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pmid:30666314
Integrated dataset on acute phase protein response in chicken challenged with Escherichia coli lipopolysaccharide endotoxin.
Anita Horvatić · Nicolas Guillemin · Haider Kaab · Dorothy McKeegan · Emily O'Reilly · Maureen Bain · Josipa Kuleš · Peter David Eckersall
Data in brief · 2018 doi:10.1016/j.dib.2018.09.103
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Complete file
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Statistical and bioinformatic analyses were performed to specify the effect of bacterial endotoxin. Plasma from chicken (N=6) challenged with Escherichia coli (LPS) (2 mg/kg body weight) was collected pre (0 h) and at 12, 24, 48, and 72 h post injection along with plasma from a control group (N=6) challenged with sterile saline. Protein identification and relative quantification were performed using Proteome Discoverer, and data were analysed using R. Gene Ontology terms were analysed by the Cytoscape application ClueGO based on Gallus gallus GO Biological Process database, and refined by REVIGO. Absolute quantification of several acute phase proteins, e.g. alpha-1-acid glycoprotein (AGP), serum amyloid A (SAA) and ovotrensferrin (OVT) was performed by immunoassays to validate the LC-MS results. The data contained within this article are directly related to our research article\"Quantitative proteomics using tandem mass tags in relation to the acute phase protein response in chicken challenged with Escherichia coli lipopolysaccharide endotoxin\" [1]. The raw mass spectrometric data generated in this study were deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD009399 (http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD009399).", "claims": [{"id": "claim-method", "statement": "A two-way ANOVA was performed to model the effect of treatment and time on the quantity of the peptides, using a linear regression model.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30666314", "locator": "sections[7] \"Statistics for proteomics\" paragraph 3", "quote": "A two-way ANOVA was performed to model the effect of treatment and time on the quantity of the peptides, using a linear regression model."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The mass spectrometry proteomics raw data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD009399MS (http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD009399). 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All other data are available within this article."]], "row_count": 9, "column_count": 2, "numeric_cells": 2, "header_rows": 0, "locator": "section[1]/table-wrap[1]#t0035"}}, {"id": "asset:table:pmid:30666314:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:d17bf17bec06aeb1f0d99bdd50a151d8c2a745702a43ac0bee82d2c4ffddfbbc", "bytes": 6004, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[3]/table-wrap[1]#t0005", "version": null, "note": "Proteins with significantly differential abundances between LPS and saline groups identified using TMT approach.", "structure": {"pmcid": "PMC6205363", "section_index": 3, "section_title": "Data", "row_count": 89, "column_count": 4}, "table": {"label": "Table 1", "caption": "Proteins with significantly differential abundances between LPS and saline groups identified using TMT approach.", "rows": [["Gene Symbol"], ["(Gallus gallus)", "Protein