Accuracy and Reproducibility in Quantification of Plasma Protein Concentrations by Mass Spectrometry without the Use of Isotopic Standards.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:26474480", "kind": "science-record", "revision": 6, "content_hash": "sha256:af86971bc5b8b72618fd8aab3613c046c3496410d48c59e867112c0a11bf59a9", "created_at": "2026-11-01T15:40:11Z", "updated_at": "2026-11-01T21:20:08Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Accuracy and Reproducibility in Quantification of Plasma Protein Concentrations by Mass Spectrometry without the Use of Isotopic Standards.", "doi": "10.1371/journal.pone.0140097", "pmid": "26474480", "authors": ["Gertjan Kramer", "Yvonne Woolerton", "Jan P van Straalen", "Johannes P C Vissers", "Nick Dekker", "James I Langridge", "Robert J Beynon", "Dave Speijer", "Auguste Sturk", "Johannes M F G Aerts"], "journal": "PloS one", "year": 2015, "abstract": "BACKGROUND: Quantitative proteomic analysis with mass spectrometry holds great promise for simultaneously quantifying proteins in various biosamples, such as human plasma. Thus far, studies addressing the reproducible measurement of endogenous protein concentrations in human plasma have focussed on targeted analyses employing isotopically labelled standards. Non-targeted proteomics, on the other hand, has been less employed to this end, even though it has been instrumental in discovery proteomics, generating large datasets in multiple fields of research.\nRESULTS: Using a non-targeted mass spectrometric assay (LCMSE), we quantified abundant plasma proteins (43 mg/mL-40 ug/mL range) in human blood plasma specimens from 30 healthy volunteers and one blood serum sample (ProteomeXchange: PXD000347). Quantitative results were obtained by label-free mass spectrometry using a single internal standard to estimate protein concentrations. This approach resulted in quantitative results for 59 proteins (cut off ≥11 samples quantified) of which 41 proteins were quantified in all 31 samples and 23 of these with an inter-assay variability of ≤ 20%. Results for 7 apolipoproteins were compared with those obtained using isotope-labelled standards, while 12 proteins were compared to routine immunoassays. Comparison of quantitative data obtained by LCMSE and immunoassays showed good to excellent correlations in relative protein abundance (r = 0.72-0.96) and comparable median concentrations for 8 out of 12 proteins tested. Plasma concentrations of 56 proteins determined by LCMSE were of similar accuracy as those reported by targeted studies and 7 apolipoproteins quantified by isotope-labelled standards, when compared to reference concentrations from literature.\nCONCLUSIONS: This study shows that LCMSE offers good quantification of relative abundance as well as reasonable estimations of concentrations of abundant plasma proteins.", "claims": [{"id": "claim-method", "statement": "Ordinary least square linear regression was used to ascertain whether there was a linear correlation between protein amount loaded and protein amount quantified on column. The mass spectrometry data, and protein and peptide identification data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository with the dataset identifier PXD000347.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26474480", "locator": "sections[9] \"Determination of linearity, LOD/LOQ, digestion efficiency and assay variability\" paragraph 2", "quote": "Ordinary least square linear regression was used to ascertain whether there was a linear correlation between protein amount loaded and protein amount quantified on column."}, {"asset": "source:pmid:26474480", "locator": "sections[24] \"Data Availability\" paragraph 2", "quote": "The mass spectrometry data, and protein and peptide identification data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository with the dataset identifier PXD000347."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The mass spectrometry data, and protein and peptide identification data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository with the dataset identifier PXD000347.