{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:32782267", "kind": "science-record", "revision": 6, "content_hash": "sha256:52936aee7f372f685c4e43e72e116f4399c7c6d5f55f8f47307473128481156a", "created_at": "2026-11-01T15:41:07Z", "updated_at": "2026-11-01T21:23:36Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "A comprehensive CHO SWATH-MS spectral library for robust quantitative profiling of 10,000 proteins.", "doi": "10.1038/s41597-020-00594-z", "pmid": "32782267", "authors": ["Kae Hwan Sim", "Lillian Chia-Yi Liu", "Hwee Tong Tan", "Kelly Tan", "Daniel Ng", "Wei Zhang", "Yuansheng Yang", "Stephen Tate", "Xuezhi Bi"], "journal": "Scientific data", "year": 2020, "abstract": "Sequential window acquisition of all theoretical fragment-ion spectra (SWATH) is a data-independent acquisition (DIA) strategy that requires a specific spectral library to generate unbiased and consistent quantitative data matrices of all peptides. SWATH-MS is a promising approach for in-depth proteomic profiling of Chinese hamster Ovary (CHO) cell lines, improving mechanistic understanding of process optimization, and real-time monitoring of process parameters in biologics R&D and manufacturing. However, no spectral library for CHO cells is publicly available. Here we present a comprehensive CHO global spectral library to measure the abundance of more than 10,000 proteins consisting of 199,102 identified peptides from a CHO-K1 cell proteome. The robustness, accuracy and consistency of the spectral library were validated for high confidence in protein identification and reproducible quantification in different CHO-derived cell lines, instrumental setups and downstream processing samples. The availability of a comprehensive SWATH CHO global spectral library will facilitate detailed characterization of upstream and downstream processes, as well as quality by design (QbD) in biomanufacturing. The data have been deposited to ProteomeXchange (PXD016047).", "claims": [{"id": "claim-method", "statement": "A Pearson correlation matrix was constructed using the intensities of all identified proteins.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32782267", "locator": "sections[18] \"Robustness of protein identification and quantification in CHO HCCF and HCPs in DSP mAb samples\" paragraph 3", "quote": "A Pearson correlation matrix was constructed using the intensities of all identified proteins."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The raw DDA data files for library generation, the search result (group files), the CHO spectral library, and the SWATH-MS acquisition data applied in the current study have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org)34via the PRIDE partner repository35,36 with the data set identifier PXD01604728.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32782267", "locator": "sections[12] \"Data Records\" paragraph 2", "quote": "The raw DDA data files for library generation, the search result (group files), the CHO spectral library, and the SWATH-MS acquisition data applied in the current study have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org)34via the PRIDE partner repository35,36 with the data set identifier PXD01604728."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "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:32782267"], "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. 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acquisition data applied in the current study have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org)34via the PRIDE partner repository35,36 with the data set identifier PXD01604728.