Table 2.
(a) The most associated protein peptides with an uncorrected P < 0.05 for the difference between 60 first-onset schizophrenia patients and 77 controls from the Cologne study. (b) The association for 12 of the 14 proteins reported in (a) and available in the 75 future schizophrenia patients and 644 controls from the neonatal study. (c) The most associated protein peptides with an uncorrected P < 0.10 for the 75 future schizophrenia patients and 644 controls from the neonatal study
| (a) Cologne study | ||||
|---|---|---|---|---|
| Protein | Peptide | First-onset schizophrenia and controls | ||
| Fold-change | P | Corrected P | ||
| Haptoglobin (HPT) | VTSIQDWVQK | 1.54 | 0.000535 | 0.0283 |
| Haptoglobin (HPT) | DYAEVGR | 1.56 | 0.000542 | 0.0283 |
| Haptoglobin (HPT) | VGYVSGWGR | 1.53 | 0.000653 | 0.0283 |
| Plasma protease C1 inhibitor (IC1) | TNLESILSYPK | 1.36 | 0.001480 | 0.0481 |
| Apolipoprotein C-III (APOC3) | GWVTDGFSSLK | −1.25 | 0.00308 | 0.0801 |
| Apolipoprotein A-IV (APOA4) | IDQNVEELK | −1.26 | 0.00829 | 0.172 |
| Plasma protease C1 inhibitor (IC1) | FQPTLLTLPR | 1.34 | 0.0116 | 0.172 |
| Apolipoprotein C-III (APOC3) | DALSSVQESQVAQQAR | −1.21 | 0.0120 | 0.172 |
| Antithrombin-III (ANT3) | FDTISEK | 1.26 | 0.0121 | 0.172 |
| Antithrombin-III (ANT3) | LPGIVAEGR | 1.25 | 0.0132 | 0.172 |
| Complement C4-A (CO4A) | VLSLAQEQVGGSPEK | 1.24 | 0.0159 | 0.188 |
| Alpha-1-antichymotrypsin (AACT) | EQLSLLDR | 1.38 | 0.0190 | 0.206 |
| Apolipoprotein A-II (APOA2) | SPELQAEAK | −1.13 | 0.0211 | 0.209 |
| Inter-alpha-trypsin inhibitor heavy chain H4 (ITIH4) | GPDVLTATVSGK | 1.18 | 0.0225 | 0.209 |
| Complement component C9 (CO9) | VVEESELAR | 1.23 | 0.0291 | 0.242 |
| Apolipoprotein C-I (APOC1) | EFGNTLEDK | −1.26 | 0.0339 | 0.242 |
| Complement component C9 (CO9) | LSPIYNLVPVK | 1.24 | 0.0354 | 0.242 |
| Complement C4-A (CO4A) | ITQVLHFTK | 1.22 | 0.0357 | 0.242 |
| Ficolin-3 (FCN3) | YGIDWASGR | 1.23 | 0.0364 | 0.242 |
| Apolipoprotein A-IV (APOA4) | ISASAEELR | −1.21 | 0.0372 | 0.242 |
| Alpha-2-antiplasmin (A2AP) | FDPSLTQR | 1.23 | 0.0412 | 0.255 |
| Beta-2-glycoprotein 1 (APOH) | EHSSLAFWK | 1.26 | 0.0488 | 0.288 |
| (b) Neonatal study | ||||
|---|---|---|---|---|
| Protein | Peptide | Future schizophrenia and controls | ||
| Fold-change | P | aOne-sided P | ||
| Haptoglobin (HPT) | VTSIQDWVQK | — | — | — |
| Haptoglobin (HPT) | DYAEVGR | — | — | — |
| Haptoglobin (HPT) | VGYVSGWGR | — | — | — |
| Plasma protease C1 inhibitor (IC1) | TNLESILSYPK | 1.001 | 0.9710 | — |
| Apolipoprotein C-III (APOC3) | GWVTDGFSSLK | 1.002 | 0.9750 | — |
| Apolipoprotein A-IV (APOA4) | IDQNVEELK | 1.123 | 0.0592 | b |
| Plasma protease C1 inhibitor (IC1) | FQPTLLTLPR | — | — | — |
| cApolipoprotein C-III (APOC3) | DALSSVQESQVAQQAR | 1.005 | 0.9200 | — |