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26474480", "locator": "sections[24] \"Data Availability\" paragraph 2", "quote": "The mass spectrometry data, and protein and peptide identification data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository with the dataset identifier PXD000347."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Spearman correlation analysis showed good-to-excellent agreement between LCMSE/HI3 peptide quantification and clinical immunoassays, and the underlying mass-spectrometry data were deposited in ProteomeXchange under identifier PXD000347.", "kind": "quantitative", "target": {"value": 0.72, "unit": "correlation coefficient", "tolerance": null, "source": "Comparison of quantitative data obtained by LCMSE and immunoassays showed good to excellent correlations in relative protein abundance (r = 0.72–0.96) and comparable median concentrations for 8 out of 12 proteins tested."}, "evidence": [{"asset": "source:pmid:26474480", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "Comparison of quantitative data obtained by LCMSE and immunoassays showed good to excellent correlations in relative protein abundance (r = 0.72–0.96) and comparable median concentrations for 8 out of 12 proteins tested."}, {"asset": "source:pmid:26474480", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "Using a non-targeted mass spectrometric assay (LCMSE), we quantified abundant plasma proteins (43 mg/mL—40 ug/mL range) in human blood plasma specimens from 30 healthy volunteers and one blood serum sample (ProteomeXchange: PXD000347)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Spearman correlation analysis showed good-to-excellent agreement between LCMSE/HI3 peptide quantification and clinical immunoassays, and the underlying mass-spectrometry data were deposited in ProteomeXchange under identifier PXD000347.", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:26474480"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:PXD000347"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:PXD000347"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:26474480", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1371/journal.pone.0140097", "sha256": "sha256:3ee69066e6f1ea97b7dd903d0ed13a2836f11a8ff54e1286be5d8216557ae873", "bytes": 65692, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1371/journal.pone.0140097", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC4608811", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PXD000347", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=PXD000347", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD000347", "version": null, "note": "The mass spectrometry data, and protein and peptide identification data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository with the dataset identifier PXD000347.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The mass spectrometry data, and protein and peptide identification data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository with the dataset identifier PXD000347.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "Quantitation of plasma protein concentrations by mass spectrometry without the use of isotopic standards. C4PR_LIV", "resolution_checked_at": "2026-10-31T18:35:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:26474480:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:5eb7fc8f61e384097771afbea5796b5865faec72d0c49177d800ba7d3ab6620f", "bytes": 815, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[4]/table-wrap[1]#pone.0140097.t001", "version": null, "note": "Reference and assay ranges clinical assays.", "structure": {"pmcid": "PMC4608811", "section_index": 4, "section_title": "Clinical Assays, reference range and assay range", "row_count": 13, "column_count": 3}, "table": {"label": "Table 1", "caption": "Reference and assay ranges clinical assays.", "rows": [["Assay", "Reference range (x106 ng/mL)", "Assay range 1 (x106 ng/mL)"], ["Albumin", "35–50", "2–60"], ["Immunoglobulin Gamma", "7.0–16.0", "3.0–50.0"], ["Serotransferrin", "2.0–3.6", "0.10–5.2"], ["Fibrinogen", "1.5–4.0", "0.3–10.0"], ["Complement C3", "0.9–1.8", "0.03–3.32"], ["Apolipoprotein A-I", "1.0–2.1", "0.03–3.32"], ["Haptoglobin", "0.3–2.0", "0.1–5.7"], ["Apolipoprotein