Table 2.
Deiminated proteins in serum-EVs of cow (Bos taurus) as identified by F95-enrichment. Deiminated proteins from serum-EVs 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. Rows highlighted in pink indicate protein hits identified in serum-EVs 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 S2.
| Protein Name | Symbol | Sequences | Total Score (p < 0.05) 1 |
|---|---|---|---|
| Serotransferrin | G3X6N3 | 75 | 4958 |
| Serotransferrin | Q29443 | 74 | 4941 |
| Complement factor H | Q28085 | 85 | 4700 |
| Alpha-2-macroglobulin | Q7SIH1 | 77 | 4633 |
| Serum albumin | A0A140T897 | 76 | 4604 |
| Complement C3 | Q2UVX4 | 83 | 4258 |
| Uncharacterised protein (CFH—Complement factor H) | F1MC45 | 61 | 3469 |
| Fibronectin | G5E5A9 | 56 | 2492 |
| Uncharacterised protein (Ceruloplasmin) | F1N076 | 37 | 1994 |
| Uncharacterised protein (uncharacterised) | F1MJK3 | 38 | 1870 |
| Uncharacterised protein (C4A—Complement C4) | E1BH06 | 35 | 1840 |
| C4b-binding protein alpha chain | Q28065 | 36 | 1761 |
| Keratin, type II cytoskeletal 5 | M0QVZ6 | 35 | 1750 |
| Hemopexin | Q3SZV7 | 30 | 1594 |
| Keratin, type I cytoskeletal 14 | F1MC11 | 29 | 1592 |
| Uncharacterised protein (uncharacterised) | G3N0V0 | 25 | 1542 |
| Histidine-rich glycoprotein | F1MKS5 | 26 | 1407 |
| Uncharacterised protein (keratin 33A (KRT33A)) | F1MXG6 | 22 | 1311 |
| KRT33A protein | A5PJJ1 | 22 | 1306 |
| Keratin 31 | Q148I8 | 22 | 1291 |
| Uncharacterised protein (uncharacterised) | G3X7F3 | 20 | 1288 |
| Keratin, type II cuticular Hb1 | Q148H4 | 25 | 1225 |
| Uncharacterised protein (keratin 34 (KRT34)) | F1MSA6 | 21 | 1209 |
| Kininogen-1 | A0A140T8C8 | 21 | 1188 |
| Kininogen-1 | P01044 | 21 | 1164 |
| Uncharacterised protein (Desmoplakin) | E1BKT9 | 27 | 1156 |
| Uncharacterised protein (keratin 86 (KRT86)) | E1B898 | 22 | 1104 |
| Apolipoprotein A-I preproprotein | V6F9A2 | 22 | 1101 |
| Uncharacterised protein (uncharacterised) | F1MVK1 | 20 | 1066 |
| Uncharacterised protein (KRT6A—Keratin, type II cytoskeletal 59 kDa, component IV) | M0QVY0 | 21 | 1049 |
| Kininogen-2 | P01045 | 19 | 1042 |
| Uncharacterised protein (KRT3—Keratin, type II cytoskeletal 68 kDa, component IB) | G3MXL3 | 21 | 1034 |
| Junction plakoglobin | Q8SPJ1 | 21 | 987 |
| Keratin, type II cytoskeletal | Q08D91 | 19 | 971 |
| Uncharacterised protein (Immunoglobulin heavy constant mu) | G5E5T5 | 16 | 938 |
| Keratin, type I cytoskeletal 17 | A0A140T867 | 17 | 890 |
| Uncharacterised protein (IGLL1—immunoglobulin lambda-like polypeptide 1) | F1MCF8 | 12 | 886 |
| Uncharacterised protein (uncharacterised) | F1MH40 | 13 | 872 |
| Uncharacterised protein (uncharacterised) | F1MZ96 | 14 | 863 |
| Keratin 10 (Epidermolytic hyperkeratosis; keratosis palmaris et plantaris) | A6QNZ7 | 15 | 854 |
| Uncharacterised protein (uncharacterised) | F1MLW7 | 10 | 849 |
