Citrullination of arginine residues by peptidyl arginine deiminase (PAD) enzymes drives autoimmune diseases. This post-translational modification was recently shown to inactivate ADAMTS13 and SERPINs which suggests involvement of citrullination in inflammation-related thrombosis. However, citrullination is notoriously difficult to detect by conventional methods, especially in complex proteomes. Here, we developed a novel citrulline probe which enables enrichment of citrullinated peptides prior to site-specific analysis via mass spectrometry (MS). We utilized this method to analyze citrullination of fibrinogen by PAD4 and show the utility of this probe for assessment of plasma protein citrullination. The citrulline probe was synthesized and its specificity was assessed by NMR. Highly purified PAD4 was used for in vitro citrullination of fibrinogen. Following tryptic digestion, citrullinated peptides were labelled with the probe. Subsequently, citrullinated peptides were enriched and analyzed by MS. Probe-specific peptide mass shift was used for reliable identification of citrullination sites using MaxQuant. The newly developed probe selectively modifies citrulline. Using a time-course of PAD4-incubated fibrinogen we measured an increasing intensity and number of citrullinated fibrinogen residues with a maximum of 52 sites. Clustered fibrinogen alpha-chain residues Arg218, Arg271, Arg458, Arg573 and Arg591 are preferentially citrullinated. Applicability of our method for complex proteomes was showcased by measuring a dose-response curve of spiked citrullinated fibrinogen in human plasma and plasma samples derived of patients with severe COVID-19. Our findings indicate that PAD4 preferentially modifies specific sites within fibrinogen that overlap with known targets of anti-citrullinated protein antibodies (ACPA). In addition, our findings provide evidence for extensive protein citrullination in patients with COVID-19.