biophysics,Karolinska Institute,SE 171 77 Stockholm,Sweden;Science for Life Laboratory,SE 171 21 Solna,Sweden |
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Abstract: | 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 decomposition 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 differentiation between very similar proteomes. In addition, PACE provides novel insights into proteome-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. |
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Keywords: | Shotgun proteomics Mass spectrometry LC-MS/MS Data reduction Cyanobacterium Arginine deprivation |
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