| Antithrombin-III (ANT3) | FDTISEK | — | — | — |
| Antithrombin-III (ANT3) | LPGIVAEGR | 1.092 | 0.0887 | 0.0444 |
| Complement C4-A (CO4A) | VLSLAQEQVGGSPEK | 1.061 | 0.1860 | — |
| cAlpha-1-antichymotrypsin (AACT) | EQLSLLDR | 1.062 | 0.2340 | — |
| cApolipoprotein A-II (APOA2) | SPELQAEAK | 1.120 | 0.0397 | b |
| Inter-alpha-trypsin inhibitor heavy chain H4 (ITIH4) | GPDVLTATVSGK | 1.015 | 0.7250 | — |
| Complement component C9 (CO9) | VVEESELAR | — | — | — |
| Apolipoprotein C-I (APOC1) | EFGNTLEDK | 1.030 | 0.5260 | — |
| cComplement component C9 (CO9) | LSPIYNLVPVK | 1.003 | 0.9700 | — |
| cComplement C4-A (CO4A) | ITQVLHFTK | 1.105 | 0.0267 | 0.01340 |
| Ficolin-3 (FCN3) | YGIDWASGR | — | — | — |
| Apolipoprotein A-IV (APOA4) | ISASAEELR | 1.087 | 0.1180 | — |
| Alpha-2-antiplasmin (A2AP) | FDPSLTQR | 1.107 | 0.0116 | 0.00580 |
| Beta-2-glycoprotein 1 (APOH) | EHSSLAFWK | 1.073 | 0.2990 | — |
| (c) Neonatal study | ||||
|---|---|---|---|---|
| Protein | Peptide | Future schizophrenia and controls | ||
| Fold-change | P | |||
| Transthyretin (TTHY) | VLDAVR | 1.156 | 0.00264 | |
| Alpha-2-antiplasmin (A2AP) | FDPSLTQR | 1.1074 | 0.0116 | |
| Protein AMBP (AMBP) | ETLLQDFR | 1.1102 | 0.0129 | |
| Serotransferrin (TRFE) | EGYYGYTGAFR | 1.1307 | 0.0166 | |
| C4b-binding protein alpha chain (C4BPA) | YTCLPGYVR | −1.1866 | 0.0204 | |
| Complement C4-A (CO4A) | ITQVLHFTK | 1.1055 | 0.0267 | |
| Tubulin alpha-4A chain (TBA4A) | EIIDPVLDR | 1.1094 | 0.0392 | |
| Apolipoprotein A-II (APOA2) | SPELQAEAK | 1.1203 | 0.0397 | |
| Clusterin (CLUS) | IDSLLENDR | 1.0977 | 0.0413 | |
| Ig gamma-3 chain C region (IGHG3) | DTLMISR | 1.0869 | 0.0418 | |
| Kininogen-1 (KNG1) | DFVQPPTK | 1.0769 | 0.0529 | |
| Ig gamma-3 chain C region (IGHG3) | NQVSLTCLVK | 1.0967 | 0.0534 | |
| Apolipoprotein A-IV (APOA4) | IDQNVEELK | 1.1225 | 0.0592 | |
| Apolipoprotein D (APOD) | VLNQELR | 1.0961 | 0.0643 | |
| Purine nucleoside phosphorylase (PNPH) | VFGFSLITNK | −1.0679 | 0.069 | |
| Apolipoprotein A-I (APOA1) | ATEHLSTLSEK | 1.0885 | 0.073 | |
| Alpha-2-antiplasmin (A2AP) | DFLQSLK | 1.0677 | 0.0844 | |
| Antithrombin-III (ANT3) | LPGIVAEGR | 1.0918 | 0.0887 | |
| Histone H4 (H4) | DAVTYTEHAK | 1.1005 | 0.0894 | |
P-values were corrected for multiple testing using the false discovery rate. The selected covariates are listed in Supplementary Table 4a. The table also includes APOA4 (IDQNVEELK), ANT3 (LPGIVAEGR), APOA2 (SPELQAEK), CO4A (ITQVLHFTK) and A2P2 (FDPSLTQR) from (b). The selected covariates are listed in Supplementary Table 4b. aOne-sided test conducted when the direction of the fold-change is consistent with that from the Cologne study and the two-sided P < 0.10. bTwo-sided P < 0.10, but direction of the fold-change is not consistent. cSame protein peptide but different transition in (b) compared to (a)