Overall, based on sequence homology, we have developed a straightforward and fast method to detect linear Ca 2+ -binding motifs from genomic information. Genome-wide analysis of EF-hand Ca 2+ -binding motifs in bacteria and virus have been analyzed with this methodology. Experimentally, we have also developed a robust and reliable grafting approach to study Ca 2+ -binding properties of continuous Ca 2+ binding sites. This novel approach has been successfully used to dissect site-specific Ca 2+ binding affinity and cooperativity among the four canonical EF-hands in the prototypical Ca 2+ -binding protein, calmodulin. The combination of these two approaches is expected to enable us to explore more Ca 2+ binding sites that are underrepresented due to the limitation of available methodology. Proteomics Comparison of Cerebrospinal Fluid of Relapsing Remitting and Primary Progressive Multiple Sclerosis BACKGROUND: Based on clinical representation of disease symptoms multiple sclerosis (MScl) patients can be divided into two major subtypes; relapsing remitting (RR) MScl (85–90%) and primary progressive (PP) MScl (10–15%). Proteomics analysis of cerebrospinal fluid (CSF) has detected a number of proteins that were elevated in MScl patients. Here we specifically aimed to differentiate between the PP and RR subtypes of MScl by comparing CSF proteins. METHODOLOGY/PRINCIPAL FINDINGS: CSF samples (n = 31) were handled according to the same protocol for quantitative mass spectrometry measurements we reported previously. In the comparison of PP MScl versus RR MScl we observed a number of differentially abundant proteins, such as protein jagged-1 and vitamin D-binding protein. Protein jagged-1 was over three times less abundant in PP MScl compared to RR MScl. Vitamin D-binding protein was only detected in the RR MScl samples. These two proteins were validated by independent techniques (western blot and ELISA) as differentially abundant in the comparison between both MScl types. CONCLUSIONS/SIGNIFICANCE: The main finding of this comparative study is the observation that the proteome profiles of CSF in PP and RR MScl patients overlap to a large extent. Still, a number of differences could be observed. Protein jagged-1 is a ligand for multiple Notch receptors and involved in the mediation of Notch signaling. It is suggested in literature that the Notch pathway is involved in the remyelination of MScl lesions. Aberration of normal homeostasis of Vitamin D, of which approximately 90% is bound to vitamin D-binding protein, has been widely implicated in MScl for some years now. Vitamin D directly and indirectly regulates the differentiation, activation of CD4+ T-lymphocytes and can prevent the development of autoimmune processes, and so it may be involved in neuroprotective elements in MScl. Multiple sclerosis (MScl) can be divided into two major subtypes based on clinical representation of disease symptoms in the patients [1] . Between 85-90% of patients can be classified as having the relapsing remitting (RR) MScl subtype, in which disease relapses are followed by periods of remission, and 10-15% of all MScl patients are diagnosed with the primary progressive (PP) subtype [2] . Even within a single large Dutch MScl pedigree of 26 patients with similar genetic background, the percentage of patients with a PP phenotype remained 15% [3] .