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The raw DDA data files for library generation, the search result (group files), the CHO spectral library, and the SWATH-MS acquisition data applied in the current study have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org)34via the PRIDE partner repository35,36 with the data set identifier PXD01604728.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "A comprehensive CHO SWATH-MS spectral library for accurate quantitative profiling of 10k proteins", "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:32782267:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:b230415a7a7224efcc9989ff9066d11fb1833ebf90332e3a996265e36f2cca7c", "bytes": 1097, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[15]/table-wrap[1]#Tab1", "version": null, "note": "Comparison of the proteome coverage between CHO global spectral library, 1D library and the latest proteomic studies on CHO-DG44 and CHO-S cells.", "structure": {"pmcid": "PMC7419519", "section_index": 15, "section_title": "Coverage of the CHO global spectral library", "row_count": 8, "column_count": 7}, "table": {"label": "Table 1", "caption": "Comparison of the proteome coverage between CHO global spectral library, 1D library and the latest proteomic studies on CHO-DG44 and CHO-S cells.", "rows": [["", "DDA files #", "Protein #a", "Protein #a (≥2 peptides)", "Peptide #a,b", "Confidence cutoff", "Data processing pipeline"], ["CHO global spectral library", "63", "10,974", "9,549", "199,102b", "99% peptides confidence& 1% protein FDR", "ProteinPilot& OneOmics"], ["CHO-K1 1D library", "3", "3,134", "2,810", "20,249b", "99% peptides confidence & 1% protein FDR", "ProteinPilot& OneOmics"], ["CHO-DG44 exponential13", "48", "N.A", "5,950", "58,128", "1% FDR", "Proteome Discoverer"], ["CHO-DG44 stationary13", "48", "N.A", "5,593", "50,194", "1% FDR", "Proteome Discoverer"], ["CHO-S exponential13", "48", "N.A", "6,089", "53,958", "1% FDR", "Proteome Discoverer"], ["CHO-S stationary13", "48", "N.A", "5,538", "48,205", "1% FDR", "Proteome Discoverer"], ["Combined CHO-DG44 and CHO-S13", "192", "N.A", "9,359", "N.A", "1% FDR", "Proteome Discoverer"]], "row_count": 8, "column_count": 7, "numeric_cells": 36, "header_rows": 1, 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combined-search spectral library"], ["Total identified proteins", "6,445", "4,310"], ["20% CV cutoff", "4,717", "2,537"], ["10% CV cutoff", "3,183", "1,414"], ["Median CV", "10.16%", "15.47%"], ["Total identified peptides", "23,971", "14,061"], ["20% CV cutoff", "16,919", "8,252"], ["10% CV cutoff", "10,325", "4,585"], ["Median CV", "11.73%", "15.42%"]], "row_count": 9, "column_count": 3, "numeric_cells": 20, "header_rows": 1, "locator": "section[16]/table-wrap[1]#Tab2"}}, {"id": "asset:table:pmid:32782267:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:f0c6764b9b50fb1132278dacd0a93eb3494002162ecca6766f8ecaa7c217f9a7", "bytes": 1013, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[17]/table-wrap[1]#Tab3", "version": null, "note": "Details of three LC-MS instrumental setups for the SWATH-MS acquisition of CHO-K1 WCL samples.", "structure": 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["LC gradient", "100 min", "95 min", "90 min"], ["Sample amount", "1 µg", "5 µg", "20 µg"]], "row_count": 9, "column_count": 4, "numeric_cells": 20, "header_rows": 1, "locator": "section[17]/table-wrap[1]#Tab3"}}, {"id": "asset:table:pmid:32782267:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:9df4a5f8285af3c95bcd1a0f3d951618980da6f5bd2085667acf89a679141e4d", "bytes": 27194, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[18]/table-wrap[1]#Tab4", "version": null, "note": "The protein areas of the 152 HCPs quantified in