Cholesterol-rich membrane microdomains, also known as lipid rafts, are specialized assemblies of membrane lipids and proteins that regulate diverse cellular events. Distinct physicochemical properties of cholesterol and sphingolipids facilitate partitioning of membrane associated proteins producing heterogeneity in the membrane bilayer. The lipid rafts are considered as signalling and sorting platforms on the cell surface that mediates clustering of signalling machinery including receptors, serine tyrosine kinases, GPI anchored and acetylated proteins. Lipid rafts are also regarded as membrane organizers that control myriads of cellular processes like endocytosis, cell adhesion and migration.Interestingly, their dysfunction has been implicated in a range of cancers, cardiovascular, and neurodegenerative diseases. Due to their apparent biological importance, various biochemical and microscopic techniques have been implemented to characterise protein constituents of cellular raft fractions along with high throughput proteomics approaches.Mass-spectrometry based proteomics profiling of lipid rafts has been pivotal in understanding the composition and spatiotemporal dynamics within these microdomains.Despite extensive proteomics research, the global protein landscape and subsequent function of lipid raft still remained elusive.In an effort to determine and understand potential lipid raft proteome profiled by multiple proteomic investigations in physiological and disease conditions this thesis describes a systematic computational approach. To achieve this, I propose and sought to fulfil three main aims (1) To develop an open source resource to characterise mammalian lipid raft proteome (2) In depth in silico characterisation of structural features and functional significance of human lipid raft associated proteins (3) To understand raft associated mechanism of tumor progression by integrative analysis of quantitative proteomics studies.In Chapter 2, I present a database for mammalian lipid raft proteome "RaftProt" (http://lipid-raft-database.di.uq.edu.au/). This online public resource is the first repository hosting a comprehensive collection lipid raft associated proteins detected through high throughput lipid raft proteomics studies. I have developed a user-friendly web platform, including number of online features, to assist searching, browsing and downloading large scale proteomics datasets. Furthermore, implementing an ontology at the backend of the RaftProt I provided a novel approach to organise and represent proteomic datasets based on anatomical features. A subset of bona-fide high confidence lipid raft proteins was proposed by applying experimental evidence based filtering criteria. Taken together, this database is a valuable resource to decipher the biological and disease specific iii organization of mammalian lipid raft proteome. Importantly, this collection effort also led the foundation for systems level characterisation of functional lipid rafts later in this project. indicate that the unifying...