| Complement C4 | P01030 | 16 | 826 |
| Uncharacterised protein (Immunoglobulin heavy constant mu) | G5E513 | 15 | 810 |
| KRT15 protein | Q17QL7 | 13 | 734 |
| Uncharacterised protein (uncharacterised) | G3N0S9 | 14 | 631 |
| Keratin, type I cytoskeletal 19 | P08728 | 12 | 625 |
| KRT4 protein | A4IFP2 | 12 | 623 |
| SERPIND1 protein | A6QPP2 | 12 | 606 |
| Uncharacterised protein (uncharacterised) | F1MLW8 | 7 | 588 |
| Histidine-rich glycoprotein | P33433 | 9 | 566 |
| Inter-alpha-trypsin inhibitor heavy chain H2 | F1MNW4 | 12 | 554 |
| Inter-alpha-trypsin inhibitor heavy chain H4 | F1MMD7 | 10 | 521 |
| Vitamin D-binding protein | F1N5M2 | 12 | 517 |
| Antithrombin-III | F1MSZ6 | 11 | 492 |
| Plasminogen | P06868 | 14 | 485 |
| Apolipoprotein A-IV | Q32PJ2 | 11 | 475 |
| Serpin A3-3 | G3N1U4 | 9 | 442 |
| Complement factor B | P81187 | 9 | 429 |
| C1QC protein | Q1RMH5 | 8 | 428 |
| Complement C1q subcomponent subunit B | Q2KIV9 | 7 | 413 |
| Uncharacterised protein (serotransferrin-like) | E1BI82 | 8 | 411 |
| Uncharacterised protein (KRT16—Keratin 16) | G3X7W8 | 9 | 407 |
| Complement C1q subcomponent subunit A | Q5E9E3 | 7 | 401 |
| Serpin A3-4 | A2I7N0 | 9 | 383 |
| Alpha-1B-glycoprotein | Q2KJF1 | 7 | 381 |
| Uncharacterised protein (uncharacterised) | G3N3Q3 | 5 | 367 |
| Uncharacterised protein (Serpin A3-5) | G8JKW7 | 7 | 366 |
| Keratin, type II cytoskeletal 78 | A6QNX5 | 7 | 356 |
| Primary amine oxidase, liver isozyme | Q29437 | 8 | 352 |
| Serpin A3-2 | A2I7M9 | 7 | 333 |
| Uncharacterised protein (uncharacterised) | F1MW79 | 6 | 330 |
| Uncharacterised protein (uncharacterised) | G3N1H5 | 5 | 325 |
| Uncharacterised protein (KRT77—Keratin 77) | G3MYU2 | 6 | 310 |
| Uncharacterised protein (uncharacterised) | E1B805 | 7 | 309 |
| Uncharacterised protein (uncharacterised) | G3MXG6 | 4 | 305 |
| Uncharacterised protein (uncharacterised) | G3MXD9 | 5 | 300 |
| Uncharacterised protein (uncharacterised) | G3N2P6 | 5 | 292 |
| Uncharacterised protein (insulin-like growth factor binding protein, acid labile subunit (IGFALS)) | F1MJZ4 | 5 | 286 |
| Adiponectin | Q3Y5Z3 | 5 | 282 |
| Alpha-2-antiplasmin | P28800 | 7 | 271 |
| Protein AMBP | F1MMK9 | 6 | 268 |
| Vitronectin | Q3ZBS7 | 5 | 264 |
| Uncharacterised protein (uncharacterised) | G5E604 | 5 | 254 |
| Desmoglein-1 | F1MIW8 | 7 | 252 |
| Fibrinogen gamma-B chain | F1MGU7 | 5 | 252 |
| Uncharacterised protein (uncharacterised) | G3MY71 | 5 | 251 |
| Annexin A2 | P04272 | 5 | 244 |
| Fibrinogen alpha chain | A5PJE3 | 5 | 243 |
| Uncharacterised protein (uncharacterised) | G3MWT1 | 3 | 241 |
| Glyceraldehyde-3-phosphate dehydrogenase | P10096 | 6 | 238 |
| Serpin A3-7 | A0A0A0MP92 | 5 | 218 |
| Plakophilin-1 | Q28161 | 4 | 216 |
| Inter-alpha-trypsin inhibitor heavy chain H1 | Q0VCM5 | 5 | 213 |
| Hemoglobin subunit beta | P02070 | 4 | 212 |
