Mass spectrometry (MS)-basedshotgun proteomics technology has been applied to identify a number of proteins underlying complex diseases. However, analysis for large-scale proteomics data remains challenging. Here, we present JUMP, a software suite for analyzing MS-based proteomic data at systems level. The JUMP suite contains many components, including MS database search engine, identification filtering, protein quantification, protein quantification, and proteogenomics. We applied the JUMP suite to analyze a large-scale tandem mass tag (TMT)-based proteomic dataset derived from Alzheimer’s disease (AD) human brain cortical tissues. We identified and quantified over 10,000 proteins fromboth normal and ADhuman brain samples at the protein FDR < 0.01. We thencharacterized 173 differentially expressed (DE) proteins between AD and normal cases. We subsequently constructed co-expression networks for DE proteins using the weighted gene correlation network analysis (WGCNA) tool. We finally integratedmulti-omics data to prioritizethe identified proteins and pathways that are involved the AD pathogenesis. In summary, oursystems-biology approaches elucidate molecular mechanismsunderlying AD.

Xusheng Wang is Bioinformatics Group Leader at St. Jude Children’s Research Hospital. He completed his Ph.D from University of California, Davis and Zhejiang University in China and postdoctoral studies from University of Tennessee Health Science Center. He has published more than 60 papers in prestigious journals, including Science, Nature Neuroscience, Nature Chemistry Biology, and Nature Communications. He also serves as Associate Editor for Front. Genet. - Evolutionary and Population Genetics and Editor for PLoS One, Front. Genet. - Genetic Disorders.