name", "P-value (FDR)", "Fold Change"], ["HPS5", "serum amyloid A protein", "2.20E-03", "1.24"], ["SERPINA3", "alpha-1-antiproteinase*", "7.89E-07", "1.02"], ["HPX", "haemopexin*", "5.35E-06", "0.79"], ["ORM1", "alpha 1-acid glycoprotein", "1.05E-05", "0.66"], ["LCN8", "extracellular fatty acid-binding protein precursor", "7.62E-03", "0.65"], ["TF", "ovotransferrin", "3.61E-06", "0.49"], ["CP", "ceruloplasmin*", "1.14E-03", "0.48"], ["SMC4", "condensin complex subunit", "1.94E-03", "0.47"], ["LOC107051143", "complement C3-like*", "2.09E-05", "0.43"], ["CFD", "complement factor D, partial*", "1.05E-04", "0.34"], ["LOC423629", "uncharacterized protein LOC423629*", "1.87E-03", "0.33"], ["LOC419851", "complement regulatory soluble protein", "9.47E-03", "0.32"], ["PIT54", "PIT 54", "1.17E-04", "0.29"], ["LOC100858647", "beta-microseminoprotein-like*", "2.99E-03", "0.28"], ["FGA", "Fibrinogen alpha chain precursor", "4.45E-05", "0.26"], ["CLU", "clusterin isoform X1*", "6.86E-03", "0.21"], ["FGB", "Fibrinogen beta chain precursor", "2.46E-04", "0.21"], ["FGG", "fibrinogen gamma chain precursor", "1.10E-04", "0.21"], ["C3", "complement C3 precursor", "1.41E-03", "0.19"], ["IGLL1", "immunoglobulin light chain variable region, partial", "1.79E-02", "0.18"], ["CFHR2", "complement factor H*", "1.64E-05", "0.17"], ["SPINK5", "ovoinhibitor", "2.87E-02", "0.17"], ["A2ML4", "alpha-2-macroglobulin-like protein 1*", "8.86E-03", "0.17"], ["VNN1", "pantetheinase precursor", "3.69E-02", "0.17"], ["APOH", "beta-2-glycoprotein 1 precursor", "3.50E-03", "0.15"], ["FETUB", "fetuin-B precursor", "8.55E-06", "0.15"], ["PLG", "plasminogen*", "3.20E-06", "0.12"], ["ATRN", "attractin isoform X3*", "3.08E-02", "0.11"], ["LOC418892", "uncharacterized protein", "2.78E-02", "0.11"], ["CST3", "cystatin precursor", "2.25E-02", "−0.10"], ["TNC", "tenascin", "4.09E-02", "−0.11"], ["ITIH3", "inter-alpha-trypsin inhibitor heavy chain H3 isoform X1*", "4.21E-02", "−0.12"], ["AGRN", "basement membrane-specific heparan sulfate proteoglycan core protein precursor", "2.51E-02", "−0.12"], ["ITIH2", "inter-alpha-trypsin inhibitor heavy chain H2 precursor", "1.96E-02", "−0.12"], ["IGFALS", "insulin-like growth factor-binding protein complex acid labile subunit isoform X1*", "3.71E-03", "−0.13"], ["HSPG2", "basement membrane-specific heparan sulfate proteoglycan core protein*", "1.79E-02", "−0.13"], ["HRG", "histidine-rich glycoprotein*", "1.51E-02", "−0.14"], ["COL5A1", "alpha 1 (V) collagen", "2.79E-02", "−0.14"], ["KNG1", "kininogen-1*", "1.19E-03", "−0.14"], ["C1QTNF3", "complement C1q tumor necrosis factor-related protein 3 isoform X1*", "8.85E-03", "−0.14"], ["F13A1", "coagulation factor XIII A chain", "4.15E-02", "−0.14"], ["LUM", "lumican precursor", "2.45E-03", "−0.14"], ["AHSG", "alpha-2-HS-glycoprotein*", "3.98E-02", "−0.14"], ["GIF", "hypothetical protein RCJMB04_7i4", "3.80E-02", "−0.15"], ["PROS1", "vitamin K-dependent protein S*", "1.42E-02", "−0.15"], ["APOA2", "apolipoprotein A-II*", "2.47E-02", "−0.16"], ["ANPEP", "aminopeptidase, partial", "2.11E-02", "−0.16"], ["LOC107056848", "cadherin-5-like, partial*", "7.56E-03", "-0.17"], ["VTN", "vitronectin precursor", "1.59E-05", "−0.17"], ["CL2", "ribonuclease CL2 precursor", "1.69E-02", "−0.17"], ["LOC107055759", "vitamin K-dependent protein S-like*", "7.86E-03", "−0.17"], ["APOA1", "apolipoprotein A-I", "1.64E-05", "−0.18"], ["FBLN1", "fibulin-1, isoform