MZDASoft-A Software Architecture that Enables Large Scale Comparison of Protein Expression Levels over Multiple Samples Based on LC-MS/MS

摘要

RATIONALEWithout 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 number of samples based on existing software architectures, because it requires access to peak elution profiles from multiple LC-MS/MS samples simultaneously.