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Nucleic Acids Research Advance Access originally published online on June 6, 2007
Nucleic Acids Research 2007 35(Web Server issue):W707-W712; doi:10.1093/nar/gkm345
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Nucleic Acids Research, 2007, Vol. 35, No. suppl_2 W707-W712
© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Articles

The Multi-Q web server for multiplexed protein quantitation

Chuan-Yih Yu, Yin-Hao Tsui, Yi-Hwa Yian, Ting-Yi Sung* and Wen-Lian Hsu

Institute of Information Science, Academia Sinica, Taipei, Taiwan, R.O.C.

*To whom correspondence should be addressed. Tel: 886-2-2788-3799 ext 1711; Fax: 886-2-2782-4814; Email: tsung{at}iis.sinica.edu.tw, Correspondence may also be addressed to Wen-Lian Hsu. Tel: 886-2-2788-3799 #1804; Fax: 886-2-2782-4814; Email: hsu{at}iis.sinica.edu.tw

Received January 31, 2007. Revised April 20, 2007. Accepted April 22, 2007.

The Multi-Q web server provides an automated data analysis tool for multiplexed protein quantitation based on the iTRAQ labeling method. The web server is designed as a platform that can accommodate various input data formats from search engines and mass spectrometer manufacturers. Compared to the previous stand-alone version, the new web server version provides many enhanced features and flexible options for quantitation. The workflow of the web server is represented by a quantitation wizard so that the tool is easy to use. It also provides a friendly interface that helps users configure their parameter settings before running the program. The web server generates a standard report for quantitation results. In addition, it allows users to customize their output reports and information of interest can be easily highlighted. The output also provides visualization of mass spectral data so that users can conveniently validate the results. The Multi-Q web server is a fully automated and easy to use quantitation tool that is suitable for large-scale multiplexed protein quantitation. Users can download the Multi-Q Web Server from http://ms.iis.sinica.edu.tw/Multi-Q-Web.


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