B-100", "0.55–1.2", "0.03–2.76"], ["Immunoglobulin Alpha", "0.7–4.0", "0.5–8.0"], ["Complement C4", "0.1–0.4", "0.01–0.8"], ["Ceruloplasmin", "0.20–0.55", "0.07–2.20"], ["Immunoglobulin Mu", "0.40–2.3", "0.25–6.50"]], "row_count": 13, "column_count": 3, "numeric_cells": 27, "header_rows": 1, "locator": "section[4]/table-wrap[1]#pone.0140097.t001"}}, {"id": "asset:table:pmid:26474480:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:3dcf57c09887bd03d9d4039fcbc00e5d68671b69f03c90a22180a350cb70c922", "bytes": 5723, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[9]/table-wrap[1]#pone.0140097.t002", "version": null, "note": "Hi3 peptide quantitative analysis of abundant plasma proteins.(50:1 substrate:enzyme, 20 hours digestion, 0.21 ug on column injection).", "structure": {"pmcid": "PMC4608811", "section_index": 9, "section_title": "Determination of linearity, LOD/LOQ, digestion efficiency and assay variability", "row_count": 61, "column_count": 11}, "table": {"label": "Table 2", "caption": "Hi3 peptide quantitative analysis of abundant plasma proteins.(50:1 substrate:enzyme, 20 hours digestion, 0.21 ug on column injection).", "rows": [["No", "Protein name", "median (ng/mL)", "IRV", "IAV", "AV", "LIN", "ST", "LOQ", "n", "FN"], ["1", "Albumin", "7.4 x107", "12", "15", "11", "0.992", "0.955", "6.0 x103", "31", "1"], ["2", "Ig gamma", "4.8 x106", "30", "17", "5", "0.985", "0.998", "8.5 x104", "31", "2"], ["3", "Serotransferrin", "2.7 x106", "19", "19", "9", "0.991", "0.976", "2.6 x105", "31", "3"], ["4", "Fibrinogen", "2.6 x106", "14", "15", "9", "0.995", "0.991", "7.0 x104", "30", "4"], ["5", "Complement C3", "2.3 x106", "17", "16", "7", "0.987", "0.974", "5.6 x104", "31", "5"], ["6", "Alpha-2-macroglobulin", "1.8 x106", "16", "11", "4", "0.990", "0.993", "5.2 x104", "31", "6"], ["7", "Apolipoprotein A-I", "1.7 x106", "29", "14", "8", "0.991", "0.976", "2.2 x104", "31", "7"], ["8", "Alpha-1-antitrypsin", "1.6 x106", "14", "16", "15", "0.985", "0.964", "2.7 x104", "31", "8"], ["9", "Haptoglobin", "1.3 x106", "26", "20", "9", "0.993", "0.991", "3.2 x104", "31", "9"], ["10", "Ig kappa chain C region", "1.0 x106", "25", "14", "8", "0.989", "0.985", "1.7 x104", "31", "10"], ["11", "Apolipoprotein B-100", "9.7 x105", "14", "15", "9", "0.966", "0.999", "2.5 x105", "31", "11"], ["12", "Hemopexin", "9.1 x105", "12", "12", "4", "0.999", "0.960", "2.1 x104", "31", "12"], ["13", "Ig alpha", "7.3 x105", "18", "17", "8", "0.998", "0.982", "2.3 x104", "31", "13"], ["14", "Complement C4", "6.8 x105", "16", "16", "14", "0.979", "-", "1.3 x105", "31", "14"], ["15", "Fibronectin", "5.0 x105", "-", "-", "32", "-", "-", "-", "22", "15"], ["16", "Ig lambda chain C region", "4.0 x105", "22", "17", "7", "0.989", "0.976", "1.5 x104", "31", "16"], ["17", "Ceruloplasmin", "3.5 x105", "22", "16", "8", "0.990", "0.992", "1.8 x104", "31", "17"], ["18", "Inter-alpha-trypsin inhibitor hc H2", "3.5 x105", "14", "18", "14", "0.991", "0.965", "2.4 x104", "31", "18"], ["19", "Complement factor H", "2.7 x105", "20", "20", "5", "0.991", "0.990", "3.3 x104", "31", "19"], ["20", "Vitamin D-binding protein", "2.7 x105", "15", "15", "9", "0.994", "0.993", "3.3 x104", "31", "20"], ["21", "Kininogen-1", "2.6 x105", "17", "14", "10", "0.989", "0.963", "3.6 x104", "31", "21"], ["22", "Alpha-2-HS-glycoprotein", "2.4 x105", "16", "13", "12", "0.990", "0.961", "4.0 x103", "31", "22"], ["23", "Plasminogen", "2.2 x105", "22", "20", "11", "0.991", "0.983", "4.7 x104", "31", "23"], ["24", "Ig mu chain C region", "2.2 x105", "26", "14", "17", "0.993", "0.997", "1.4 x104", "31", "24"], ["25", "Apolipoprotein A-II", "2.0 x105", "27", "17", "6", "0.995", "0.988", "2.4 x104", "31", "25"], ["26", "Alpha-1-antichymotrypsin", "1.8 x105", "16", "6", "6", "0.989", "0.961", "6.0 x103", "31", "26"], ["27", "Inter-alpha-trypsin inhibitor hc H1", "1.8 x105", "16", "-", "18", "0.993", "-", "4.4 x104", "31", "27"], ["28", "Alpha-1-acid glycoprotein 1", "1.7 x105", "41", "16", "10", "0.990", "0.971", "6.0 x103", "31", "28"], ["29", "Beta-2-glycoprotein 1", "1.7 x105", "11", "31", "7", "0.993", "0.966", "7.2 x104", "31", "29"], ["30", "Inter-alpha-trypsin inhibitor hc H4", "1.7 