Sialylation is one of the altered protein glycosylations associated with cancer development. The sialoglycoproteins in cancer cells, however, largely remain unidentified because of the lack of a method for quantitative analysis of sialoglycoproteins. This manuscript presents a high throughput method for quantitative analysis of N-linked sialoglycoproteins using conditional hydrazide chemistry, liquid chromatography, and tandem mass spectrometry. We further applied the sialoglycoproteomic method to the profiling of breast cancer tissues and compared findings with the results from the total glycoproteomic analysis using the original hydrazide chemistry method. We identified altered expression of sialoglycoproteins, as well as the total glycoprotein changes associated with breast cancer. Using lectin and Western blot analysis, we characterized one of the sialoglycoproteins, versican, and confirmed that versican was most sialylated and elevated in breast cancer. Furthermore, we showed that versican was detected in both cancer epithelial cells and peritumoral stromal cells using immunohistochemistry. Tissue microarray analysis revealed that epithelial expression of versican had significant relations to lymph node metastasis and pathological stages. This is the first quantitative sialoglycoproteomic and glycoproteomic analysis of breast cancer and noncancerous tissues. These findings present a significant addition of the method to the identification of altered expression of sialylated glycoproteins associated with breast cancer development. Molecular & Cellular Proteomics 11: 10.1074/mcp.M111.011403, 1-10, 2012.Aberrant protein glycosylations are known to be associated with tumorigenesis and cancer progression steps including oncogenic transformation, tumor invasion, and metastasis (1). In breast cancer, elevated concentrations of highly glycosylated proteins, such as mucins, are associated with increased tumor burden and poor prognosis (2). Several glycosylation changes including sialylation, fucosylation, increased branching of N-glycans, and incomplete biosynthesis resulting in truncated glycans are commonly found in cancer (3). By existing as terminal sugars on glycans attached to proteins and lipid moieties, sialic acids play critical roles in intermolecular interactions and the formation of cellular characteristics (4). Altered expression of sialylated glycoproteins has been discovered in many carcinomas such as colon, acute myeloid, leukemia, cervix, and brain tumors (5-14). Furthermore, partial removal of sialic acids on cell surface has also been shown to increase both cell adhesion and aggregation in the pancreatic cancer cells (15), which confirmed that sialylation indeed contributes to cell metastasis.Recent development in MS technology has fueled high throughput analyses of glycoproteins (16,17). Current strategies in studying glycoproteins generally start with enrichment of glycoproteins or glycopeptides from complex mixtures using different physical-chemical methods followed by identification and quanti...