Pinpointing new protein and phosphoprotein biomarkers in rheumatoid arthritis by high-resolution label-free mass spectrometry analysis of liquid biopsies

Rheumatoid arthritis is an autoimmune inflammatory disease that attacks the joints, leading to joint destruction, if left untreated. The disease affects 0.5 to 1 % of the population in developed countries and causes great impairment to those affected and may even lead to early mortality, since the disease is usually correlated to cardiovascular events. Premature diagnosis and treatment are of the utmost importance, since it has been proved that people who began treatment within 3 months of disease onset had better outcomes, usually being able to avoid cartilage destruction in the joints. This work has the primary goal of identifying potential biomarkers in serum samples of patients with rheumatoid arthritis. Another objective was to check the phosphoproteome for differently phosphorylated peptides. In order to achieve these goals, we employed liquid chromatography-mass spectrometry to perform Label-Free Quantification of the non-phosphorylated fraction of the proteome, as well as for identifying the peptide sequences and phosphorylation present on the phosphoproteome of the different conditions. We compared serum samples from rheumatoid arthritis to healthy donors and to patients with systemic lupus erythematosus, another autoimmune disease characterised by chronic inflammation. We were able to identify 43 proteins, that were differently expressed between rheumatoid arthritis and healthy subjects. 12 of these were specific to rheumatoid arthritis. We were also able to identify 41 peptides that possessed different phosphorylation patterns between rheumatoid arthritis and healthy subjects. It was also possible to identify a kinase that appears to be active in rheumatoid arthritis, but not in healthy subjects