Table 1.
Deiminated proteins in bovine serum (Bos taurus), as identified by F95-enrichment and LC-MS/MS analysis. Deiminated proteins from serum were isolated by immunoprecipitation using the pan-deimination F95 antibody. The resulting F95-enriched eluate was then analysed by LC-MS/MS and peak list files submitted to Mascot. Bos taurus species-specific peptide sequence hits are listed, showing number of sequences for protein hits and total score. Blue highlighted rows indicate protein hits identified in whole sera only. Uncharacterised proteins based on LC-MS/MS search were further confirmed in STRING, based on the protein symbol, and protein identification from STRING, where retrieved, is shown in brackets ([]). For further full LC-MS/MS analysis of all protein hits see Supplementary Table S1.
| Protein Name | Symbol | Sequences | Total Score (p < 0.05) 1 |
|---|---|---|---|
| Serotransferrin | G3X6N3 | 76 | 5712 |
| Serotransferrin | Q29443 | 76 | 5711 |
| Complement factor H | Q28085 | 77 | 5123 |
| Alpha-2-macroglobulin | Q7SIH1 | 77 | 5079 |
| Serum albumin | A0A140T897 | 59 | 3944 |
| Uncharacterised protein [complement factor H] | F1MC45 | 54 | 3745 |
| Complement C3 | Q2UVX4 | 68 | 3483 |
| Uncharacterised protein [ceruloplasmin] | F1N076 | 44 | 2712 |
| Embryo-specific fibronectin 1 | B8Y9S9 | 37 | 2263 |
| Hemopexin | Q3SZV7 | 30 | 2019 |
| Uncharacterised protein [complement C4A] | E1BH06 | 34 | 1997 |
| C4b-binding protein alpha chain | Q28065 | 33 | 1841 |
| Kininogen-1 | A0A140T8C8 | 23 | 1505 |
| Kininogen-1 | P01044 | 22 | 1449 |
| Histidine-rich glycoprotein | F1MKS5 | 26 | 1432 |
| Uncharacterised protein (uncharacterised) | F1MJK3 | 26 | 1291 |
| Kininogen-2 | P01045 | 19 | 1271 |
| Uncharacterised protein (uncharacterised) | G3X7F3 | 16 | 1259 |
| Uncharacterised protein (uncharacterised) | G3N0V0 | 19 | 1186 |
| Apolipoprotein A-I preproprotein | V6F9A2 | 19 | 1122 |
| Uncharacterised protein (uncharacterised) | F1MVK1 | 17 | 953 |
| SERPIND1 protein | A6QPP2 | 16 | 865 |
| Uncharacterised protein (uncharacterised) | F1MZ96 | 13 | 837 |
| Uncharacterised protein [Bos taurus immunoglobulin lambda-like polypeptide 1 (IGLL1)] | F1MLW7 | 10 | 815 |
| Uncharacterised protein [Bos taurus immunoglobulin lambda-like polypeptide 1 (IGLL1)] | F1MCF8 | 10 | 796 |
| Uncharacterised protein [Immunoglobulin heavy constant mu] | G5E5T5 | 12 | 784 |
| Uncharacterised protein [Immunoglobulin heavy constant mu] | G5E513 | 10 | 732 |
| Uncharacterised protein (uncharacterised) | G3N0S9 | 12 | 648 |
| Histidine-rich glycoprotein | P33433 | 12 | 623 |
| Alpha-2-antiplasmin | P28800 | 11 | 531 |
| Uncharacterised protein (uncharacterised) | F1MLW8 | 5 | 434 |
