The invention provides applications of deoxyhypusine dioxygenase, namely, DOHH, or a fragment thereof in preparation of a reagent for diagnosis of anti-citrullinated protein antibody negative (ACPA-negative) rheumatoid arthritis (RA). In the method, a high-density protein chip is hybridized with RA serum to screen 35 proteins, which are candidate auto-antigens of the ACPA-negative RA. It is identified that four protein antigens, DOHH, DUSP11, PTX3 and PAGE5, have high sensitivity and specificity in ACPA-negative serum of the RA, wherein the four protein antigens are all novel auto-antigens. The method shows that the DOHH, DUSP11, PTX3 and PAGE5 can be used as diagnosis markers for the ACPA-negative RA.