SP# Protein Name Protein ID Sequence Ref. % RT shift 1 α-enolase P06733.2 13-DS R/Cit GNPTVEVDLFTSKGLFR-32 [20] 2.4 2 - P06733.2 266-DPS R/Cit YISPDQLADLYKSFIK-285 [20] 3.0 3 - P06733.2 415-EELGSKAKFAG R/Cit NF R/Cit NPLAK-434 [20] 1.6 4 Vimentin AAH66956 31-VTTSTRTYSLGSAL R/Cit PSTSR-50 [21] 1.4 5 - AAH66956 136-EQLKGQGKS R/Cit LGDLYEEEMR-155 [21] 2.6 6 - AAH66956 371-NMKEEMARHL R/Cit EYQDLLNVK-390 [21] 1.4 7 - AAH66956 371-NMKEEMA R/Cit HLREYQDLLNVK-390 [21] 2.0 8 protein-arginine deiminase type-4 NP_036519.2 201-LHVA R/Cit SEMDKV R/Cit VFQAT R/Cit GK-220 [30] 3.6 9 - NP_036519 375-GLKEFPIK R/Cit VMGPDFGYVTR-394 [30] 3.4 10 - NP_036519 480-PAPDRKGFRLLLASP R/Cit SCYK-499 [30] 2.0 11 C-X-C motif chemokine 10 P02778.2 24-LS R/Cit TVRCTCISISNQPVNPR-43 [31] 1.6 12 tubulin polymerization promoting protein p25 α ACB10579 72-EMHGKNWSKLC R/Cit DCQVIDGR-91 [22] 1.6 13 - ACB10579 154-SGVTKAISSPTVS R/Cit LTDTTK-173 [22] 1.4 14 Fibrinogen α-chain P02671 29-AEGGGV R/Cit GPRVVE R/Cit HQSACK-48 [32] 0 15 - P02671 562-SHHPGIAEFPS R/Cit GKSSSYSK-581 [32] 0.4 16 - P02671 583-FTSSTSYN R/Cit GDSTFESKSYK-602 [32] 1.0 17 Myelin basic protein P02686.3 158-A R/Cit HGFLP R/Cit HRDTGILDSIGR-177 [33] 2.6 18 - P02686.3 245-LSRFSWGAEGQ R/Cit PGFGYGGR-264 [33] 2.0 19 - P02686.3 257-PGFGYGG R/Cit ASDYKSAHKGFK-276 [33] 0.6 20 - P02686.3 284-LSKIFKLGG R/Cit DSRSGSPMAR-303 [33] 0.6 21 Fibrinogen β-chain P02675 266-Y R/Cit VYCDMNTENGGWTVIQNR-285 [24] 0 22 - P02675 254-MYLIQPDSSVKPY R/Cit VYCDMR-273 [24] 3.4 23 - P02675 55-EAPSL R/Cit PAPPPISGGGYRAR-74 [24] 2.0 24 Fibrinogen γ-chain P02679.3 132-SI R/Cit YLQEIYNSNNQKIVNLK-151 [24] 3.0

Table 1: The complete list of synthetic peptides (SP) derived from human proteins, along with protein accession number, amino acid position, the reference to the citrullinated protein, and the observed RT shift between the citrulline and arginine version of the peptide. Bold letters indicates expected tryptic cleavage sites, and Cit indicates citrulline.