D precursor", "3.85E-02", "−0.18"], ["APOA4", "apolipoprotein A-IV precursor", "4.10E-04", "−0.19"], ["IL6ST", "interleukin-6 receptor subunit beta precursor", "4.32E-05", "−0.20"], ["TFRC", "chicken transferrin receptor", "2.19E-04", "−0.20"], ["SPARC", "basement-membrane protein 40 precursor", "3.29E-02", "−0.20"], ["F13B", "coagulation factor XIII B chain isoform X1*", "9.61E-03", "−0.20"], ["LOC100857892", "sushi, nidogen and EGF-like domain-containing protein 1 isoform X1*", "8.56E-03", "−0.20"], ["LOC107050076", "IgGFc-binding protein-like, partial*", "4.78E-03", "−0.21"], ["SERPINF1", "pigment epithelium-derived factor precursor", "3.03E-06", "−0.21"], ["CLEC3B", "tetranectin precursor", "7.32E-03", "−0.22"], ["SERPINC1", "antithrombin-III*", "1.39E-06", "−0.23"], ["SERPINA4", "serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 4 precursor", "3.23E-04", "−0.23"], ["LOC771012", "coagulation factor X-like*", "4.19E-03", "−0.23"], ["ENO1", "alpha-enolase", "6.46E-03", "−0.23"], ["LOC100858068", "IgGFc-binding protein-like, partial*", "2.32E-02", "−0.23"], ["RBP4A", "E Chain E, Retinol Binding Protein Complexed With Transthyretin", "2.26E-04", "-0.25"], ["FN1", "fibronectin, partial", "9.44E-03", "−0.26"], ["SERPINA5", "alpha-1-antitrypsin isoform X1*", "2.49E-04", "−0.28"], ["TGFBI", "transforming growth factor-beta-induced protein ig-h3 precursor", "3.84E-06", "−0.28"], ["HBG2", "beta-globin", "1.46E-02", "−0.29"], ["LCAT", "lecithin-cholesterol acyltransferase, partial", "1.14E-02", "−0.29"], ["C4", "complement C4 precursor", "3.37E-02", "−0.30"], ["ALPP", "intestinal-type alkaline phosphatase*", "1.27E-02", "−0.30"], ["POSTN", "periostin precursor", "3.16E-06", "−0.32"], ["COL1A1", "collagen alpha-1(I) chain*", "2.52E-05", "−0.36"], ["SCARA5", "scavenger receptor class A member 5 isoform X1*", "1.97E-02", "−0.36"], ["LOC776376", "pentraxin-related precursor", "1.82E-02", "−0.39"], ["HBAD", "alpha-D globin", "3.10E-02", "−0.43"], ["COL6A1", "collagen alpha-1(VI) chain precursor", "2.07E-06", "−0.44"], ["CPN2", "carboxypeptidase N subunit 2*", "2.11E-05", "−0.46"], ["LRRC15", "uncharacterized protein LRRC15*", "2.11E-05", "−0.46"], ["HBAA", "hemoglobin subunit alpha-A chain", "7.37E-03", "−0.48"], ["KRT8", "keratin, type II cytoskeletal 8*", "3.35E-02", "−0.50"], ["LOC107055417", "keratin, type II cytoskeletal 8-like, partial*", "3.35E-02", "−0.50"], ["COL1A2", "collagen alpha-2(I) chain precursor", "7.52E-04", "−0.51"]], "row_count": 89, "column_count": 4, "numeric_cells": 217, "header_rows": 2, "locator": "section[3]/table-wrap[1]#t0005"}}, {"id": "asset:table:pmid:30666314:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:27a693fb0f7a37ab02b14c744f6814b0d242fc32dfc2e11f19801deee308f388", "bytes": 1393, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[3]/table-wrap[2]#t0010", "version": null, "note": "Proteins with significantly differential abundances during time in chicken challenged with Escherichia coli lipopolysaccharide endotoxin.", "structure": {"pmcid": "PMC6205363", "section_index": 3, "section_title": "Data", "row_count": 20, "column_count": 6}, "table": {"label": "Table 2", "caption": "Proteins with significantly differential abundances during time in chicken challenged with Escherichia coli lipopolysaccharide endotoxin.", "rows": [["Gene symbol", "P value (FDR)", "Fold change (12 h/0 