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pmid:32575983
Top-Down Proteomics of Human Saliva Discloses Significant Variations of the Protein Profile in Patients with Mastocytosis.
Simone Serrao · Davide Firinu · Alessandra Olianas · Margherita Deidda · Cristina Contini · Federica Iavarone · M Teresa Sanna · Mozhgan Boroumand · Francisco Amado · Massimo Castagnola · Irene Messana · Stefano Del Giacco · Barbara Manconi · Tiziana Cabras
Journal of proteome research · 2020 doi:10.1021/acs.jproteome.0c00207
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Experiment
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Analysis
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Complete file
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A cutaneous subtype (CM) is distinguished from a systemic one (SM); SM patients can be grouped into SM with (SM+C) or without (SM-C) additional cutaneous lesions, and their classification is often challenging. This study was purposed to highlight variations in the salivary proteome of patients with different mastocytosis subtypes and compared to healthy controls. A top-down proteomics approach coupled to a label-free quantitation revealed salivary profiles in patients different from those of controls and a down-regulation of peptides/proteins involved in the mouth homeostasis and defense, such as statherin, histatins, and acidic proline-rich proteins (aPRPs), and in innate immunity and inflammation, such as the cathepsin inhibitors, suggesting a systemic condition associated with an exacerbated inflammatory state. The up-regulation of antileukoproteinase and S100A8 suggested a protective role against the disease status. The two SM forms were distinguished by the lower levels of truncated forms of aPRPs, statherin, P-B peptide, and cystatin D and the higher levels of thymosin β4 and α-defensins 1 and 4 in SM-C patients with respect to SM+C. Data are available via ProteomeXchange with identifier PXD017759.", "claims": [{"id": "claim-method", "statement": "The comparisons between the three groups of patients and that of the controls and between the three groups of patients have been performed with Mann–Whitney and Welch-corrected t tests, depending on the distribution (skewed or normal) and the variance (unequal or homogeneous). 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(theor)", "m/z (charge) for XIC search", "[M + H]+ ± SD exper. (theor)", "PTMs", "m/z (charge) for MS/MS"], ["Acid proline-rich proteins (PRP-1 and PRP-3 types)a"], ["PRP-1 (P02810)", "22.2", "15515 ± 2 (15514–15,515)", "1293.9(+12), 1194.4(+13), 1035.3(+15), 970.7(+16), 913.6(+17)", "15506.1 ± 0.1 (15506.24–15507.22)", "Q1 pyroglutamination, S8 and S22 phosphorylation", "1293.68(+12); 1194(+13); 1035.28 (+15); 970.58 (+16); 862.85(+18)"], ["PRP-1 1P", "22.9", "15435 ± 2 (15434–15,435)", "1287.2(+12), 1188.3(+13), 1030.0(+15), 