In the present study, we aimed to discover and verify proteins with differential abundance in cerebrospinal fluid (CSF) from patients with early multiple sclerosis compared to controls. iTRAQ and Orbitrap MS was used to compare the CSF proteome of patients with clinically isolated syndrome (CIS) (n = 5), patients with relapsing-remitting multiple sclerosis that had CIS at the time of lumbar puncture (n = 5), and controls with other inflammatory neurological disease (n = 5). Of more than 1200 identified proteins, five were selected as biomarker candidates. Selected reaction monitoring (SRM) was used to verify the biomarker candidates in a larger patient and control cohort (n = 132). We also included proteins reported as differentially abundant in multiple sclerosis in the literature for SRM verification. We found differential abundance of 11 proteins after verification, of which the five proteins alpha-1-antichymotrypsin, contactin-1, apolipoprotein D, clusterin, and kallikrein-6 show potential as diagnostic markers for multiple sclerosis. This study forms the basis for further biomarker verification studies in even larger sample cohorts, to determine if these proteins have clinical relevance as biomarkers for multiple sclerosis.