h)", "Fold change (24 h/0 h)", "Fold change (48 h/0 h)", "Fold change (72 h/0 h)"], ["A2ML4", "1.57E-02", "0.34", "0.44", "0.31", "0.19"], ["AHSG", "1.06E-02", "−0.43", "−0.15", "−0.04", "0.13"], ["APOA2", "1.37E-02", "−0.36", "−0.49", "−0.19", "−0.30"], ["C3", "4.39E-02", "0.18", "0.35", "0.35", "0.19"], ["CFD", "1.89E-02", "0.42", "0.61", "0.62", "0.43"], ["COL1A1", "3.39E-02", "−0.62", "−0.42", "−0.42", "−0.23"], ["CP", "3.16E-03", "1.02", "1.05", "0.51", "0.21"], ["FGA", "9.93E-03", "0.29", "0.38", "0.23", "0.03"], ["FGB", "1.03E-02", "0.26", "0.34", "0.24", "0.03"], ["FGG", "9.19E-03", "0.23", "0.33", "0.23", "0.01"], ["HPS5", "5.44E-03", "2.27", "1.35", "0.35", "-0.29"], ["HPX", "7.81E-03", "0.76", "1.20", "1.21", "0.94"], ["ITIH2", "4.46E-02", "−0.19", "−0.05", "0.02", "0.04"], ["LCN8", "1.82E-02", "1.78", "1.02", "0.66", "0.21"], ["ORM1", "5.01E-03", "0.93", "1.18", "0.76", "0.42"], ["POSTN", "2.18E-02", "0.06", "−0.30", "−0.35", "−0.15"], ["SERPINA3", "4.31E-03", "1.24", "1.35", "0.99", "0.73"], ["TF", "1.54E-02", "0.51", "0.55", "0.41", "0.30"], ["TGFBI", "1.50E-02", "−0.34", "−0.52", "−0.29", "−0.24"]], "row_count": 20, "column_count": 6, "numeric_cells": 99, "header_rows": 1, "locator": "section[3]/table-wrap[2]#t0010"}}, {"id": "asset:table:pmid:30666314:5", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:33c68b7dabced4c3e85eefcfe32a7387849d3154bbf06592c5445033c3e91062", "bytes": 2765, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[3]/table-wrap[3]#t0015", "version": null, "note": "GO terms over-represented in chicken challenged with Escherichia coli lipopolysaccharide endotoxin vs saline group.", "structure": {"pmcid": "PMC6205363", "section_index": 3, "section_title": "Data", "row_count": 26, "column_count": 8}, "table": {"label": "Table 3", "caption": "GO terms over-represented in chicken challenged with Escherichia coli lipopolysaccharide endotoxin vs saline group.", "rows": [["GOID", "GOTerm", "Term p-value", "Genes", "Cluster", "Redundant", "Leader", "Group"], ["GO:0072378", "blood coagulation, fibrin clot formation", "1.18E-12", "6", "No specific", "", "", "GO:0052547"], ["GO:0031589", "cell-substrate adhesion", "1.76E-04", "7", "No specific", "", "Yes", "GO:0031589"], ["GO:0015893", "drug transport", "6.75E-03", "4", "Negative", "", "", "GO:1902042"], ["GO:0035987", "endodermal cell differentiation", "5.95E-04", "3", "Negative", "", "", "GO:0052547"], ["GO:0030198", "extracellular matrix organization", "6.46E-03", "4", "Negative", "", "", "GO:0043062"], ["GO:0043062", "extracellular structure organization", "8.25E-04", "6", "Negative", "", "Yes", "GO:0043062"], ["GO:0030195", "negative regulation of blood coagulation", "1.75E-06", "5", "Positive", "Yes", "", "NA"], ["GO:0010951", "negative regulation of endopeptidase activity", "9.55E-18", "16", "Negative", "Yes", "", "NA"], ["GO:2000352", "negative regulation of endothelial cell apoptotic process", "4.89E-04", "3", "Positive", "", "", "GO:1902042"], ["GO:1902042", "negative regulation of extrinsic apoptotic signaling pathway via death domain receptors", "4.17E-04", "3", "Positive", "", "Yes", "GO:1902042"], ["GO:0031639", "plasminogen activation", "3.14E-04", "3", "Positive", "", "", "GO:0052547"], ["GO:0070527", "platelet aggregation", "4.19E-03", "3", "Positive", "Yes", "", "NA"], ["GO:0022409", "positive regulation of cell-cell