965.7(+16), 908.9(+17)", "15426.1 ± 0.1 (15426.27–15427.26)", "Q1 pyroglutamination, S8 or S22 phosphorylation", "1287.01(+12); 1188.3(+13); 1030.0 (+15)"], ["PRP-1 0P", "23.2", "15355 ± 2 (15354–15,355)", "1280.5(+12), 1182.1(+13), 1024.6(+15), 960.7(+16), 904.2(+17)", "15346.1 ± 0.1 (15346.31–15347.29)", "Q1 pyroglutamination", "1534.42 (+10); 904.08 (+17)"], ["PRP-1 3P", "21.6", "15595 ± 2 (15594–15,595)", "1418.7(+11), 1300.5(+12), 1200.6(+13), 1040.6(+15), 975.7(+16)", "15585.8 ± 0.1 (15586.21–15587.19)", "Q1 pyroglutamination, S8, S17, and S22 phosphorylation", "1733.70 (+9); 1560.08 (+10); 1114.61 (+14); 975.56 (+16)"], ["PRP-3 (P02810)", "22.8", "11161 ± 1 (11161–11,162)", "1595.5(+7), 1396.2(+8), 1015.7(+11), 931.1(+12), 859.6(+13)", "11155.01 ± 0.07 (11156.08–11157.06)", "Q1 pyroglutamination, S8 and S22 phosphorylation", "931.09(+12); 798.07(+14); 745.00(+15)"], ["PRP-3 1P", "23.4", "11081 ± 1 (11081–11,082)", "1584.1(+7), 1386.2(+8), 1008.4(+11), 924.5(+12), 853.4(+13)", "11075.98 ± 0.07 (11076.11–11077.09)", "Q1 pyroglutamination, S8 or S22 monophosphorylation", "1386.13(+8); 1008.28(+11); 853.31(+13)"], ["PRP-3 0P", "23.8", "11001 ± 1 (11001–11,002)", "1376.2(+8), 1101.2(+10), 917.8(+12) 786.8(+14)", "10996.01 ± 0.07 (10996.14–10997.13)", "Q1 pyroglutamination", "1001.10(+11); 786.72(+14)"], ["PRP-3 desR6", "22.8", "11004 ± 1 (11005–11,006)", "1573.2(+7), 1223.8(+9), 1001.5(+11), 847.6(+13)", "10999.85 ± 0.07 (10999.97–11000.96)", "C-term. R106 removal from PRP-3", "1001.45(+11); 918.08(+12)"], ["P-C peptide (P02810)", "15.0", "4370.9 ± 0.4 (4370.8)", "1457.9(+3), 1093.7(+4)", "4369.19 ± 0.03 (4369.20)", "", "1457.07(+3); 1093.05(+4); 874.64(+5); 729.04(+6)"], ["Statherin"], ["statherin (P02808)", "29.2", "5380.0 ± 0.5 (5379.7)", "1794.2(+3), 1345.9(+4), 1076.9(+5)", "5377.46 ± 0.03 (5377.45)", "S2 and S3 phosphorylation", "1793.17(+3); 1345.12(+4); 1076.30(+5)"], ["statherin 1P", "28.9", "5299.9 ± 0.5 (5299.7)", "1767.6(+3), 1325.9(+4), 1060.9(+5)", "5297.46 ± 0.03 (5297.48)", "S2 or S3 phosphorylation", "1325.12(+4); 1060.30(+5)"], ["statherin des-F43", "27.8", "5232.4 ± 0.5 (5232.5)", "1745.1(+3), 1309.1(+4), 1047.5(+5)", "5230.39 ± 0.03 (5230.38)", "C-term. F43 removal from statherin", "1744.13(+3); 1308.35(+4); 1046.88(+5)"], ["statherin desT42-F43", "27.9", "5131.2 ± 0.5 (5131.4)", "1711.4(+3), 1283.8(+4), 1027.2(+5)", "5129.34 ± 0.03 (5129.33)", "C-term. T42 and F43 removal from statherin", "1710.45(+3); 1283.09(+4); 1026.67(+5)"], ["statherin desD1", "28.7", "5264.7 ± 0.5 (5264.6)", "1755.9(+3), 1317.2(+4), 1053.9(+5)", "5262.43 ± 0.03 (5262.42)", "N-term D1 removal from statherin", "1754.81(+3); 1316.36(+4); 1053.29(+5)"], ["statherin des1-9", "28.5", "4127.9 ± 0.4 (4127.6)", "1376.9(+3), 1032.9(+4)", "4126.00 ± 0.02 (4125.99)", "removal of D1SSEEKFLR9 from statherin", "1376.00(+3); 1032.25(+4)"], ["statherin des1-10", "28.0", "3971.3 ± 0.4 (3971.4)", "1986.7(+2), 1324.8(+3)", "3969.88 ± 0.02 (3969.89)", "Removal of D1SSEEKFLRR10 from statherin", "1323.96(+3); 993.22(+4)"], ["statherin des1-13", "27.5", "3645.2 ± 0.4 (3645.0)", "1823.6(+2), 1216.1(+3)", "3643.69 ± 0.02 (3643.68)", "Removal of D1SSEEKFLRRIGR13 from statherin", "1215.23(+3); 911.68(+4)"], ["P-B peptide"], ["P-B peptide (P02814)", "30.0", "5792.9 ± 0.5 (5792.7)", "1932.0(+3), 1449.2(+4), 1159.6(+5)", "5790.05 ± 0.04 (5790.04)", "", "1930.68(+3); 1448.27(+4); 1158.82(+5)"], ["P-B des1-4", "30.0", "5371.0 ± 0.5 (5371.3)", "1791.4(+3), 1343.8(+4), 1075.3(+5)", "5368.83 ± 0.03 (5368.82)", "removal of Q1RGP4 from P-B", "1790.25(+3); 1342.96(+4); 1074.57(+5)"], ["P-B des1-5", "30.3", "5215.0 ± 0.5 (5215.1)", "1739.4(+3), 1304.8(+4), 1044.0(+5)", "5212.74 ± 0.03 (5212.73)", "removal of Q1RGPR5 from P-B", "1303.93(+4); 1043.35(+5)"], ["P-B des1-7", "30.1", "5060.1 ± 0.5 (5060.9)", "1688.0(+3), 1266.2(+4), 1013.2(+5)", "5058.66 ± 0.03 (5058.65)", "removal of Q1RGPRGP7 from P-B", "1686.88(+3); 1265.42(+4); 1012.54(+5)"], ["P-B des1-12", "27.5", "4549.0 ± 0.5 (4549.3)", "1517.5(+3), 1138.3(+4)", "4547.41 ± 0.02 (4547.41)", "removal of Q1RGPRGPYPPGP12 from P-B", "1137.61(+4)"], ["Histatins"], ["Hst-1 (P15515)", "21.9", "4928.2 ± 0.5 (4928.2)", "1644.1(+3), 1233.5(+4)", "4926.19 ± 0.03 (4926.20)", "S2 phosphorylation", "986.05(+5); 821.87(+6); 704.61(+7)"], ["Hst-1 0P", "22.0", "4848.2 ± 0.5 (4848.2)", "1617.4(+3), 1213.5(+4)", "4846.24 ± 0.03 (4846.23)", "", "970.05(+5)"], ["Hst-3 (P15516)", "17.7", "4062.2 ± 0.4 (4062.4)", "1355.1(+3), 1016.6(+4)", "4060.97 ± 0.02 (4060.98)", "", "1015.99(+4); 813.00(+5); 677.67(+6)"], ["Hst-3 1/25", "14.3", "3192.4 ± 0.3 (3192.5)", "1065.1(+3), 799.1(+4)", "3191.63 ± 0.02 (3191.62)", "removal of S26NYLYDN32 from Hst-3", "400.09(+8); 456.95(+9)"], ["Hst-3 1/24", "14.6", "3036.5 ± 0.3 (3036.3)", "1013.2(+3), 760.1(+4)", "3035.53 ± 0.02 (3035.52)", "removal of S26NYLYD31 from Hst-3", "608.11(+5); 506.93(+6); 434.65(+7)"], ["Cystatins"], ["cystatin A (P01040)", "31.8", "11005 ± 2 (11006.5)", "1001.59(+11), 1101.59(+10), 1223.94(+9), 1376.81(+8), 1573.36(+7), 1835.42(+6)", "11000.65 ± 0.07 (11000.67)", "", "1376.83(+8); 847.74(+13); 787.19(+14); 734.85(+15);"], ["cystatin A Nα-Ac", "33", "11047 ± 2 (11048.5)", "1005.41(+11), 1105.85(+10), 1228.61(+9), 1382.06(+8), 1579.36(+7), 1842.42(+6)", "11042.55 ± 0.07 (11042.68)", "N-terminal acetylation", "1381.79(+8); 789.98(+14)"], ["cystatin B-SSG (P04080)", "32.8", "11486 ± 2 (11486.9)", "1915.5(+6), 1642.0(+7), 1436.9(+8), 1277.3(+9), 1149.7(+10), 1045.3(+11)", "11480.61 ± 0.07 (11480.68)", "N-terminal acetylation, C3 glutathionylation", "1436.72(+8); 1277.31(+9); 766.91(+15), 718.79(+16)"], ["cystatin C (P01034)", "35.1", "13342 ± 2 (13343.1)", "1483.57(+9), 1335.32(+10), 1214.02(+11), 1112.93(+12), 1027.40(+13)", "13335.31 ± 0.08 (13335.58)", "2 