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Nucleic Acids Research 2006 34(Web Server issue):W258-W263; doi:10.1093/nar/gkl245
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© The Author 2006. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@oxfordjournals.org

Article

MODi : a powerful and convenient web server for identifying multiple post-translational peptide modifications from tandem mass spectra

Sangtae Kim, Seungjin Na1, Ji Woong Sim2, Heejin Park3, Jaeho Jeong4, Hokeun Kim5, Younghwan Seo6, Jawon Seo4, Kong-Joo Lee4 and Eunok Paek1,*

Research Center for Computer Technology, Hanyang University Seoul, 133-791, Korea 1 Department of Mechanical and Information Engineering, University of Seoul Seoul 130-743, Korea 2 School of Computer Science and Engineering, Seoul National University Seoul 151-742, Korea 3 College of Information and Communications, Hanyang University Seoul 133-791, Korea 4 Center for Cell Signaling Research, Division of Molecular Life Sciences and College of Pharmacy, Ewha Womans University Seoul 120-750, Korea 5 Functional Proteomics Center, Korea Institute of Science and Technology Seoul 136-791, Korea 6 Lab Frontier Co. Ltd Seoul 120-750, Korea

*To whom correspondence should be addressed. Tel: +82 2 2210 2680; Fax: +82 2 2248 5110; Email: paek{at}uos.ac.kr

Received February 14, 2006. Revised March 14, 2006. Accepted March 29, 2006.

MODi (http://modi.uos.ac.kr/modi/) is a powerful and convenient web service that facilitates the interpretation of tandem mass spectra for identifying post-translational modifications (PTMs) in a peptide. It is powerful in that it can interpret a tandem mass spectrum even when hundreds of modification types are considered and the number of potential PTMs in a peptide is large, in contrast to most of the methods currently available for spectra interpretation that limit the number of PTM sites and types being used for PTM analysis. For example, using MODi, one can consider for analysis both the entire PTM list published on the unimod webpage (http://www.unimod.org) and user-defined PTMs simultaneously, and one can also identify multiple PTM sites in a spectrum. MODi is convenient in that it can take various input file formats such as .mzXML, .dta, .pkl and .mgf files, and it is equipped with a graphical tool called MassPective developed to display MODi's output in a user-friendly manner and helps users understand MODi's output quickly. In addition, one can perform manual de novo sequencing using MassPective.


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