the DSP mAb samples.", "structure": {"pmcid": "PMC7419519", "section_index": 18, "section_title": "Robustness of protein identification and quantification in CHO HCCF and HCPs in DSP mAb samples", "row_count": 153, "column_count": 12}, "table": {"label": "Online-only Table 1", "caption": "The protein areas of the 152 HCPs quantified in the DSP mAb samples.", "rows": [["Protein Id", "Protein Description", "MW[Cal.]", "pI", "OM_MEAN", "OM_STDEV", "PrA_MEAN", "PrA_STDEV", "CEX_MEAN", "CEX_STDEV", "AEX_MEAN", "AEX_STDEV"], ["NP_001230908.1", "Tubulin alpha-1b chain", "49872.57", "4.94", "3.32E + 05", "3.27E + 03", "7.22E + 03", "6.02E + 03", "4.89E + 03", "2.63E + 03", "5.02E + 03", "7.77E + 02"], ["NP_001230912.1", "Aminoacyl trna synthase complex-interacting multifunctional protein 2", "35386.3", "7.69", "4.49E + 04", "2.56E + 03", "9.17E + 02", "2.03E + 02", "1.21E + 02", "1.51E + 02", "8.43E + 01", "1.03E + 02"], ["NP_001230968.1", "Elongation factor 2", "94879.53", "6.41", "2.76E + 05", "1.25E + 03", "7.25E + 03", "3.12E + 03", "6.66E + 03", "2.89E + 02", "3.30E + 04", "3.47E + 04"], ["NP_001231030.1", "Tubulin beta-5 chain", "49098.5", "4.78", "1.74E + 05", "6.85E + 03", "1.53E + 04", "4.50E + 03", "8.98E + 03", "1.86E + 03", "3.73E + 03", "5.01E + 02"], ["NP_001231196.1", "Aminoacyl trna synthase complex-interacting multifunctional protein 1", "39699.01", "9.37", "7.32E + 04", "2.43E + 03", "4.62E + 03", "1.54E + 03", "4.15E + 03", "3.58E + 02", "1.78E + 04", "3.30E + 03"], ["NP_001231202.1", "Golgi apparatus protein 1 precursor", "128275.35", "6.34", "1.09E + 05", "1.25E + 03", "4.90E + 03", "2.88E + 03", "9.20E + 03", "3.19E + 03", "1.82E + 03", "7.37E + 02"], ["NP_001231331.1", "Elongation factor 1-alpha 1", "51088.98", "9.1", "9.01E + 05", "2.23E + 04", "4.14E + 04", "4.97E + 03", "3.96E + 03", "1.43E + 03", "4.94E + 03", "1.11E + 03"], ["NP_001231783.1", "Glyceraldehyde-3-phosphate dehydrogenase", "36823.87", "8.49", "3.71E + 06", "5.56E + 04", "3.12E + 03", "9.96E + 02", "3.64E + 03", "1.26E + 03", "4.50E + 03", "1.84E + 03"], ["NP_001233603.1", "Beta-2-microglobulin precursor", "13159.28", "6.89", "3.73E + 05", "7.79E + 03", "2.49E + 03", "3.94E + 02", "2.36E + 03", "7.15E + 02", "2.67E + 03", "4.81E + 02"], ["NP_001233622.2", "Protein disulfide-isomerase precursor", "56286.34", "4.77", "1.52E + 06", "0.00E + 00", "4.46E + 03", "1.69E + 03", "3.17E + 03", "1.35E + 03", "2.55E + 03", "4.42E + 02"], ["NP_001233630.1", "Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit beta-1", "37597.95", "5.61", "2.01E + 04", "2.05E + 02", "1.16E + 03", "1.36E + 02", "2.89E + 03", "2.74E + 03", "9.19E + 02", "3.78E + 02"], ["NP_001233634.1", "Trifunctional purine biosynthetic protein adenosine-3", "111688.02", "6.45", "1.21E + 05", "1.63E + 03", "3.00E + 03", "9.37E + 02", "6.61E + 03", "2.50E + 03", "4.98E + 03", "3.23E + 03"], ["NP_001233654.1", "Phosphoglycerate kinase 1", "46112.78", "8.02", "4.09E + 05", "9.42E + 03", "7.58E + 03", "3.47E + 03", "5.90E + 03", "3.62E + 03", "1.21E + 04", "8.00E + 03"], ["NP_001233658.1", "Heat shock cognate 71 kda protein", "71436.1", "5.24", "9.90E + 05", "1.70E + 03", "7.60E + 03", "8.28E + 03", "3.71E + 03", "1.67E + 03", "2.60E + 03", "3.55E + 02"], ["NP_001233662.1", "T-complex protein 1 subunit alpha", "61483.7", "5.71", "4.73E + 05", "4.55E + 03", "1.17E + 04", "2.24E + 03", "2.75E + 03", "1.15E + 03", "4.32E + 03", "2.34E + 03"], ["NP_001233668.1", "Endoplasmic reticulum chaperone bip precursor", "72320.76", "5.07", "6.88E + 06", "1.36E + 05", "8.76E + 03", "5.77E + 03", "2.19E + 04", "2.21E + 04", "8.08E + 03", "3.65E + 03"], ["NP_001233670.1", "Hypoxia up-regulated protein 1 