disulfide bridges", "1112.81(+12); 890.50(+15)"], ["cystatin C Mox", "35.3", "13358 ± 1 (13358.4)", "1485.28(+9), 1336.85(+10), 1215.41(+11), 1114.21(+12), 1028.58(+13)", "13351.60 ± 0.08 (13351.57)", "M14 oxidation of cystatin C", "1114.23(+12); 954.20(+14)"], ["cystatin D-R26 des1-8 (P28325)", "38.0", "13163 ± 2 (13163.0)", "1646.40 (+8), 1463.60 (+9), 1317.30 (+10), 1197.60 (+11), 1097.90 (+12), 1013.50 (+13)", "13155.25 ± 0.08 (13155.48)", "removal of G1SASAQSR8, 2 disulfide bridges", "941.09(+14); 823.71(+16)"], ["cystatin D-R26 des1-5", "37.7", "13517 ± 2 (13517.3)", "1690.70(+8), 1502.90(+9), 1352.70 (+10), 1229.80 (+11), 1127.4 (+12), 1040.40 (+13)", "13509.41 ± 0.08 (13509.65)", "Q1 pyroglutamination after removal of G1SASA5, 2 disulfide bridges", "1502.63(+9), 1040.87(+13) 966.48(+14); 845.72(+16)"], ["cystatin S (P01036)", "35.3", "14186 ± 2 (14185)", "1774.3(+8), 1577.2(+9), 1419.6(+10), 1290.6(+11), 1183.2(+12), 1092.2(+13), 1014.3(+14)", "14176.61 ± 0.08 (14176.81)", "2 disulfide bridges", "946.58(+15); 835.22(+17)"], ["cystatin S1", "35.3", "14266 ± 2 (14265)", "1784.3(+8), 1586.1(+9), 1427.6(+10), 1297.9(+11), 1189.8(+12), 1098.4(+13), 1020.0(+14)", "14256.66 ± 0.09 (14256.77)", "S3 phosphorylation of cystatin S, 2 disulfide bridges", "1098.37(+13); 1019.69(+14); 951.91(+15)"], ["cystatin S1ox", "35.3", "14281 ± 2 (14280.7)", "1786.40(+8), 1589.70 (+9), 1429.30 (+10), 1299.50 (+11), 1191.30 (+12), 1099.70 (+13)", "14272.66 ± 0.09 (14272.77)", "W23 oxidation of cystatin S1", "1299.08(+11); 1099.36(+13); 894.67(+16)"], ["cystatin S2", "35.3", "14346 ± 2 (14345)", "1794.3(+8), 1595.0(+9), 1435.6(+10), 1305.2(+11), 1196.5(+12), 1104.5(+13), 1025.7(+14)", "14336.58 ± 0.09 (14336.74)", "S1 and S3 phosphorylation of cystatin S, 2 disulfide bridges", "957.31(+15); 897.55(+16)"], ["cystatin SN (P01037)", "34.6", "14312 ± 2 (14313)", "1790.0(+8), 1591.2(+9), 1432.2(+10), 1302.1(+11), 1193.7(+12), 1101.9(+13), 1023.3(+14)", "14304.03 ± 0.09 (14304.09)", "2 disulfide bridges", "1023.29(+14); 796.01(+18); 716.50(+20)"], ["cystatin SNox", "34.6", "14328 ± 2 (14328)", "1792.30(+8), 1593.20 (+9), 1434.00 (+10), 1303.30 (+11), 1195.20 (+12), 1103.30 (+13)", "14320.09 ± 0.09 (14319.84)", "2 disulfide bridges, W23 oxidation", "843.64(+17); 754.26(+19); 717.35(+20); 682.52(+21)"], ["cystatin SA (P09228)", "36.8", "14347 ± 2 (14346)", "1794.4(+8), 1595.1(+9), 1435.7(+10), 1305.3(+11), 1196.6(+12), 1104.6(+13), 1025.8(+14)", "14337.87 ± 0.09 (14338.01)", "1 disulfide bridge", "897.50(+16); 844.88(+17); 798.78(+18);"], ["Antileukoproteinase"], ["SLPI (P03973)", "26.2", "11709 ± 1 (11710)", "1952.64(+6), 1673.84(+7), 1464.73(+8), 1302.10(+9)", "11702.41 ± 0.07 (11702.36)", "8 disulfide bridges", "1171.82(+10); 1065.47(+11); 976.69(+12); 837.45(+14)"], ["α-Defensins"], ["α-defensin 1 (P59665)", "23.5", "3442.5 ± 0.3 (3442.1)", "1772.03(+2), 1148.36(+3), 