title: In silico proteome-wide amino aCid and elemental composition (PACE) analysis of expression proteomics data provides a fingerprint of dominant metabolic processes.
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.
authors.affiliation: Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institute, SE 171 77 Stockholm, Sweden.
authors.forename: David M
authors.initials: DM
authors.lastname: Good
authors.forename: Anwer
authors.initials: A
authors.lastname: Mamdoh
authors.forename: Harshavardhan
authors.initials: H
authors.lastname: Budamgunta
authors.forename: Roman A
authors.initials: RA
authors.lastname: Zubarev
mesh_terms: D000596:Amino Acids / Q000032:analysis* / Q000378:metabolism; D045744:Cell Line, Tumor; D019295:Computational Biology / Q000379:methods*; D015536:Down-Regulation; D004926:Escherichia coli / Q000737:chemistry / Q000378:metabolism; D006801:Humans; D020543:Proteome / Q000737:chemistry* / Q000378:metabolism; D040901:Proteomics; D013312:Stress, Physiological; D046939:Synechocystis / Q000737:chemistry / Q000378:metabolism; D013696:Temperature
chemical_list: D000596:Amino Acids; D020543:Proteome
keywords: Arginine deprivation; Cyanobacterium; Data reduction; LC–MS/MS; Mass spectrometry; Shotgun proteomics
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