precursor", "110471.62", "5.09", "3.43E + 05", "7.59E + 03", "5.95E + 03", "1.69E + 03", "6.10E + 03", "1.63E + 03", "1.03E + 04", "2.59E + 03"], ["NP_001233673.1", "Glutathione s-transferase p 1", "23222.26", "7.64", "1.62E + 06", "4.19E + 04", "9.83E + 03", "2.55E + 03", "2.60E + 03", "8.25E + 02", "6.29E + 03", "9.27E + 02"], ["NP_001233694.1", "Peroxiredoxin-1", "22005.86", "8.22", "8.50E + 06", "8.64E + 04", "3.60E + 04", "1.86E + 04", "9.51E + 03", "2.96E + 03", "6.97E + 03", "4.04E + 03"], ["NP_001233703.1", "Protein disulfide-isomerase a3 precursor", "55844.01", "5.98", "7.40E + 05", "1.00E + 04", "1.79E + 03", "7.72E + 01", "3.03E + 03", "2.08E + 03", "2.21E + 03", "5.15E + 02"], ["NP_001233750.1", "Heat shock protein hsp 90-alpha", "81056.75", "4.96", "8.92E + 05", "2.16E + 03", "6.99E + 03", "2.39E + 03", "8.07E + 03", "2.29E + 03", "3.73E + 03", "1.68E + 03"], ["XP_027243210.1", "Heat shock protein hsp 90-beta isoform x11", "80061.51", "4.97", "2.74E + 06", "1.63E + 04", "2.50E + 04", "1.98E + 04", "1.10E + 04", "7.37E + 03", "7.83E + 03", "7.34E + 03"], ["XP_027243827.1", "T-complex protein 1 subunit delta", "59603.81", "8.24", "4.07E + 05", "3.40E + 03", "8.46E + 03", "2.71E + 03", "8.78E + 03", "3.65E + 03", "2.24E + 03", "7.59E + 02"], ["XP_027243857.1", "Malate dehydrogenase, cytoplasmic", "36934.45", "6.17", "3.58E + 05", "9.43E + 03", "3.64E + 03", "1.53E + 03", "2.93E + 03", "4.38E + 02", "2.79E + 03", "9.83E + 02"], ["XP_027243958.1", "Peptidyl-prolyl cis-trans isomerase a isoform x2", "18135.48", "8.44", "5.95E + 05", "9.10E + 03", "1.92E + 03", "7.67E + 02", "3.08E + 03", "1.31E + 03", "6.03E + 03", "3.23E + 03"], ["XP_027244682.1", "Lipoprotein lipase isoform x2", "52415.96", "7.94", "1.39E + 05", "2.87E + 03", "1.30E + 04", "7.08E + 03", "7.10E + 03", "8.53E + 02", "6.92E + 03", "3.47E + 03"], ["XP_027245386.1", "Transketolase", "68892.71", "7.56", "7.23E + 05", "6.94E + 03", "8.12E + 03", "4.97E + 03", "5.61E + 03", "1.13E + 03", "5.71E + 03", "2.30E + 03"], ["XP_027246103.1", "Clusterin", "49430.24", "5.52", "3.08E + 06", "1.64E + 05", "8.56E + 04", "8.95E + 03", "5.42E + 03", "3.52E + 02", "4.63E + 03", "2.33E + 03"], ["XP_027246161.1", "Cathepsin b", "37487.37", "5.73", "1.61E + 06", "2.16E + 04", "7.52E + 03", "7.48E + 03", "9.78E + 03", "2.58E + 03", "3.36E + 03", "1.06E + 03"], ["XP_027246369.1", "Proteasome activator complex subunit 2", "26429.15", "5.56", "1.13E + 05", "2.36E + 03", "4.70E + 03", "1.97E + 02", "4.90E + 03", "3.34E + 02", "3.57E + 03", "2.35E + 03"], ["XP_027246859.1", "N(4)-(beta-n-acetylglucosaminyl)-l-asparaginase", "38261.44", "7.12", "1.23E + 06", "9.43E + 03", "1.15E + 04", "1.37E + 03", "6.19E + 03", "1.30E + 03", "1.29E + 04", "3.62E + 03"], ["XP_027246972.1", "Acid ceramidase isoform x2", "49761.99", "8.82", "1.50E + 06", "8.16E + 03", "1.59E + 04", "5.97E + 03", "8.56E + 03", "6.78E + 03", "6.29E + 03", "4.22E + 02"], ["XP_027247933.1", "Matrix metalloproteinase-19", "58055.66", "7.71", "2.96E + 05", "4.19E + 03", "1.28E + 04", "4.63E + 03", "3.88E + 03", "5.13E + 02", "5.59E + 03", "3.10E + 03"], ["XP_027247964.1", "Proliferation-associated protein 2g4", "43569.39", "6.26", "3.38E + 05", "3.74E + 03", "5.78E + 03", "6.43E + 02", "3.73E + 03", "1.88E + 03", "3.38E + 03", "2.79E + 03"], ["XP_027248157.1", "T-complex protein 1 subunit beta", "59161.48", "6.01", "2.12E + 05", "5.79E + 03", "1.05E + 04", "2.92E + 03", "4.84E + 03", "2.46E + 03", "5.70E + 03", "3.22E + 03"], ["XP_027248343.1", "Endoplasmin", "88686.92", "4.75", "1.27E + 06", "1.25E + 04", "1.99E + 04", "9.46E + 03", "5.93E + 03", "2.39E + 02", "5.95E + 03", "3.77E + 03"], ["XP_027248903.1", "T-complex protein 1 subunit