MZDASoft: a software architecture that enables large-scale comparison of protein expression levels over multiple samples based on liquid chromatography/tandem mass spectrometry

Rapid Communications in Mass Spectrometry : RCM
Mehrab Ghanat BariJianqiu Zhang

Abstract

Without accurate peak linking/alignment, only the expression levels of a small percentage of proteins can be compared across multiple samples in Liquid Chromatography/Mass Spectrometry/Tandem Mass Spectrometry (LC/MS/MS) due to the selective nature of tandem MS peptide identification. This greatly hampers biomedical research that aims at finding biomarkers for disease diagnosis, treatment, and the understanding of disease mechanisms. A recent algorithm, PeakLink, has allowed the accurate linking of LC/MS peaks without tandem MS identifications to their corresponding ones with identifications across multiple samples collected from different instruments, tissues and labs, which greatly enhanced the ability of comparing proteins. However, PeakLink cannot be implemented practically for large numbers of samples based on existing software architectures, because it requires access to peak elution profiles from multiple LC/MS/MS samples simultaneously. We propose a new architecture based on parallel processing, which extracts LC/MS peak features, and saves them in database files to enable the implementation of PeakLink for multiple samples. The software has been deployed in High-Performance Computing (HPC) environments. The core part o...Continue Reading

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Citations

Jun 25, 2017·BMC Bioinformatics·Sirajul SalekinJianqiu Michelle Zhang

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