861.52(+4)", "3440.45 ± 0.02 (3440.519)", "3 disulfide bridges", "861.14(+4); 689.11(+5)"], ["α-defensin 2 (P59665/6)", "23.5", "3370.7 ± 0.3 (3370.9)", "1686.49(+2), 1124.66(+3), 843.75(+4)", "3370.41 ± 0.02 (3370.484)", "3 disulfide bridges", "843.61(+4); 675.10(+5)"], ["α-defensin 3 (P59666)", "23.5", "3485.8 ± 0.3 (3486.1)", "1744.03(+2), 1163.03(+3), 872.52(+4)", "3484.53 ± 0.02 (3484.509)", "3 disulfide bridges", "872.11(+4); 698.09(+5)"], ["α-defensin 4 (P12838)", "27.2", "3709.1 ± 0.3 (3709.4)", "1855.71(+2), 1237.48(+3), 928.36(+4)", "3707.68 ± 0.02 (3707.767)", "3 disulfide bridges", "928.18(+4); 742.74(+5);"], ["Thymosin β4"], ["Tβ4 (P62328)", "18.5", "4963.7 ± 0.5 (4963.5)", "1655.51(+3), 1241.88(+4), 993.71(+5)", "4961.47 ± 0.03 (4961.494)", "N-terminal acetylation", "710.08(+7), 621.32(+8)"], ["S100A proteins"], ["S100A8 (P05109)", "40.4", "10834 ± 2 (10834.6)", "1355.3(+8), 1204.8(+9), 1084.5(+10), 985.9(+11)", "10827.41 ± 0.07 (10828.66)", "", "903.62(+12); 834.11(+13); 774.75(+14)"], ["S100A8 SNO", "40.8", "10863 ± 2 (10863.5)", "1358.9(+8), 1208.1(+9), 1087.3(+10), 988.6(+11)", "10857.37 ± 0.07 (10857.65)", "C42 nitrosylation", "1087.49(+10); 680.03(+16); 640.03(+17)"], ["S100A8 hyperoxidized", "39.3", "10915 ± 2 (10914.6)", "1365.3(+8), 1213.7(+9), 1092.5(+10), 993.2(+11)", "10908.40 ± 0.07 (10908.63)", "C42-SO3H, W54 dioxidation or C42-SO3H, W54, and M78 oxidation", "993.20(+11); 910.37(+12); 683.16(+16); 642.85(+17)"], ["S100A9(S) (P06702)", "42.2", "12690 ± 2 (12689.3)", "1410.9(+9), 1269.9(+10), 1154.6(+11), 1058.4(+12), 977.1(+13)", "12682.21 ± 0.08 (12682.29)", "N-term. Acetylation after M1TCKM5 removal", "1410.67(+9); 1269.93(+10); 977.22(+13); 793.95(+16); 747.48(+17); 705.85(+18);"], ["S100A9(S) 1P", "42.2", "12770 ± 2 (12769.3)", "1419.8(+9), 1277.9(+10), 1161.8(+11), 1065.1(+12), 983.3(+13)", "12762.05 ± 0.08 (12762.26)", "T108 phosphorylation of S100A9(S)", "1161.66(+11); 798.96(+16); 710.29(+18)"], ["S100A9(S)ox", "41.3", "12706 ± 2 (12705.3)", "1412.7(+9), 1271.5(+10), 1156.0(+11), 1059.8(+12), 978.3(+13)", "12698.14 ± 0.08 (12698.29)", "M89, or 78 or 76 or 58 oxidation of S100A9(S)", "1271.41(+10); 1155.92(+11); 908.51(+14)"], ["S100A9(S)ox 1P", "41.3", "12786 ± 2 (12785.3)", "1421.9(+9), 1279.5(+10), 1163.3(+11), 1066.4(+12), 984.5(+13)", "12778.21 ± 0.08 (12778.25)", "T108 phosphorylation of S100A9(S)ox", "1419.82(+9); 983.26(+13); 913.10(+14)"]], "row_count": 64, "column_count": 7, "numeric_cells": 355, "header_rows": 1, "locator": "section[6]/table-wrap[1]#tbl2"}}, {"id": "asset:table:pmid:32575983:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:abf58967b1d8178cc9fd9ab79bd07f8993cdb2d176bd48ae907ef9ecef227df1", "bytes": 5282, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[10]/table-wrap[1]#tbl3", "version": null, "note": "XIC Peak Areas Values (Mean ± SD), Frequencies, and p Values Obtained by Statistical