Compared with the whole proteome, phosphoproteins were more significantly represented in the biological processes of RNA metabolism, DNA metabolism and cellular component organization, while N-glycoproteins were more likely to take part in various processes such as cell adhesion, cell-cell signaling, developmental processes, and stress response. This suggests again that protein phosphorylation plays important roles in intracellular processes while protein N-glycosylation is mainly involved in extracellular processes. Since subproteome enrichment reduces the complexity of samples and facilitates MS analysis, it has been predicted that it will improve the sensitivity of protein identification significantly. With the concurrent analysis of proteome, phosphoproteome and glycoproteome, it is convenient to determine whether subproteome enrichment improves the sensitivity of protein identification significantly in a single analysis and reduces the inter-experimental variation between proteome and subproteome analysis. In this study, 200 phosphoproteins or glycoproteins were identified solely from phosphopeptides and/or glycopeptides but not identified from unmodified peptides in ERLIC04, suggesting that the subproteome enrichment led to the identification of some low-abundance proteins. Based on the functional analysis using AmiGO Go Slimmer, 9% of these proteins were involved in signal transduction, a significantly higher percentage than that in whole proteome and in the phosphoproteome and glycoproteome overall. Since most proteins involved in signal transduction are of relatively low abundance, the results indicate that subproteome enrichment improves the sensitivity of identification of low-abundance proteins. Checking the listings of these 27 proteins in the SWISS-PROT database: 23 of them were annotated ����evidence at transcript level����; 1 had no SWISS-PROT entry; only 3 were annotated ����evidence at protein level����. This sketchy record seems to confirm that most of them are of low abundance. In addition, subproteome enrichment leads to the identification of many low-abundance proteins with known important functions that cannot be identified from whole proteome analysis. For example, ONX-0914 960374-59-8 integrin alpha-5/beta-6 and angiopoietin-like 3 are identified only in the Sorafenib PTM-enriched fraction. Integrin alpha-5/ beta-6 is a receptor for fibronectin and cytotactin, and their binding inhibits tumor growth, angiogenesis and metastasis. Angiopoietin-like 3, present at extremely low levels in kidney, can bind integrin alpha-5/beta-3, which induces cell adhesion and migration and regulates angiogenesis. The expression of many other cancer related genes, such as CD63, CD36, Cd164, Gpld1, Ace and Braf, was also detected only from the set of enriched modified peptides.