adhesion", "3.36E-03", "4", "Positive", "", "", "GO:0031589"], ["GO:0045921", "positive regulation of exocytosis", "4.19E-03", "3", "Positive", "Yes", "", "NA"], ["GO:0090277", "positive regulation of peptide hormone secretion", "4.94E-04", "4", "Positive", "", "", "GO:1902042"], ["GO:0050714", "positive regulation of protein secretion", "4.76E-03", "4", "Positive", "Yes", "", "NA"], ["GO:0045907", "positive regulation of vasoconstriction", "6.99E-04", "3", "Positive", "", "", "GO:0052547"], ["GO:0072376", "protein activation cascade", "2.79E-13", "9", "No specific", "", "", "GO:0052547"], ["GO:0016485", "protein processing", "1.58E-03", "5", "Positive", "Yes", "", "NA"], ["GO:0030193", "regulation of blood coagulation", "6.70E-08", "7", "No specific", "Yes", "", "NA"], ["GO:0010810", "regulation of cell-substrate adhesion", "9.15E-03", "3", "Negative", "Yes", "", "NA"], ["GO:0051336", "regulation of hydrolase activity", "1.52E-10", "20", "Negative", "", "", "GO:0052547"], ["GO:0052547", "regulation of peptidase activity", "1.62E-17", "18", "Negative", "", "Yes", "GO:0052547"], ["GO:0051592", "response to calcium ion", "4.15E-03", "3", "Positive", "", "", "GO:1902042"], ["GO:0042060", "wound healing", "7.79E-07", "10", "Negative", "Yes", "", "NA"]], "row_count": 26, "column_count": 8, "numeric_cells": 91, "header_rows": 1, "locator": "section[3]/table-wrap[3]#t0015"}}, {"id": "asset:table:pmid:30666314:6", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:366a827b0bee3f1202f60bd97113c832b90c07c2cde56b68358a6d97aff71d8f", "bytes": 1600, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[3]/table-wrap[4]#t0020", "version": null, "note": "GO terms over-represented in chicken challenged with Escherichia coli lipopolysaccharide endotoxin during time.", "structure": {"pmcid": "PMC6205363", "section_index": 3, "section_title": "Data", "row_count": 15, "column_count": 7}, "table": {"label": "Table 4", "caption": "GO terms over-represented in chicken challenged with Escherichia coli lipopolysaccharide endotoxin during time.", "rows": [["GOID", "GOTerm", "Term p-value", "Genes", "Redundant", "Leader", "Group"], ["GO:0006953", "acute-phase response", "7.12E-06", "3", "", "", "GO:0072376"], ["GO:0010951", "negative regulation of endopeptidase activity", "3.40E-05", "4", "", "", "GO:0072376"], ["GO:0072376", "protein activation cascade", "6.11E-07", "4", "", "Yes", "GO:0072376"], ["GO:0034116", "positive regulation of heterotypic cell-cell adhesion", "4.60E-07", "3", "", "Yes", "GO:0034116"], ["GO:0051592", "response to calcium ion", "5.96E-05", "3", "", "", "GO:0072376"], ["GO:0070527", "platelet aggregation", "5.32E-05", "3", "Yes", "", "GO:0072376"], ["GO:0045921", "positive regulation of exocytosis", "5.32E-05", "3", "Yes", "", "GO:0072376"], ["GO:0042730", "fibrinolysis", "3.15E-06", "3", "", "", "GO:0072376"], ["GO:0045907", "positive regulation of vasoconstriction", "7.12E-06", "3", "", "", "GO:0072376"], ["GO:0050714", "positive regulation of protein secretion", "1.72E-04", "3", "Yes", "", "GO:0072376"], ["GO:0090277", "positive regulation of peptide hormone secretion", "4.96E-05", "3", "", "", "GO:0072376"], ["GO:0031639", "plasminogen activation", "3.15E-06", "3", "", "", "GO:0072376"], ["GO:1902042", "negative regulation of extrinsic apoptotic signaling pathway via death domain receptors", "3.99E-06", "3", "", "", "GO:0072376"], ["GO:2000352", "negative regulation of endothelial