How to use




  Contact us

  User Manu

Welcome to our site!

We are the group in research and developing tools for protein identification using Peptide-Mass Fingerprinting Data. The software "ProteinDecision" was designed with the probabily theory and implemented in Jave. Users can obtain the following information at our site:

1.Users can Find the introduction and learn how to use it.

2.Users can download the product and use it for free.

3.Users are welcome for consultation


ProteinDecision is a computer software for identifying protein by serching against protein database with the input Peptide-Mass Fingerprinting Data. It can handle the issues of selecting peaks from mass spectrum, transforming database format, displaying the top ranks of identification result, and detailed information for each ranking. We used a novel scoring function by considering the distribution of matching a mass-to-charge and peak intensity in a database based on the MOWSE frequency table and developed a statistic model to evaluate the confidence of the score and make an improvement for ranking proteins for identification.

How to use it

The software include the following features that users can learn to use:

1.It supports FASTA database format

2.It uses a novel scoring schema - PBSF that can efficiently identify protein

3.It has a statistical model to evaluate the score confidence

4.It allows users set their own running parameters

4.It has a java-based user-friendly interface

Learn how to use the features here


ProteinDecision is free of charge to users. It can be downloaded from here

After the download, users can unzip the software package using winzip and have it installed at any place on the computer. Make sure to install JRE5.0 or Higher before you can run it properly.

Users can down load the users manu or after downloading the software, click "help-> help" to activate the manu file. It is in pdf format which requires Acrobat Reader installed in advance.


ProteinDecision is NOT a software for commercial use. We can not guarantee our services all along the time. However, we will keep on working on it and have it updated. Any feedback or advice is greatly appreciated.


This work has been supported by MU-Monsanto Program and a National Science Foundation grant NSF/ITRIIS-0407204.developed by Zhao Song, Chao Zhang and Dong Xu. Zhao is also supported by Shumaker Fellowship.

Contact us

ProteinDecision is developed by Zhao Song, Chao Zhang and Dong Xu. We will acknowledge lab members for helpful discussion and feed back information.

If you have any comments or advice, feel free to contact us at:

Dong Xu, Chairman of Computer Science Department

Digital Biology Laboratory, University Of Missouri-Columbia, MO, 65211





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