Protein name Protein ID Sequence Mod.Res. Actin, cytoplasmic 1 P60709 85-IWHHTFYNEL Cit VAPEEHPVLLTEAPLNPK-113 96 α-1-antitrypsin P01009 218-WE Cit PFEVKDTEEEDFHVDQVTTVK-241 220 α-2-macroglobulin P01023 704-VGFYESDVMG Cit GHAR-719 715 Apolipoprotein A-I P02647 231-AKPALEDL Cit QGLLPVLESFK-250 239 Apolipoprotein A-IV P06727 276-GNL Cit GNTEGLQK-287 279 Apolipoprotein C-III P02656 45-DALSSVQESQVAQQA Cit GWVTDGFSSLK-71 60 Apolipoprotein E P02649 186-EGAE Cit GLSAIR-198 190 Apolipoprotein L1 O14791 321-VNEPSILEMS Cit GVK-334 331 Complement C1r subcomponent P00736 472-MGNFPWQVFTNIHG Cit GGGALLGDR-494 484 Complement C3 P01024 1285-DAPDHQELNLDVSLQLPS Cit-1303 1303 Complement C4-A P0C0L4 1350-QI Cit GLEEELQFSLGSK-1365 1352 Fibrinogen α-chain P02671 582-QFTSSTSYN Cit GDSTFESK-599 591 Fibrinogen α-chain P02671 481-EVVTSEDGSDCPEAMDLGTLSGIGTLDGF Cit HR-512 510 Fibrinogen α-chain P02671 259-MELERPGGNEIT Cit GGSTSYGTGSETESPR-287 272 Fibrinogen α-chain P02671 115-GDFSSANN Cit DNTYNR-129 123 Fibrinogen β-chain P02675 53-Cit EEAPSLRPAPPPISGGGYR-72 53 Fibronectin P02751 253-GNLLQCICTGNG Cit GEWK-269 265 Fibronectin P02751 2335-RPGGEPSPEGTTGQSYNQYSQ Cit YHQR-2360 2354 Haptoglobin P00738 117-L Cit TEGDGVYTLNNEK-131 118 Ig κ-chain V-III region GOL P04206 46-LLMYGASS Cit ATGIPDRFSGSGSGTDFTLTISR-78 55 Inter-α-trypsin inhi-bitor heavy chain H2 P19823 136-TVG Cit ALYAQAR-146 139 Inter-α-trypsin inhi-bitor heavy chain H4 Q14624 658-MNF Cit PGVLSSR-669 661 Plasminogen P00747 88-M Cit DVVLFEK-96 89 Protein AMBP P02760 294-GPC Cit AFIQLWAFDAVK-309 297 Proteoglycan 4 Q92954 187-NSAAN Cit ELQK-196 191 Proteoglycan 4 Q92954 1307-AIGPSQTHTI Cit IQYSPARLAYQDK-1330 1317 Proteoglycan 4 Q92954 1285-RPALNYPVYGETTQV Cit R-1301 1300 Prothrombin P00734 453-YNW Cit ENLD Cit DIALMK-467 456,461 Prothrombin P00734 434-YE Cit NIEK-440 436 Serum albumin P02768 97-LCTVATL Cit ETYGEMADCCAK-117 105

Table 2: The complete list of proteins where citrulline has been annotated directly and unambiguously on the fragment. Bold protein name indicates newly identified citrullinated RA synovial fluid proteins. All other proteins have been found by van Beers JJ et al. [17] to contain citrulline.