cell apoptotic process", "4.80E-06", "3", "", "", "GO:0072376"]], "row_count": 15, "column_count": 7, "numeric_cells": 56, "header_rows": 1, "locator": "section[3]/table-wrap[4]#t0020"}}, {"id": "asset:table:pmid:30666314:7", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:071c2db3fd4254bb8ea018386a87357dc7a23fb9f58ebfc7cafd79e7af374509", "bytes": 495, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[3]/table-wrap[5]#t0025", "version": null, "note": "P-values of group and time effects on alpha-1-acid glycoprotein (AGP), serum amyloid A (SAA), and ovotransferrin (OVT) proteins quantified by ELISA.", "structure": {"pmcid": "PMC6205363", "section_index": 3, "section_title": "Data", "row_count": 4, "column_count": 5}, "table": {"label": "Table 5", "caption": "P-values of group and time effects on alpha-1-acid glycoprotein (AGP), serum amyloid A (SAA), and ovotransferrin (OVT) proteins quantified by ELISA.", "rows": [["Protein", "Group", "Group x time", "Time - LPS group", "Time – saline group"], ["AGP", "<0.001", "<0.001", "<0.001", "NS"], ["SAA", "<0.001", "<0.001", "<0.001", "NS"], ["OVT", "<0.001", "<0.001", "<0.001", "NS"]], "row_count": 4, "column_count": 5, "numeric_cells": 9, "header_rows": 1, "locator": "section[3]/table-wrap[5]#t0025"}}, {"id": "asset:table:pmid:30666314:8", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:68d12d24846f6c5d644b9860315e9c4fd4513c32c66b69b157f4e8e6c6668444", "bytes": 1267, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[3]/table-wrap[6]#t0030", "version": null, "note": "Time effect for alpha-1-acid glycoprotein (AGP), serum amyloid A (SAA), and ovotransferrin (OVT) proteins quantified by ELISA. A. Effect of group (LPS versus saline) for each time point, saline used as reference to compare. B. Effect of time on proteins fold change compared with 0 h (reference level).", "structure": {"pmcid": "PMC6205363", "section_index": 3, "section_title": "Data", "row_count": 17, "column_count": 7}, "table": {"label": "Table 6", "caption": "Time effect for alpha-1-acid glycoprotein (AGP), serum amyloid A (SAA), and ovotransferrin (OVT) proteins quantified by ELISA. A. Effect of group (LPS versus saline) for each time point, saline used as reference to compare. B. Effect of time on proteins fold change compared with 0 h (reference level).", "rows": [["A. Group effect (LPS versus saline) for each time point"], ["", "", "0 h", "12 h", "24 h", "48 h", "72 h"], ["AGP", "Fold change", "−0.04", "1.29", "1.68", "1.18", "0.96"], ["P value", "NS", "<0.01", "<0.01", "<0.05", "NS"], ["SAA", "Fold change", "0.73", "5.21", "1.90", "1.71", "0.01"], ["P value", "NS", "<0.01", "<0.01", "<0.05", "NS"], ["OVT", "Fold change", "−0.06", "0.78", "1.05", "0.90", "0.62"], ["P value", "NS", "<0.01", "<0.01", "<0.01", "<0.1"], [""], ["B. 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The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["PXD009399"], "resolved_accessions": ["PXD009399"], "statements": ["The mass spectrometry proteomics raw data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD009399MS (http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD009399). All other data are available within this article."], "basis": "The paper names PXD009399 in ProteomeXchange Consortium via the PRIDE partner repository and the accession resolves in the repository. 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