x105", "43", "10", "7", "0.993", "0.995", "2.0 x104", "31", "30"], ["31", "Complement factor B", "1.5 x105", "25", "52", "11", "0.995", "0.974", "2.5 x104", "31", "31"], ["32", "Clusterin", "1.5 x105", "10", "17", "10", "0.990", "0.958", "1.7 x104", "31", "32"], ["33", "Alpha-1B-glycoprotein", "1.4 x105", "18", "12", "9", "0.989", "0.955", "1.0 x104", "31", "33"], ["34", "Prothrombin", "1.4 x105", "16", "23", "51", "0.993", "0.974", "1.7 x104", "31", "34"], ["35", "Antithrombin-III", "1.4 x105", "20", "19", "7", "0.984", "0.962", "5.0 x103", "31", "35"], ["36", "Plasma protease C1 inhibitor", "1.3 x105", "19", "18", "10", "0.964", "0.966", "1.1 x104", "31", "36"], ["37", "Vitronectin", "1.1 x105", "13", "13", "10", "0.995", "0.982", "1.4 x104", "28", "37"], ["38", "Apolipoprotein A-IV", "1.0 x105", "18", "16", "9", "0.994", "0.972", "9.0 x103", "31", "38"], ["39", "C4b-binding protein alpha chain", "1.0 x105", "18", "13", "35", "0.996", "0.997", "1.5 x104", "31", "39"], ["40", "Histidine-rich glycoprotein", "9.0 x104", "21", "13", "10", "0.976", "0.958", "8.0 x103", "31", "40"], ["No", "Protein name", "median (ng/mL)", "IRV", "IAV", "AV", "LIN", "ST", "LOQ", "n", "FN"], ["41", "Gelsolin", "7.0 x104", "23", "36", "11", "0.990", "-", "3.5 x104", "22", "41"], ["42", "Heparin cofactor 2", "6.6 x104", "17", "-", "100", "0.991", "-", "1.1 x104", "11", "42"], ["43", "Afamin", "5.7 x104", "16", "12", "15", "0.998", "0.954", "1.0 x105", "18", "43"], ["44", "Angiotensinogen", "5.7 x104", "19", "16", "5", "0.989", "0.992", "1.1 x104", "30", "44"], ["45", "Paraoxonase/arylesterase 1", "5.1 x104", "22", "-", "22", "0.982", "0.999", "7.0 x103", "23", "45"], ["46", "Alpha-1-acid glycoprotein 2", "5.0 x104", "44", "15", "13", "0.999", "0.958", "4.0 x103", "31", "46"], ["47", "Hemoglobin subunit alpha", "4.1 x104", "40", "-", "7", "0.991", "-", "3.0 x103", "31", "47"], ["48", "Apolipoprotein C-III", "3.9 x104", "32", "27", "20", "-", "0.978", "1.4 x104", "31", "48"], ["49", "Protein AMBP", "3.9 x104", "26", "10", "16", "0.825", "0.949", "7.0 x103", "22", "49"], ["50", "Hemoglobin subunit beta", "3.8 x104", "17", "42", "8", "0.992", "0.983", "4.0 x103", "31", "50"], ["51", "Pregnancy zone protein", "3.6 x104", "64", "64", "75", "0.959", "0.998", "7.0 x103", "15", "-"], ["52", "Zinc alpha 2 glycoprotein", "3.3 x104", "24", "12", "212", "0.772", "0.971", "4.0 x103", "20", "51"], ["53", "Apolipoprotein E", "3.1 x104", "19", "6", "11", "0.996", "0.964", "1.7 x104", "27", "52"], ["54", "CD5 antigen like protein", "2.5 x104", "8", "7", "15", "-", "0.997", "1.3 x104", "19", "-"], ["55", "Haptoglobin-related protein", "2.3 x104", "24", "24", "21", "0.968", "0.995", "3.0 x103", "16", "53"], ["56", "Retinol-binding protein 4", "2.2 x104", "20", "-", "27", "-", "-", "-", "14", "54"], ["57", "Apolipoprotein D", "2.1 x104", "-", "-", "13", "-", "-", "-", "20", "55"], ["58", "Apolipoprotein C-I", "1.6 x104", "-", "-", "11", "-", "-", "-", "26", "56"], ["59", "Apolipoprotein C-II", "1.6 x104", "-", "23", "7", "-", "0.922", "-", "19", "57"]], "row_count": 61, "column_count": 11, "numeric_cells": 569, "header_rows": 0, "locator": "section[9]/table-wrap[1]#pone.0140097.t002"}}, {"id": "asset:table:pmid:26474480:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:ecce183fc31e1f304cb5ada09210ca2cab76f08a1988b10d9f738cf8a1a8c33b", "bytes": 847, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[18]/table-wrap[1]#pone.0140097.t003", "version": null, "note": "Intra-assay variation comparison of Hi3 peptide quantitation to targeted proteomics studies of plasma proteins.", "structure": {"pmcid": "PMC4608811", "section_index": 18, "section_title": "HI3 peptide quantitation: reliability", "row_count": 7, "column_count": 4}, "table": {"label": "Table 3", "caption": "Intra-assay variation comparison of Hi3 peptide quantitation to targeted proteomics studies of plasma proteins.", "rows": [["Source of Data", "Intra-assay CV", "CV≤ 20%", "CV≤ 30%"], ["HI3 peptide quantitation data from this study.", "16% (6–64%)", "82%", "90%"], ["Targeted Proteomics study [12] using isotopic labels.", "8% (7–12%)", "100%", "100%"], ["Targeted Proteomics study [16] using isotopic