gamma", "60267.3", "6.23", "3.02E + 05", "4.03E + 03", "4.27E + 03", "1.29E + 03", "3.08E + 04", "2.08E + 04", "3.22E + 03", "4.42E + 02"], ["XP_027249017.1", "Thrombospondin-3 isoform x1", "105716.58", "4.4", "2.32E + 04", "1.44E + 03", "3.39E + 03", "1.95E + 03", "7.44E + 03", "1.00E + 03", "3.86E + 03", "4.02E + 03"], ["XP_027249018.1", "Thrombospondin-3 isoform x2", "104721.34", "4.4", "1.79E + 05", "7.72E + 03", "7.11E + 03", "5.20E + 03", "8.59E + 03", "4.08E + 03", "1.81E + 04", "1.98E + 04"], ["XP_027249169.1", "Protein s100-a6 isoform x1", "9841.82", "5.3", "8.07E + 06", "1.67E + 05", "1.60E + 04", "5.65E + 03", "4.65E + 03", "3.21E + 03", "7.52E + 03", "7.43E + 03"], ["XP_027249297.1", "Semaphorin-3e", "85922.37", "7.95", "1.44E + 05", "2.87E + 03", "4.62E + 03", "1.20E + 03", "1.70E + 03", "3.49E + 02", "5.89E + 03", "4.68E + 03"], ["XP_027249460.1", "Extracellular matrix protein 1 isoform x1", "62257.78", "6.36", "1.72E + 04", "5.79E + 02", "1.28E + 03", "1.40E + 02", "2.50E + 03", "2.60E + 03", "6.91E + 02", "2.97E + 02"], ["XP_027249462.1", "Extracellular matrix protein 1 isoform x3", "60267.3", "6.98", "1.34E + 05", "1.89E + 03", "1.83E + 04", "1.84E + 04", "7.95E + 03", "4.12E + 03", "3.93E + 03", "1.67E + 03"], ["XP_027249711.1", "Importin-5 isoform x2", "118212.37", "4.82", "8.57E + 04", "4.24E + 02", "5.88E + 03", "9.94E + 02", "5.75E + 03", "9.18E + 02", "6.82E + 03", "6.38E + 02"], ["XP_027250030.1", "Macrophage migration inhibitory factor", "12716.95", "6.8", "8.91E + 04", "4.48E + 03", "1.40E + 03", "1.11E + 03", "6.31E + 03", "1.85E + 03", "5.03E + 03", "3.27E + 03"], ["XP_027251765.1", "Glyceraldehyde-3-phosphate dehydrogenase", "39367.26", "6.67", "3.67E + 04", "5.91E + 02", "2.07E + 03", "1.31E + 03", "1.19E + 03", "2.51E + 02", "2.12E + 03", "9.94E + 02"], ["XP_027251842.1", "Keratin, type ii cytoskeletal 2 epidermal isoform x2", "71767.85", "6.46", "1.50E + 06", "9.43E + 03", "6.13E + 03", "9.39E + 02", "3.48E + 03", "3.28E + 03", "7.69E + 03", "3.48E + 03"], ["XP_027252444.1", "Keratin, type ii cytoskeletal 1b isoform x2", "65243.5", "8.51", "1.04E + 06", "1.63E + 04", "1.28E + 03", "1.46E + 03", "4.72E + 02", "5.08E + 02", "1.58E + 03", "1.56E + 03"], ["XP_027252959.1", "Fibronectin isoform x3", "264291.46", "5.57", "3.89E + 04", "7.41E + 02", "1.21E + 03", "3.47E + 02", "7.93E + 02", "4.26E + 02", "2.39E + 04", "3.24E + 04"], ["XP_027252960.1", "Fibronectin isoform x4", "264180.88", "5.58", "1.52E + 05", "1.08E + 04", "7.22E + 03", "3.35E + 03", "2.28E + 04", "7.94E + 03", "1.34E + 04", "7.40E + 03"], ["XP_027252964.1", "Fibronectin isoform x8", "254228.48", "5.77", "8.16E + 04", "3.45E + 03", "6.85E + 03", "1.04E + 03", "3.82E + 03", "1.30E + 03", "2.41E + 03", "7.61E + 02"], ["XP_027252965.1", "Fibronectin isoform x9", "251463.92", "5.83", "2.30E + 05", "5.19E + 03", "3.07E + 03", "7.38E + 02", "5.71E + 03", "2.44E + 03", "4.73E + 03", "1.71E + 03"], ["XP_027252966.1", "Fibronectin isoform x10", "251021.59", "5.57", "6.16E + 04", "2.45E + 03", "3.39E + 03", "1.18E + 03", "3.09E + 03", "1.74E + 03", "2.11E + 03", "2.59E + 02"], ["XP_027252967.1", "Fibronectin isoform x11", "250911.01", "5.59", "1.53E + 05", "1.89E + 03", "4.97E + 03", "2.78E + 03", "9.17E + 03", "2.75E + 03", "9.79E + 03", "6.14E + 03"], ["XP_027252968.1", "Fibronectin isoform x12", "240958.61", "5.8", "1.54E + 05", "4.50E + 03", "1.46E + 04", "1.30E + 04", "2.95E + 03", "1.30E + 03", "6.90E + 03", "7.39E + 02"], ["XP_027254100.1", "Alpha-enolase isoform x2", "47992.67", "6", "4.97E + 05", "1.13E + 04", "3.68E + 03", "1.84E + 03", "1.32E + 04", "2.97E + 03", "6.68E + 03", "2.77E + 03"], ["XP_027255561.1", "Basement membrane-specific heparan