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

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.