Analysis by Comparing the Three Patients’ Groups with Respect to the Controls and Each Othera", "structure": {"pmcid": "PMC8008451", "section_index": 10, "section_title": "Quantitative Comparison between Controls and Patients", "row_count": 49, "column_count": 7}, "table": {"label": "Table 3", "caption": "XIC Peak Areas Values (Mean ± SD), Frequencies, and p Values Obtained by Statistical Analysis by Comparing the Three Patients’ Groups with Respect to the Controls and Each Othera", "rows": [["", "", "XIC peak area ×108 (mean ± SD) and frequency", "p values"], ["no.", "protein/peptide", "CM", "SM", "Ctrls", "CM vs Ctrls", "SM vs Ctrls"], ["#1", "PRP-1", "17.8 ± 10.1 (6/6)", "27.4 ± 27.2 (35/35)", "99.9 ± 70.9 (48/48)", "<0.0001 ↓CM", "< 0.0001 ↓SM"], ["#2", "PRP-1 1P", "2.5 ± 3.1 (5/6)", "3.7 ± 5.2 (29/35)", "12.8 ± 12.9 (47/48)", "0.002 ↓CM", "< 0.0001 ↓SM"], ["#3", "PRP-1 0P", "(0/6)", "0.09 ± 0.3 (6/35)", "0.5 ± 0.9 (22/48)", "NA", "0.003 ↓SM"], ["#4", "PRP-1 3P", "0.2 ± 0.2 (4/6)", "0.4 ± 0.6 (22/35)", "2.0 ± 1.9 (44/48)", "0.002 ↓CM", "< 0.0001 ↓SM"], ["#5", "PRP-3", "5.9 ± 4.4 (6/6)", "9.5 ± 11.3 (33/35)", "35.1 ± 29.3 (48/48)", "0.0002 ↓CM", "< 0.0001 ↓SM"], ["#6", "PRP-3 1P", "1.1 ± 1.0 (6/6)", "1.5 ± 1.8 (29/35)", "4.9 ± 4.1 (47/48)", "0.002 ↓CM", "< 0.0001 ↓SM"], ["#7", "PRP-3 0P", "(0/10)", "0.004 ± 0.02 (2/35)", "0.4 ± 1.1 (18/48)", "NA", "0.0003 ↓SM"], ["#8", "PRP-3 desR106", "3.1 ± 2.7 (6/6)", "2.8 ± 5.9 (26/35)", "3.8 ± 6.2 (40/48)", "•", "•"], ["#9", "P-C peptide", "4.1 ± 4.4 (6/6)", "7.0 ± 10.0 (33/35)", "20.4 ± 16.2 (48/48)", "0.001 ↓CM", "< 0.0001 ↓SM"], ["#10", "statherin", "5.4 ± 6.6 (5/6)", "6.0 ± 6.6 (34/35)", "13.4 ± 10.1 (47/47)", "0.02 ↓CM", "0.0001 ↓SM"], ["#11", "Stath. 1P", "0.2 ± 0.2 (3/6)", "0.1 ± 0.2 (17/35)", "0.3 ± 0.4 (32/47)", "•", "0.03 ↓SM"], ["#12", "Stath. des-F43", "1.1 ± 1.0 (6/6)", "1.0 ± 0.9 (34/35)", "1.9 ± 1.8 (46/47)", "•", "0.006 ↓SM"], ["#13", "Stath. desT42-F43", "0.7 ± 0.4 (6/6)", "0.4 ± 0.4 (25/35)", "0.7 ± 0.7 (46/47)", "•", "•"], ["#14", "Stath. desD1", "0.7 ± 0.9 (5/6)", "0.5 ± 0.5 (31/35)", "0.8 ± 0.8 (46/47)", "•", "0.02 ↓SM"], ["#15", "Stath. des1-9", "0.1 ± 0.2 (5/6)", "0.2 ± 0.4 (18/35)", "0.7 ± 0.7 (40/47)", "•", "< 0.0001 ↓SM"], ["#16", "Stath. des1-10", "0.2 ± 0.2 (5/6)", "0.3 ± 0.4 (24/35)", "0.5 ± 0.5 (44/47)", "•", "0.001 ↓SM"], ["#17", "Stath. des1-13", "0.1 ± 0.1 (4/6)", "0.1 ± 0.2 (22/35)", "0.3 ± 0.2 (45/47)", "0.04 ↓CM", "< 0.0001 ↓SM"], ["#18", "P-B peptide", "7.6 ± 7.9 (6/6)", "9.2 ± 7.8 (34/35)", "21.9 ± 14.3 (47/47)", "0.004 ↓CM", "< 0.0001 ↓SM"], ["#19", "P-B des1-4", "0.9 ± 0.6 (6/6)", "1.0 ± 0.8 (31/35)", "1.5 ± 1.7 (39/48)", "•", "•"], ["#20", "P-B des1-5", "3.0 ± 3.6 (6/6)", "1.8 ± 2.4 (30/35)", "2.3 ± 2.8 (42/48)", "•", "•"], ["#21", "P-B des1-7", "1.7 ± 0.9 (6/6)", "1.7 ± 1.5 (32/35)", "4.4 ± 2.8 (47/48)", "0.007 ↓CM", "< 0.0001 ↓SM"], ["#22", "P-B des1-12", "0.8 ± 0.4 (6/6)", "0.6 ± 0.6 (31/35)", "1.0 ± 1.4 (46/48)", "•", "•"], ["#23", "Hst-1", "1.1 ± 1.6 (4/6)", "1.1 ± 1.5 (24/35)", "2.9 ± 2.9 (34/48)", "•", "0.02 ↓SM"], ["#24", "Hst-1 0P", "(0/6)", "0.2 ± 0.3 (15/35)", "0.4 ± 0.7 (23/48)", "NA", "•"], ["#25", "Hst-3", "0.01 ± 0.03 (1/6)", "0.3 ± 0.6 (12/35)", "1.2 ± 1.7 (26/48)", "NA", "0.008 ↓SM"], ["#26", "Hst-3 1/25", "(0/6)", "0.04 ± 0.1 (6/35)", "0.9 ± 1.2 (25/48)", "NA", "0.0001 ↓SM"], ["#27", "Hst-3 1/24", "(0/6)", "0.8 ± 1.7 (15/27)", "3.0 ± 3.4 (40/48)", "NA", "< 0.0001 ↓SM"], ["#28", "Cyst. A", "2.0 ± 1.4 (6/6)", "1.2 ± 1.2 (35/35)", "2.2 ± 1.9 (47/48)", "•", "0.001 ↓SM"], ["#29", "Cyst B (all proteoforms)", "1.3 ± 1.1 (6/6)", "1.2 ± 1.2 (34/35)", "1.4 ± 1.3 (43/48)", "•", "•"], ["#30", "Cyst. C (all proteoforms)", "0.03 ± 0.07 (1/6)", "0.05 ± 0.2 (3/35)", "0.6 ± 0.7 (32/48)", "NA", "< 0.0001 ↓SM"], ["#31", "Cyst. D-R26 des1-5", "0.4 ± 0.9 (1/6)", "0.5 ± 0.8 (19/35)", "0.8 ± 1.1 (28/48)", "NA", "•"], ["#32", "Cyst. D-R26 des1-8", "(0/6)", "0.06 ± 0.1 (11/35)", "0.1 ± 0.2 (15/48)", "NA", "•"], ["#33", "Cyst. S", "(0/6)", "0.3 ± 0.7 (11/35)", "2.5 ± 0.5 (29/48)", "NA", "0.0007 ↓SM"], ["#34", "Cyst. S1 (all proteoforms)", "11.3 ± 12.7 (6/6)", "4.5 ± 3.8 (33/35)", "10.3 ± 10.6 (45/48)", "•", "0.002 ↓SM"], ["#35", "Cyst. S2", "1.9 ± 3.0 (2/6)", "2.2 ± 3.6 (22/35)", "3.8 ± 3.9 (45/48)", "•", "0.002 ↓SM"], ["#36", "Cyst. SN (all proteoforms)", "10.2 ± 13.8 (4/6)", "9.2 ± 11.1 (31/35)", "20.7 ± 17.1 (47/48)", "•", "0.0005 ↓SM"], ["#37", "Cyst. SA", "0.9 ± 1.9 (2/6)", "0.8 ± 2.1 (9/35)", "2.9 ± 3.8 (35/48)", "•", "<0.0001 ↓SM"], ["#38", "Tβ4", "0.4 ± 0.3 (5/6)", "0.4 ± 0.5 (24/35)", "0.8 ± 1.0 (30/48)", "•", "•"], ["#39", "α-defensin 1", "1.1 ± 0.7 (6/6)", "1.4 ± 1.9 (33/35)", "1.9 ± 2.9 (41/48)", "•", "•"], ["#40", "α-defensin 2", "0.8 ± 0.6 (6/6)", "0.7 ± 0.9 (31/35)", "1.3 ± 1.7 (37/48)", "•", "•"], ["#41", "α-defensin 3", "0.6 ± 0.7 (5/6)", "0.3 ± 0.4 (21/35)", "0.8 ± 1.3 (30/48)", "•", "•"], ["#42", "α-defensin 4", "0.2 ± 0.1 (3/6)", "0.1 ± 0.2 (15/35)", "0.3 ± 0.4 (23/48)", "•", "•"], ["#43", "S100A9(S) + (S)ox", "1.3 ± 1.5 (4/6)", "1.5 ± 1.9 (24/35)", "2.3 ± 2.7 (39/48)", "•", "•"], ["#44", "S100A9(S) 1P + (S)ox 1P", "0.4 ± 0.5 (3/6)", "0.6 ± 1.0 (16/35)", "0.5 ± 1.0 (17/48)", "•", "•"], ["#45", "SLPI", "0.2 ± 0.3 (3/6)", "0.2 ± 0.8 (18/35)", "0.1 ± 0.20 (10/48)", "•", "0.005 ↑SM"], ["#46", "S100A8 (all proteoforms)", "0.5 ± 1.1 (1/6)", "0.6 ± 1.1 (14/35)", "0.2 ± 0.6 (9/48)", "NA", "0.02 ↑SM"], ["#47", "S100A8-SNO", "0.5 ± 1.1 (1/6)", "0.3 ± 0.7 (8/35)", "0.1 ± 0.5 (6/48)", "NA", "•"]], "row_count": 49, "column_count": 7, "numeric_cells": 263, "header_rows": 2, "locator": "section[10]/table-wrap[1]#tbl3"}}, {"id": "asset:table:pmid:32575983:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:a1905f171d1bc6d3b40026923a10bf24cb17ef2c110aed3852a417f46b60af36", "bytes": 