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J. Biol. Chem., Vol. 281, Issue 41, 30315-30318, October 13, 2006

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Antigen Processing of a Short Viral Antigen by Proteasomes^*

Daniel López¹, Olga Calero, Mercedes Jiménez, Margarita García-Calvo, and Margarita Del Val^¶

From the Unidad de Proteómica and ^¶Unidad de Inmunología Viral, Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28220 Madrid, Spain and Department of Enzymology, Merck Research Laboratories, Rahway, New Jersey 07065

Mass spectrometry (MS)-based methods coupled to reverse phase chromatography separation are a useful technology to analyze complex peptide pools that are comprised of different peptides with unrelated sequences. In antigen presentation, proteasomes generate a set of short peptides that are closely related and overlapping and in some instances may even have identical retention times and identical masses. In these situations, micro-liquid chromatography-MS/MS focused on each theoretical parent ion followed by manual interpretation optimizes the identification of generated peptides. The results suggest that the degradation of short antigens by the proteasome occurs by sequential cleavage.

Received for publication, June 22, 2006 , and in revised form, July 18, 2006.

^* This work was supported by grants from the Programa Ramón y Cajal, Comunidad de Madrid, Instituto de Salud Carlos III, Fundación FIPSE, and Fondo de Investigaciones Sanitarias de la SS (to D. L.) and from the Ministerio de Educación y Ciencia, Comunidad de Madrid, and Instituto de Salud Carlos III (to M. D. V.). The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.

¹ To whom correspondence and reprint requests should be addressed. Tel.: 34 91 822 37 08; Fax: 34 91 509 79 19; E-mail: dlopez{at}isciii.es.

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