| Hemoglobin subunit beta | P02070 | 6 | 422 |
| Vitamin D-binding protein | F1N5M2 | 9 | 420 |
| Alpha-1-antiproteinase | P34955 | 8 | 418 |
| Adiponectin | Q3Y5Z3 | 6 | 411 |
| Uncharacterised protein (uncharacterised) | F1MW79 | 7 | 403 |
| ECM1 protein | A5PJT7 | 8 | 395 |
| Complement C1q subcomponent subunit B | Q2KIV9 | 8 | 390 |
| Plasma kallikrein | Q2KJ63 | 8 | 385 |
| Inter-alpha-trypsin inhibitor heavy chain H4 | F1MMD7 | 6 | 367 |
| C1QC protein | Q1RMH5 | 5 | 347 |
| Uncharacterised protein [Serpin A3-5; Serine protease inhibitor] | G8JKW7 | 6 | 338 |
| Apolipoprotein A-IV | F1N3Q7 | 7 | 338 |
| Inter-alpha-trypsin inhibitor heavy chain H2 | F1MNW4 | 6 | 338 |
| Selenoprotein P | P49907 | 6 | 323 |
| Plasminogen | E1B726 | 6 | 302 |
| Complement C1q subcomponent subunit A | Q5E9E3 | 5 | 300 |
| Uncharacterised protein [Bos taurus insulin-like growth factor binding protein, acid labile subunit (IGFALS)] | F1MJZ4 | 6 | 277 |
| Thrombospondin-1 | F1N3A1 | 7 | 273 |
| Serpin A3-3 | G3N1U4 | 5 | 271 |
| Protein HP-20 homolog | Q2KIT0 | 5 | 269 |
| Uncharacterised protein (uncharacterised) | G5E604 | 4 | 234 |
| Inter-alpha-trypsin inhibitor heavy chain H1 | Q0VCM5 | 4 | 234 |
| Uncharacterised protein (uncharacterised) | E1B805 | 5 | 232 |
| Uncharacterised protein (uncharacterised) | G3MXD9 | 3 | 209 |
| Uncharacterised protein [Bos taurus immunoglobulin lambda-like polypeptide 1 (IGLL1)] | G3N2D7 | 3 | 204 |
| Keratin, type II cytoskeletal 7 | Q29S21 | 4 | 199 |
| Keratin, type I cytoskeletal 14 | F1MC11 | 4 | 199 |
| Uncharacterised protein [Heparan sulfate proteoglycan 2] | F1MER7 | 4 | 195 |
| Alpha-2-HS-glycoprotein | cRAPR1|FETUA_BOVIN | 4 | 190 |
| Uncharacterised protein (uncharacterised) | G3N1H5 | 2 | 187 |
| Serpin A3-8 | A0A0A0MP89 | 3 | 184 |
| Complement factor B | P81187 | 4 | 183 |
| Protein AMBP | F1MMK9 | 5 | 181 |
| Serpin A3-2 | A2I7M9 | 4 | 180 |
| Antithrombin-III | F1MSZ6 | 5 | 176 |
| Paraoxonase 1 | Q2KIW1 | 4 | 174 |
| Gelsolin | F1MJH1 | 3 | 171 |
| Uncharacterised protein (uncharacterised) | G3N3Q3 | 2 | 168 |
| Complement C5a anaphylatoxin | F1MY85 | 3 | 166 |
| Uncharacterised protein (uncharacterised) | G5E5H2 | 3 | 162 |
| Serpin A3-7 | A0A0A0MP92 | 4 | 160 |
| C1QTNF3 protein | A7MB82 | 3 | 160 |
| Uncharacterised protein [Bos taurus serotransferrin-like] | E1BI82 | 4 | 157 |
| Uncharacterised protein [Apolipoprotein B] | E1BNR0 | 4 | 150 |
| Primary amine oxidase, liver isozyme | Q29437 | 3 | 137 |
| Coagulation factor XI | F1MUT4 | 2 | 127 |
| Hepatocyte growth factor-like protein | E1BDW7 | 2 | 121 |
| Fibrinogen beta chain | F1MAV0 | 3 | 108 |
| Immunoglobulin J chain | Q3SYR8 | 2 | 107 |