1053, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[1]#tbl4", "version": null, "note": "Results of Correlation Analysis between Salivary Proteins/Peptides and Tryptase Levels in SM Patients and in the Subgroup SM-Ca", "structure": {"pmcid": "PMC8008451", "section_index": 12, "section_title": "Correlation Analysis with Tryptase and with Oral Aphtosis and GI Symptoms", "row_count": 14, "column_count": 6}, "table": {"label": "Table 4", "caption": "Results of Correlation Analysis between Salivary Proteins/Peptides and Tryptase Levels in SM Patients and in the Subgroup SM-Ca", "rows": [["", "SM (n = 35)", "SM-C (n = 8)", ""], ["protein/peptide", "p value", "R", "p value", "R", "distinctive between SM-C and SM+C"], ["PRP-1 1P", "", "", "0.04 (+)", "0.77", ""], ["PRP-3 1P", "", "", "0.03 (+)", "0.77", ""], ["PRP-3 desR106", "", "", "0.007 (+)", "0.88", "Y (↑ in SM-C)"], ["Statherin desD1", "", "", "0.01 (+)", "0.86", ""], ["Statherin des1-10", "0.03 (+)", "0.40", "0.02 (+)", "0.79", ""], ["Statherin des1-13", "0.02 (+)", "0.40", "0.02 (+)", "0.79", ""], ["P-B des1-4", "0.02 (+)", "0.38", "0.002 (+)", "0.93", ""], ["P-B des1-5", "", "", "0.02 (+)", "0.81", "Y (↑ in SM-C)"], ["P-B des1-7", "", "", "0.01 (+)", "0.86", ""], ["P-B des1-12", "", "", "0.006 (+)", "0.89", ""], ["Cystatin D-R26 des1-5", "0.02 (+)", "0.40", "0.005 (+)", "0.90", "Y (↑ in SM-C)"], ["Thymosin β4", "", "", "0.005 (−)", "–0.84", "Y (↓ in SM-C)"]], "row_count": 14, "column_count": 6, "numeric_cells": 45, "header_rows": 2, "locator": "section[12]/table-wrap[1]#tbl4"}}], "gaps": ["asset:data:geo:PXD017759 not downloaded", "asset:data:geo:PXD017759 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "group_comparison", "specific": "welch_t_test", "label": "Group comparison", "dsl_operations": ["welch_t"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 1.0, "band": "reordered", "quote": "The comparisons between the three groups of patients and that of the controls and between the three groups of patients have been performed with Mann–Whitney and Welch-corrected t tests, depending on the distribution (skewed or normal) and the variance (unequal or homogeneous). Correlation analyses, between the XIC peak area of the proteins/peptides under analysis and the tryptase levels of each patient, were performed with the Spearman test and considered significant when the p value was <0.05."}}], "targets": [], "gaps": []}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["welch_t"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: welch_t_test."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["PXD017759"], "resolved_accessions": ["PXD017759"], "statements": ["Data are available via ProteomeXchange with identifier PXD017759."], "basis": "The paper names PXD017759 in ProteomeXchange Consortium via the PRIDE partner repository and the accession resolves in the repository. 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