sulfate proteoglycan core protein isoform x2", "485013.53", "6.12", "7.95E + 05", "1.04E + 04", "3.00E + 03", "2.41E + 02", "2.78E + 03", "3.88E + 02", "2.47E + 03", "1.50E + 02"], ["XP_027255877.1", "T-complex protein 1 subunit epsilon", "59824.97", "5.34", "3.69E + 05", "3.68E + 03", "3.49E + 03", "2.88E + 03", "1.57E + 04", "1.21E + 04", "9.98E + 03", "7.76E + 03"], ["XP_027256703.1", "Peptidyl-prolyl cis-trans isomerase c isoform x2", "23443.43", "7.77", "6.34E + 05", "1.01E + 04", "6.93E + 03", "2.65E + 03", "2.64E + 03", "1.03E + 03", "6.95E + 03", "4.44E + 03"], ["XP_027259082.1", "Transitional endoplasmic reticulum atpase isoform x2", "89129.25", "5.14", "1.47E + 05", "5.44E + 03", "3.57E + 03", "3.16E + 02", "1.49E + 03", "4.15E + 02", "3.68E + 03", "1.89E + 03"], ["XP_027259718.1", "Myosin-9 isoform x2", "216741.11", "5.53", "1.07E + 05", "2.87E + 03", "7.70E + 03", "3.08E + 03", "1.05E + 04", "2.62E + 03", "1.45E + 04", "8.49E + 03"], ["XP_027259782.1", "Eukaryotic translation initiation factor 3 subunit l", "62368.36", "5.93", "8.15E + 04", "3.27E + 03", "1.89E + 03", "4.26E + 02", "3.65E + 03", "3.71E + 03", "1.04E + 03", "4.07E + 02"], ["XP_027260200.1", "Serine protease htra1 isoform x2", "53079.46", "8.07", "3.94E + 05", "3.74E + 03", "8.62E + 03", "2.82E + 03", "5.98E + 03", "1.59E + 03", "1.10E + 04", "1.50E + 03"], ["XP_027260201.1", "Serine protease htra1 isoform x3", "51863.05", "8.07", "1.01E + 06", "1.28E + 04", "1.24E + 04", "9.94E + 03", "7.87E + 03", "1.46E + 03", "6.79E + 03", "3.04E + 03"], ["XP_027260557.1", "Lysosome-associated membrane glycoprotein 1", "44564.63", "6.31", "4.37E + 04", "5.38E + 03", "1.38E + 03", "9.38E + 02", "7.66E + 02", "4.51E + 02", "1.87E + 03", "2.03E + 03"], ["XP_027260936.1", "Inter-alpha-trypsin inhibitor heavy chain h5 isoform x2", "105274.25", "8.44", "2.58E + 05", "4.55E + 03", "8.44E + 03", "3.31E + 03", "1.21E + 04", "1.76E + 03", "1.03E + 04", "5.14E + 03"], ["XP_027261047.1", "Vimentin", "51531.31", "5.06", "6.48E + 05", "8.99E + 03", "6.89E + 03", "1.49E + 03", "6.15E + 03", "1.20E + 03", "1.08E + 04", "1.92E + 03"], ["XP_027263120.1", "Phosphoglycerate mutase 1 isoform x2", "28087.88", "6.67", "4.00E + 05", "1.14E + 04", "3.20E + 03", "5.68E + 02", "2.80E + 03", "1.33E + 03", "3.80E + 03", "2.32E + 03"], ["XP_027263985.1", "Lactadherin isoform x5", "54185.28", "8.13", "7.15E + 04", "1.60E + 03", "3.87E + 04", "2.55E + 04", "8.11E + 03", "4.41E + 03", "1.00E + 04", "2.25E + 03"], ["XP_027263987.1", "Lactadherin isoform x7", "47218.6", "8.15", "7.42E + 04", "3.09E + 03", "4.13E + 04", "2.40E + 04", "2.71E + 04", "8.87E + 03", "7.45E + 03", "2.58E + 03"], ["XP_027264128.1", "Elongation factor 1-gamma", "48324.42", "6.36", "4.77E + 05", "1.67E + 04", "1.37E + 04", "6.62E + 03", "6.75E + 04", "2.97E + 04", "1.07E + 04", "5.08E + 03"], ["XP_027264138.1", "Neutral alpha-glucosidase ab isoform x1", "106822.41", "5.72", "9.50E + 04", "3.31E + 03", "1.14E + 03", "4.22E + 02", "8.78E + 02", "3.61E + 02", "8.97E + 02", "3.95E + 02"], ["XP_027264139.1", "Neutral alpha-glucosidase ab isoform x2", "104389.6", "5.64", "1.13E + 05", "2.05E + 03", "2.83E + 03", "1.63E + 03", "2.97E + 03", "5.28E + 02", "3.32E + 03", "7.89E + 02"], ["XP_027264402.1", "Cofilin-1", "18356.65", "8.22", "1.77E + 05", "2.49E + 03", "1.63E + 04", "2.38E + 03", "7.33E + 03", "3.25E + 03", "7.15E + 03", "1.52E + 03"], ["XP_027264538.1", "Glutathione s-transferase p 2 isoform x2", "24549.25", "9.15", "6.72E + 05", "1.45E + 04", "5.93E + 03", "2.07E + 03", "3.97E + 03", "7.10E + 02", "6.04E + 03", "6.45E + 02"], ["XP_027264700.1", "Cathepsin d", "45117.54", "6.54", "3.14E + 06", "8.52E + 04", "4.20E + 03", "1.77E + 03", "3.69E + 03", "2.46E + 02", "7.13E + 03", "8.45E + 02"], ["XP_027265239.1", "Nidogen-1 isoform x3", "137785.42", "5.07", "2.26E + 05", "2.16E + 03", "8.47E + 03", "4.13E + 03", "8.31E + 03", "1.15E + 03", "1.26E + 04", "9.76E + 03"], ["XP_027265604.1", "Vesicular integral-membrane protein vip36", "39367.26", "6.46", "3.50E + 05", "4.55E + 03", "4.76E + 03", "1.73E + 03", "2.83E + 03", "2.49E + 02", "4.31E + 03", "3.65E + 03"], ["XP_027265952.1", "Nucleobindin-2 isoform x1", "47660.93", "4.97", "7.63E + 04", "2.52E + 03", "1.71E + 03", "6.58E + 02", "4.59E + 03", "3.33E + 03", "2.87E + 03", "6.01E + 02"], ["XP_027265953.1", "Nucleobindin-2 isoform x2", "46444.52", "5.05", "1.04E + 06", "2.76E + 04", "5.90E + 03", "4.83E + 02", "2.61E + 03", "8.63E + 02", "9.13E + 03", "2.25E + 03"], ["XP_027267107.1", "Peptidyl-prolyl cis-trans isomerase b", "23885.76", "9.59", "1.60E + 06", "4.71E + 03", "3.04E + 03", "3.90E + 02", "3.38E + 03", "2.36E + 02", "4.35E + 03", "1.07E + 03"], ["XP_027267400.1", "Glucosidase 2 subunit beta isoform x2", "58055.66", "4.41", "5.89E + 05", "6.68E + 03", "5.13E + 03", "1.24E + 03", "6.16E + 03", "2.30E + 03", "4.47E + 03", "6.21E + 02"], ["XP_027267710.1", "Complement c1q tumor necrosis factor-related protein 5 isoform x3", "26871.47", "5.94", "1.02E + 06", "3.98E + 04", "3.60E + 03", "2.52E + 03", "3.18E + 03", "1.11E + 03", "3.28E + 03", "9.85E + 02"], ["XP_027267915.1", "Neural cell adhesion molecule 1 isoform x4", "123852.06", "4.71", "5.10E + 05", "4.32E + 03", "8.72E + 03", "3.14E + 03", "4.99E + 03", "2.91E + 03", "7.09E + 03", "2.69E + 02"], ["XP_027267916.1", "Neural cell adhesion molecule 1 isoform x5", "93994.87", "4.8", "5.32E + 04", "1.45E + 03", "1.36E + 03", "5.10E + 02", "8.44E + 02", "9.77E + 01", "2.43E + 03", "3.37E + 02"], ["XP_027267917.1", "Neural cell adhesion molecule 1 isoform x6", "93884.29", "4.79", "2.57E + 05", "8.73E + 03", "3.11E + 03", "3.85E + 02", "1.78E + 03", "8.40E + 02", "8.69E + 03", "2.27E + 03"], ["XP_027267919.1", "Neural cell adhesion molecule 1 isoform x8", "93773.71", "4.8", "1.11E + 05", "3.30E + 03", "5.21E + 03", "3.36E + 03", "2.83E + 03", "3.41E + 03", "1.36E + 03", "2.69E + 02"], ["XP_027267920.1", "Neural cell adhesion molecule 1 isoform x9", "80393.26", "4.77", "2.91E + 05", "2.45E + 03", "8.57E + 03", "3.57E + 03", "2.03E + 03", "1.79E + 02", "5.70E + 03", "1.60E + 03"], ["XP_027267921.1", "Neural cell adhesion molecule 1 isoform x10", "80282.68", "4.79", "1.15E + 05", "2.05E + 03", "9.81E + 03", "1.40E + 03", "3.19E + 03", "1.23E + 03", "3.04E + 03", "3.02E + 02"], ["XP_027268152.1", "T-complex protein 1 subunit theta isoform x2", "60599.05", "5.43", "3.22E + 05", "4.71E + 02", "3.87E + 03", "1.01E + 03", "1.34E + 04", "3.84E + 03", "9.09E + 03", "5.29E + 03"], ["XP_027268153.1", "T-complex protein 1 subunit theta isoform x3", "54959.35", "5.19", "2.89E + 05", "4.50E + 03", "4.77E + 03", "2.10E + 03", "1.82E + 03", "2.87E + 01", "1.98E + 03", "8.82E + 02"], ["XP_027269607.1", "Beta-glucuronidase isoform x4", "72431.34", "6.28", "1.78E + 05", "5.72E + 03", "4.30E + 03", "3.84E + 03", "2.62E + 03", "6.07E + 02", "1.72E + 03", "1.38E + 02"], ["XP_027269616.1", "T-complex protein 1 subunit zeta", "58719.15", "6.46", "1.72E + 05", "3.09E + 03", "6.45E + 03", "1.93E + 03", "2.54E + 03", "1.32E + 03", "5.12E + 03", "4.02E + 03"], ["XP_027269644.1", "Gtp-binding nuclear protein ran isoform x2", "23885.76", "7.01", "5.37E + 05", "1.03E + 04", "6.36E + 03", "2.76E + 03", "7.70E + 03", "4.69E + 03", "6.51E + 03", "3.57E + 03"], ["XP_027269956.1", "Phospholipase b-like 2", "64690.59", "5.9", "1.10E + 06", "4.78E + 04", "3.95E + 04", "4.71E + 04", "1.53E + 