| Alpha-1-antiproteinase | P34955 | 4 | 209 |
| Keratin, type II | A0JND2 | 4 | 198 |
| Actin, cytoplasmic 1 | F1MRD0 | 5 | 197 |
| Keratin, type I cytoskeletal 28 | Q148H6 | 4 | 194 |
| Thrombospondin-1 | F1N3A1 | 6 | 192 |
| Keratin, type I cytoskeletal 20 | F1MPK1 | 4 | 191 |
| ECM1 protein | A5PJT7 | 5 | 188 |
| Uncharacterised protein (Bos taurus immunoglobulin lambda-like polypeptide 1 (IGLL1)) | G3N2D7 | 3 | 186 |
| Selenoprotein P | P49907 | 5 | 184 |
| Uncharacterised protein (uncharacterised) | A0A0A0MPA0 | 4 | 176 |
| Gelsolin | F1MJH1 | 4 | 175 |
| Lactotransferrin | P24627 | 4 | 169 |
| Fibrinogen beta chain | F1MAV0 | 5 | 162 |
| Uncharacterised protein (uncharacterised) | G5E5H2 | 3 | 156 |
| Protein HP-20 homolog | Q2KIT0 | 3 | 151 |
| Uncharacterised protein (TGM1—Transglutaminase 1) | F1MBB7 | 2 | 143 |
| Actin, gamma-enteric smooth muscle | F1MKC4 | 4 | 143 |
| Uncharacterised protein (CD5L—CD5 molecule-like) | F1N514 | 4 | 131 |
| Complement component C7 | F1N045 | 4 | 128 |
| Uncharacterised protein (APOB—Apolipoprotein B) | E1BNR0 | 4 | 119 |
| Arginase-1 | Q2KJ64 | 3 | 119 |
| Alpha-S1-casein | CASA1_BOVIN | 2 | 115 |
| Uncharacterised protein (uncharacterised) | G3N028 | 2 | 114 |
| Alpha-2-HS-glycoprotein | cRAPR1|FETUA_BOVIN | 2 | 106 |
| Paraoxonase 1 | Q2KIW1 | 3 | 106 |
| Beta-2-glycoprotein 1 | A0A140T843 | 2 | 97 |
| Uncharacterised protein (uncharacterised) | G5E5V1 | 2 | 89 |
| Uncharacterised protein (Histone H2B family) | E1B7N8 | 2 | 88 |
| Complement component 1, r subcomponent | A5D9E9 | 3 | 83 |
| Histone H2A | A0A0A0MP90 | 2 | 80 |
| Uncharacterised protein (SLK-STE20-like kinase) | G3X696 | 3 | 80 |
| Prothrombin | P00735 | 2 | 79 |
| Peroxiredoxin-2 | Q9BGI3 | 3 | 79 |
| Uncharacterised protein (uncharacterised) | G3MZE0 | 1 | 69 |
| Uncharacterised protein (complement component 8, alpha polypeptide (C8A)) | F1MX87 | 1 | 69 |
| Uncharacterised protein (C1orf68—Chromosome 1 open reading frame 68) | G3N3D3 | 2 | 68 |
| Complement C5a anaphylatoxin | F1MY85 | 2 | 63 |
| Uncharacterised protein (complement factor I (CFI)) | F1N4M7 | 1 | 61 |
| Uncharacterised protein (armadillo repeat gene deleted in velocardiofacial syndrome (ARVCF)) | E1BPV1 | 2 | 59 |
| Uncharacterised protein (NEK10-Uncharacterised protein; NIMA-related kinase 10) | E1BHZ1 | 2 | 58 |
| Keratin associated protein 13-1 | A1A4M9 | 2 | 57 |
| Uncharacterised protein (uncharacterised) | F1MSF0 | 2 | 57 |
| Histone H4 | E1B9M9 | 1 | 56 |
| Gamma-glutamylcyclotransferase | Q32LE4 | 1 | 55 |
| Uncharacterised protein (JAKMIP2—Janus kinase and microtubule interacting protein 2) | G5E551 | 2 | 54 |
| TOX high mobility group box family member 4 | Q0P5K4 | 1 | 53 |
| Uncharacterised protein (TBC1D32—TBC1 domain family, member 32) | F1N7V1 | 2 | 51 |
| Proteasome subunit alpha type-6 | Q2YDE4 | 1 | 50 |
