We develop and apply computational methods of mass spectrometry (MS)-based proteomics for formulating the processes of complex phenotype/diseases by integrating genome/transcriptome data and biological network. Our ambitious is to prioritize key proteins with differential expression, variations or modifications in disease, as well as identify clinical biomarker, predict functional sub-network/pathways, interpret mechanisms underneath specific molecular processes or states by means of developing statistic models and bioinformatic approaches.