Date of Award

Spring 2015

Degree Type


Degree Name

Master of Science (MS)


Computer and Information Technology

First Advisor

John Springer

Committee Chair

John Springer

Committee Member 1

Michael Kane

Committee Member 2

Eric Matson


Proteomics is the study of the structure and behavior of proteins. In order to perform this kind of an analysis, proteins are broken down into their constituent peptides, and values of different parameters are recorded. The amount of this kind of data collected is very large, and therefore analysis of this data becomes time-consuming. To overcome this issue, there have been several software developed for processing protein data. With a large number of software solutions available in the market, the decision about which one to use is hard for the end-user. The expectations from such a software for each user vary. Apart from the end-users, there are software developers working on improving the quality of the existing software by implementing suitable optimization techniques. This study therefore proposes a comparison framework for software solutions for proteomics that will benefit the readers by providing all the information required in order to make a decision about the software that is suitable for their needs.