In the context of the prosperous development of Proteomics in life science, protein quantification, especially these based on Mass Spectrometry (short for MS) method, becomes an essential part of research. In our previous work, we developed a new software package called QuantWiz for high performance Liquid Chromatography (short for LC)-MS-based label-free protein quantification. We solved those problems of portability, applicability and longtime running existed in other software for protein quantification based on MS method. In this paper, we first compared the LC-MS-based label-free protein quantification accuracy of QuantWiz with the well-known Census software package. Then we designed and implemented a distributed memory version parallel algorithm for QuantWiz. Finally, we performed scalability testing of our new parallel algorithm and showed that our new parallel algorithm can scale up to 512 processes on Dawning 5000A.

QuantWiz: A scalable parallel software package for label-free protein quantification

Nowadays Proteomics becomes more and more popular in life science. Protein quantification, especially based on mass spectrometry (short for MS) method, is perceived as an essential part of research on proteomics. There have been some algorithms and software for protein quantification based on MS. But they have difficulties on portability, applicability and longtime running. To solve these problems, we developed a new domestic parallel software package called QuantWiz for high performance Liquid Chromatography (short for LC)-MS-based label-free protein quantification. In this paper, we described the framework design and prototype development of this high performance software package firstly. Also, user interface developed for the visualization of QuantWiz is introduced. Finally, we showed implementation of the parallelization version and performance of some experiments on this software package.

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Zelin Hu

Papers

QuantWiz: A Parallel Software Package for LC-MS-based Label-Free Protein Quantification