| Uncharacterised protein (KIAA1009 ortholog) | F1MZ01 | 2 | 50 |
| Uncharacterised protein (MYO5B—Myosin VB) | F1MMQ6 | 2 | 50 |
| Uncharacterised protein (Phospholipid phosphatase related 4) | F1MJ26 | 2 | 49 |
| Uncharacterised protein (MGA—MGA, MAX dimerization protein) | E1BKB7 | 2 | 49 |
| Uncharacterised protein (GOLGB1—Golgin B1) | E1BKZ5 | 2 | 47 |
| Histone H3 | E1BGN3 | 1 | 46 |
| Uncharacterised protein (CROCC—Ciliary rootlet coiled-coil, rootletin) | E1BBS9 | 3 | 46 |
| Protein FAM149B1 | A0JNF3 | 2 | 45 |
| Alpha-enolase | F1MB08 | 2 | 45 |
| Uncharacterised protein (UBR4—Ubiquitin protein ligase E3 component n-recognin 4) | E1BHT5 | 3 | 45 |
| Complement component C9 | Q3MHN2 | 1 | 44 |
| Uncharacterised protein (DOCK8—Bos taurus dedicator of cytokinesis 8 (DOCK8)) | E1BNA6 | 2 | 44 |
| Uncharacterised protein (KPRP—Keratinocyte proline-rich protein) | E1BLN6 | 1 | 44 |
| Uncharacterised protein (CCDC14—Coiled-coil domain containing 14) | F1MS02 | 2 | 43 |
| Uncharacterised protein (Strawberry notch homolog 1(Drosophila)) | E1BMP8 | 3 | 42 |
| DNA-directed RNA polymerase subunit beta | A5PJW8 | 1 | 42 |
| Uncharacterised protein (CRYGN-Crystallin, gamma N) | E1BDQ1 | 1 | 42 |
| Flotillin-1 | Q08DN8 | 1 | 41 |
| Uncharacterised protein (SMG6—Uncharacterised protein; Bos taurus smg-6 homolog, nonsense mediated mRNA decay factor (C. elegans) (SMG6)) | E1BFK4 | 2 | 41 |
| C1QTNF3 protein | A7MB82 | 1 | 41 |
| Uncharacterised protein (Protocadherin gamma subfamily B, 1) | F1MCA2 | 1 | 40 |
| Uncharacterised protein (Death-associated protein kinase 1) | F1MRL0 | 1 | 39 |
| Acyl-coenzyme A thioesterase THEM4 | A1A4L1 | 1 | 37 |
| Uncharacterised protein (Centrosomal protein 104kDa) | E1BND2 | 1 | 37 |
| C8G protein | A8YXZ2 | 1 | 36 |
| Uncharacterised protein (SERPINB12—Serpin family B member 12) | E1BDF5 | 1 | 36 |
| Uncharacterised protein (SLAMF9 SLAM family member 9) | E1BNF9 | 1 | 36 |
| Complement C1s subcomponent | Q0VCX1 | 1 | 36 |
| Uncharacterised protein (methyltransferase like 3 (METTL3)) | F1MX80 | 1 | 35 |
| Uncharacterised protein (SPAG9—Sperm associated antigen 9) | F1MZ69 | 1 | 35 |
| Adenosylhomocysteinase | Q3MHL4 | 1 | 35 |
| Uncharacterised protein (HIVEP3—Human immunodeficiency virus type I enhancer binding protein 3) | F1MBK6 | 1 | 34 |
| Coagulation factor V | F1N0I3 | 1 | 33 |
| Uncharacterised protein (VPREB1—Uncharacterised protein) | F1N160 | 1 | 33 |
| Uncharacterised protein (SERPING1) | E1BMJ0 | 1 | 33 |
| PPARD protein | A4IFL4 | 32 | |
| Uncharacterised protein | F1MZ93 | 1 | 32 |
| Uncharacterised protein (NCBP1—Nuclear cap binding protein subunit 1) | E1BMM0 | 1 | 32 |
| Transthyretin | O46375 | 1 | 32 |
| Uncharacterised protein (Cryptochrome-1) | F1MXB2 | 1 | 32 |
| Tubulin alpha chain | F1MNF8 | 1 | 31 |
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.