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Fully automated software solution for protein quantitation by global metabolic labeling with stable isotopes

Bindschedler, L. V. and Cramer, R. (2011) Fully automated software solution for protein quantitation by global metabolic labeling with stable isotopes. Rapid Communications in Mass Spectrometry, 25 (11). pp. 1461-1471. ISSN 1097-0231

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To link to this article DOI: 10.1002/rcm.4872

Abstract/Summary

Metabolic stable isotope labeling is increasingly employed for accurate protein (and metabolite) quantitation using mass spectrometry (MS). It provides sample-specific isotopologues that can be used to facilitate comparative analysis of two or more samples. Stable Isotope Labeling by Amino acids in Cell culture (SILAC) has been used for almost a decade in proteomic research and analytical software solutions have been established that provide an easy and integrated workflow for elucidating sample abundance ratios for most MS data formats. While SILAC is a discrete labeling method using specific amino acids, global metabolic stable isotope labeling using isotopes such as (15)N labels the entire element content of the sample, i.e. for (15)N the entire peptide backbone in addition to all nitrogen-containing side chains. Although global metabolic labeling can deliver advantages with regard to isotope incorporation and costs, the requirements for data analysis are more demanding because, for instance for polypeptides, the mass difference introduced by the label depends on the amino acid composition. Consequently, there has been less progress on the automation of the data processing and mining steps for this type of protein quantitation. Here, we present a new integrated software solution for the quantitative analysis of protein expression in differential samples and show the benefits of high-resolution MS data in quantitative proteomic analyses.

Item Type:Article
Refereed:Yes
Divisions:Faculty of Life Sciences
Faculty of Life Sciences > School of Chemistry, Food and Pharmacy > Department of Chemistry
Interdisciplinary centres and themes > Chemical Analysis Facility (CAF)
ID Code:21939
Additional Information:Presented at the combined meetings of the BMSS Special Interest Group on Stable Isotopes (BMSS ISO-SIG), the Stable Isotopes Mass Spectrometry Users' Group (SIMSUG) and COST action 'Stable Isotopes in Biosphere-Atmosphere-Earth System Research' (SIBAE) held at Exeter University 27–30 April, 2010
Publisher:Wiley

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