| Uncharacterised protein (uncharacterised) | G3MXB5 | 2 | 100 |
| Uncharacterised protein [CD5 molecule-like] | F1N514 | 2 | 94 |
| Uncharacterised protein (uncharacterised) | G3MXG6 | 2 | 94 |
| Complement component C9 | Q3MHN2 | 2 | 87 |
| Complement component C6 | F1MM86 | 3 | 86 |
| Uncharacterised protein (uncharacterised) | G5E5V1 | 2 | 86 |
| Hemoglobin subunit alpha | P01966 | 2 | 85 |
| Uncharacterised protein (uncharacterised) | G3N028 | 2 | 75 |
| Fibrinogen alpha chain | A5PJE3 | 1 | 74 |
| Vitronectin | Q3ZBS7 | 2 | 73 |
| Alpha-1B-glycoprotein | Q2KJF1 | 1 | 66 |
| Coagulation factor XII | F1MTT3 | 1 | 65 |
| Uncharacterised protein (uncharacterised) | F1MSF0 | 2 | 63 |
| Prothrombin | P00735 | 1 | 61 |
| Uncharacterised protein [Nidogen 1] | F1MWN3 | 1 | 57 |
| Protein HP-25 homolog 2 | Q2KIU3 | 1 | 57 |
| Clusterin | F1MWI1 | 1 | 55 |
| Contactin-1 | F1MVI0 | 1 | 54 |
| Polymeric immunoglobulin receptor | F1MR22 | 2 | 51 |
| Uncharacterised protein [Sperm associated antigen 9] | F1MZ69 | 2 | 51 |
| Uncharacterised protein [Ankyrin repeat domain 11] | E1BAT5 | 2 | 51 |
| Beta-2-glycoprotein 1 | A0A140T843 | 1 | 50 |
| Carboxypeptidase N catalytic chain | Q2KJ83 | 1 | 49 |
| Uncharacterised protein [complement component 8, alpha polypeptide (C8A)] | F1MX87 | 1 | 48 |
| Fibrinogen gamma-B chain | F1MGU7 | 1 | 48 |
| Uncharacterised protein [ADAM metallopeptidase with thrombospondin type 1 motif, 13] | F1MVP0 | 1 | 47 |
| Uncharacterised protein [Talin 1] | F1MDH3 | 1 | 46 |
| Complement C1s subcomponent | Q0VCX1 | 1 | 46 |
| Uncharacterised protein [CL43—Collectin-43] | F1MFY6 | 1 | 45 |
| Complement component C7 | F1N045 | 1 | 44 |
| CLEC11A protein | A5D7L1 | 1 | 43 |
| Uncharacterised protein [KCTD12—Potassium channel tetramerization domain containing 12] | G3N3D4 | 1 | 43 |
| Uncharacterised protein [BRIP1—BRCA1 interacting protein C-terminal helicase 1] | E1BNG9 | 1 | 39 |
| Cadherin-1 | F1N619 | 1 | 39 |
| Ubiquitin carboxyl-terminal hydrolase isozyme L5 | Q9XSJ0 | 1 | 38 |
| CPN2 protein | A6QP30 | 1 | 37 |
| Acyl-coenzyme A thioesterase THEM4 | A1A4L1 | 1 | 37 |
| Uncharacterised protein [SLAMF9—SLAM family member 9] | E1BNF9 | 1 | 36 |
| Uncharacterised protein [MED12; Mediator complex subunit 12] | F1MZ95 | 1 | 35 |
| Transthyretin | O46375 | 1 | 33 |
| Voltage-dependent L-type calcium channel subunit beta-3 | Q9MZL3 | 1 | 33 |
1 Ions score is −10*Log(P), where P is the probability that the observed match is a random event. Individual ions scores > 31 indicated identity or extensive homology (p < 0.05). Protein scores were derived from ions scores as a non-probabilistic basis for ranking protein hits.