labels.", "6% (1–18%)", "100%", "100%"], ["Targeted Proteomics study [15] using isotopic labels.", "5% (1–20%)", "100%", "100%"], ["Targeted Proteomics study [13] using isotopic labels.", "9% (5–60%)", "93%", "98%"], ["Targeted Proteomics study [14] without isotopic labels.", "12% (5–40%)", "76%", "88%"]], "row_count": 7, "column_count": 4, "numeric_cells": 25, "header_rows": 1, "locator": "section[18]/table-wrap[1]#pone.0140097.t003"}}, {"id": "asset:table:pmid:26474480:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:300d6ddc503fa17f900bdc8e8fd30cdc8674f7506fa67853383868a5b725da53", "bytes": 1305, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[19]/table-wrap[1]#pone.0140097.t004", "version": null, "note": "Comparison of quantification of abundant plasma proteins by HI3 peptide quantitation and clinical immunoassays.", "structure": {"pmcid": "PMC4608811", "section_index": 19, "section_title": "Comparing HI3 peptide with standard clinical immunoassay quantitation", "row_count": 14, "column_count": 9}, "table": {"label": "Table 4", "caption": "Comparison of quantification of abundant plasma proteins by HI3 peptide quantitation and clinical immunoassays.", "rows": [["Protein", "HI3 peptide quantitation", "Immunoassay", "r"], ["median (ng/mL)", "intra-assay CV1(%)", "inter-assay CV2(%)", "n1", "median (ng/mL)", "inter-assay CV3(%)", "n2"], ["Albumin", "7.4 x107", "15", "12", "31", "4.7 x107", "2", "31", "0.72"], ["Immunoglobulin γ", "4.8 x106", "17", "30", "31", "9.6 x106", "2", "31", "0.86"], ["Transferrin", "2.7 x106", "19", "19", "31", "2.7 x106", "2", "31", "0.75"], ["Fibrinogen", "2.6 x106", "15", "14", "30", "1.6 x106", "3", "30", "0.81*"], ["Complement C3", "2.3 x106", "16", "17", "31", "1.0 x106", "2", "31", "0.86"], ["Apolipoprotein A-I", "1.7 x106", "14", "29", "31", "1.5 x106", "4", "31", "0.86"], ["Haptoglobin", "1.3 x106", "20", "26", "31", "1.2 x106", "2", "31", "0.92"], ["Apolipoprotein B-100", "1.0 x106", "15", "14", "31", "0.9 x106", "3", "31", "0.85"], ["Immunoglobulin α", "0.7 x106", "17", "18", "31", "1.8 x106", "1", "31", "0.93"], ["Complement C4", "0.7 x106", "16", "16", "29", "0.2 x106", "3", "31", "0.76"], ["Ceruloplasmin", "0.4 x106", "16", "22", "31", "0.3 x106", "5", "31", "0.89"], ["Immunoglobulin μ", "0.2 x106", "14", "26", "31", "1.0 x106", "3", "31", "0.96"]], "row_count": 14, "column_count": 9, "numeric_cells": 97, "header_rows": 2, "locator": "section[19]/table-wrap[1]#pone.0140097.t004"}}], "gaps": ["asset:data:geo:PXD000347 not downloaded", "asset:data:geo:PXD000347 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "regression_modelling", "specific": "ols", "label": "Regression modelling", "dsl_operations": ["ols_fit"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["predictors_and_outcome"], "evidence": {"score": 1.0, "band": "reordered", "quote": "Ordinary least square linear regression was used to ascertain whether there was a linear correlation between protein amount loaded and protein amount quantified on column. The mass spectrometry data, and protein and peptide identification data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository with the dataset identifier PXD000347."}}], "targets": [{"id": "target-published-estimate", "claim_id": "claim-target-result", "operation": "ols_fit", "expected_value": 0.72, "unit": "correlation coefficient", "tolerance": null, "state": "complete", "note": "The published estimate as the reader quoted it from the paper. 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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": ["PXD000347"], "resolved_accessions": ["PXD000347"], "statements": ["The mass spectrometry data, and protein and peptide identification data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository with the dataset identifier PXD000347."], "basis": "The paper names PXD000347 in ProteomeXchange Consortium via PRIDE and the accession resolves in the repository. 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The mass spectrometry data, and protein and peptide identification data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository with the dataset identifier PXD000347."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}