title: Automated protein turnover calculations from 15N partial metabolic labeling LC/MS shotgun proteomics data.
abstract: Protein turnover is a well-controlled process in which polypeptides are constantly being degraded and subsequently replaced with newly synthesized copies. Extraction of composite spectral envelopes from complex LC/MS shotgun proteomics data can be a challenging task, due to the inherent complexity of biological samples. With partial metabolic labeling experiments this complexity increases as a result of the emergence of additional isotopic peaks. Automated spectral extraction and subsequent protein turnover calculations enable the analysis of gigabytes of data within minutes, a prerequisite for systems biology high throughput studies. Here we present a fully automated method for protein turnover calculations from shotgun proteomics data. The approach enables the analysis of complex shotgun LC/MS 15N partial metabolic labeling experiments. Spectral envelopes of 1419 peptides can be extracted within an hour. The method quantifies turnover by calculating the Relative Isotope Abundance (RIA), which is defined as the ratio between the intensity sum of all heavy (15N) to the intensity sum of all light (14N) and heavy peaks. To facilitate this process, we have developed a computer program based on our method, which is freely available to download at http://promex.pph.univie.ac.at/protover.
authors.affiliation: Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria.
authors.forename: David
authors.initials: D
authors.lastname: Lyon
authors.affiliation: Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria.
authors.forename: Maria Angeles
authors.initials: MA
authors.lastname: Castillejo
authors.affiliation: Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria.
authors.forename: Christiana
authors.initials: C
authors.lastname: Staudinger
authors.affiliation: Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria.
authors.forename: Wolfram
authors.initials: W
authors.lastname: Weckwerth
authors.affiliation: Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria.
authors.forename: Stefanie
authors.initials: S
authors.lastname: Wienkoop
authors.affiliation: Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria.
authors.forename: Volker
authors.initials: V
authors.lastname: Egelhofer
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D001331:Automation; D002853:Chromatography, Liquid; D006801:Humans; D007553:Isotope Labeling; D013058:Mass Spectrometry; D008969:Molecular Sequence Data; D010455:Peptides / Q000737:chemistry / Q000378:metabolism; D059748:Proteolysis; D040901:Proteomics / Q000379:methods*
chemical_list: D010455:Peptides
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