To the best of our knowledge, this is the first time that VLPs purified by conventional purification and concentration methods were compared in terms of yield, purity, morphological integrity, antigenicity and functionality. The results show that NoV GII-4 VLPs purified twice by sucrose density gradient centrifugation followed by ultrafiltration maintain their icosahedral capsid structure and their capacity to bind HBGAs. Urine Peptidomic and Targeted Plasma Protein Analyses in the Diagnosis and Monitoring of Systemic Juvenile Idiopathic Arthritis PURPOSE: Systemic juvenile idiopathic arthritis is a chronic pediatric disease. The initial clinical presentation can mimic other pediatric inflammatory conditions, which often leads to significant delays in diagnosis and appropriate therapy. SJIA biomarker development is an unmet diagnostic/prognostic need to prevent disease complications. EXPERIMENTAL DESIGN: We profiled the urine peptidome to analyze a set of 102 urine samples, from patients with SJIA, Kawasaki disease (KD), febrile illnesses (FI), and healthy controls. A set of 91 plasma samples, from SJIA flare and quiescent patients, were profiled using a customized antibody array against 43 proteins known to be involved in inflammatory and protein catabolic processes. RESULTS: We identified a 17-urine-peptide biomarker panel that could effectively discriminate SJIA patients at active, quiescent, and remission disease states, and patients with active SJIA from confounding conditions including KD and FI. Targeted sequencing of these peptides revealed that they fall into several tight clusters from seven different proteins, suggesting disease-specific proteolytic activities. The antibody array plasma profiling identified an SJIA plasma flare signature consisting of tissue inhibitor of metalloproteinase-1 (TIMP1), interleukin (IL)-18, regulated upon activation, normal T cell expressed and secreted (RANTES), P-Selectin, MMP9, and L-Selectin. CONCLUSIONS AND CLINICAL RELEVANCE: The urine peptidomic and plasma protein analyses have the potential to improve SJIA care and suggest that SJIA urine peptide biomarkers may be an outcome of inflammation-driven effects on catabolic pathways operating at multiple sites. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s12014-010-9058-8) contains supplementary material, which is available to authorized users. Clinical Relevance Sensitive and specific diagnostic biomarkers for systemic onset juvenile idiopathic arthritis (SJIA) would allow its differentiation from other febrile illnesses, such as Kawasaki disease (KD) or acute infections (febrile illness (FI)) and facilitate prompt initiation of appropriate treatment at disease onset. Early treatment may reduce the risk of long-term complications and subsequent disabilities. In addition, biomarkers that distinguish intercurrent SJIA flare from infection in patients with known SJIA would be clinically useful, as would markers that predict impending disease flare or responder status to particular therapies, or provide an early indication of a treatment response. Finally, biomarkers may provide clues to unanswered questions concerning SJIA pathogenesis. Our comparative analysis of SJIA, KD, and FI urine peptidomes identified a small subset of the urine peptidome that effectively discriminates SJIA patients in the active, quiescent, and remission disease states, and also discriminates patients with active SJIA from confounding conditions including KD and FI. Urine peptide diagnostic and prognostic biomarkers could be of clinical use, especially for serial sampling of pediatric SJIA patients. Targeted sequencing revealed that these peptide markers fall into several tight clusters indicating SJIA-specific proteolytic events. Plasma cataloging analysis of the normal plasma peptidome shows that at least some of these nested peptide markers originate in the circulation. A customized antibody array was used to compare the plasma abundance of proteins known to be involved in inflammatory and protein catabolic processes, revealing a SJIA flare signature. Taken altogether, the urine peptidomic and plasma protein and peptide analyses suggest a testable model that SJIA urine peptide biomarkers may be an outcome of inflammation-driven effects on catabolic pathways operating at multiple sites.