04", "1.01E + 04", "7.36E + 03", "1.74E + 03"], ["XP_027270355.1", "Transforming protein rhoa", "21342.36", "5.83", "1.56E + 05", "1.25E + 03", "2.82E + 03", "4.60E + 02", "2.38E + 03", "5.30E + 02", "3.50E + 03", "1.43E + 03"], ["XP_027270673.1", "Pyruvate kinase pkm isoform x1", "58719.15", "6.69", "8.65E + 05", "1.64E + 04", "1.27E + 04", "7.34E + 03", "2.17E + 03", "6.46E + 02", "4.50E + 03", "2.64E + 03"], ["XP_027270674.1", "Pyruvate kinase pkm isoform x2", "58719.15", "6.88", "1.09E + 06", "2.36E + 04", "8.46E + 03", "3.88E + 03", "6.72E + 03", "3.48E + 03", "5.74E + 03", "2.39E + 03"], ["XP_027270675.1", "Pyruvate kinase pkm isoform x3", "57060.42", "8.65", "8.09E + 05", "2.66E + 04", "1.53E + 04", "5.98E + 03", "4.50E + 03", "3.28E + 03", "8.36E + 03", "2.70E + 03"], ["XP_027270716.1", "Lysyl oxidase homolog 1 isoform x2", "67012.81", "6.57", "1.94E + 05", "4.71E + 02", "7.19E + 03", "3.63E + 03", "8.20E + 03", "2.73E + 03", "7.55E + 03", "1.64E + 03"], ["XP_027270812.1", "Chondroitin sulfate proteoglycan 4", "256882.45", "5.41", "2.63E + 05", "5.72E + 03", "1.03E + 04", "9.31E + 03", "1.06E + 04", "4.45E + 03", "1.45E + 04", "6.25E + 03"], ["XP_027271096.1", "Beta-galactosidase isoform x3", "75859.39", "8.58", "4.32E + 04", "2.36E + 03", "1.06E + 03", "1.24E + 02", "1.81E + 03", "7.72E + 02", "9.83E + 03", "2.59E + 03"], ["XP_027271097.1", "Beta-galactosidase isoform x4", "73868.91", "6.71", "3.52E + 05", "7.41E + 03", "4.27E + 03", "5.47E + 02", "4.18E + 03", "1.49E + 03", "5.98E + 03", "2.17E + 03"], ["XP_027271619.1", "Elongation factor 1-alpha 1", "50646.65", "7.9", "8.78E + 05", "4.10E + 04", "1.19E + 02", "8.16E + 01", "5.76E + 01", "5.97E + 01", "1.89E + 02", "1.39E + 02"], ["XP_027271991.1", "Malate dehydrogenase, mitochondrial isoform x2", "37376.78", "8.93", "1.35E + 05", "4.03E + 03", "3.97E + 03", "1.35E + 03", "3.21E + 03", "8.13E + 02", "3.77E + 03", "8.51E + 02"], ["XP_027272021.1", "Plasminogen activator inhibitor 1 isoform x2", "44454.04", "7.2", "4.74E + 06", "1.02E + 05", "7.43E + 03", "2.19E + 03", "7.02E + 03", "2.94E + 03", "9.84E + 03", "5.02E + 03"], ["XP_027272044.1", "Procollagen c-endopeptidase enhancer 1", "51752.47", "8.16", "2.76E + 05", "7.59E + 03", "7.26E + 03", "3.63E + 03", "5.78E + 03", "1.27E + 03", "5.10E + 03", "3.45E + 02"], ["XP_027272591.1", "Complement c3", "184229.95", "6.2", "6.09E + 04", "2.70E + 03", "5.08E + 03", "1.33E + 03", "1.07E + 04", "3.60E + 03", "5.28E + 03", "1.91E + 03"], ["XP_027272776.1", "Laminin subunit beta-1 isoform x5", "197499.81", "4.78", "2.42E + 05", "4.71E + 02", "6.80E + 03", "3.52E + 03", "1.80E + 03", "5.07E + 02", "1.12E + 04", "5.03E + 03"], ["XP_027272779.1", "Laminin subunit beta-1 isoform x3", "186662.75", "4.76", "1.91E + 05", "5.44E + 03", "3.96E + 03", "4.81E + 02", "3.41E + 03", "1.03E + 03", "6.88E + 03", "2.99E + 03"], ["XP_027272780.1", "Laminin subunit beta-1 isoform x4", "162666.42", "4.7", "6.79E + 04", "1.57E + 03", "1.64E + 03", "9.69E + 02", "2.11E + 03", "9.24E + 02", "4.12E + 03", "5.00E + 02"], ["XP_027273163.1", "Laminin subunit gamma-1 isoform x2", "177705.6", "4.99", "1.16E + 05", "3.86E + 03", "9.84E + 03", "9.17E + 03", "4.12E + 03", "1.37E + 03", "4.26E + 03", "3.94E + 02"], ["XP_027274751.1", "Immunoglobulin superfamily member 8 isoform x3", "66902.23", "7.94", "7.24E + 04", "1.28E + 03", "2.32E + 03", "6.47E + 02", "6.75E + 03", "4.73E + 03", "3.08E + 03", "5.51E + 02"], ["XP_027274961.1", "Legumain", "48435", "6.07", "3.01E + 06", "3.40E + 04", "6.31E + 03", "1.19E + 03", "5.76E + 03", "2.85E + 03", "6.16E + 03", "4.75E + 03"], ["XP_027275654.1", "Cathepsin z", "33838.15", "7.52", "3.29E + 06", "4.64E + 04", "1.44E + 04", "6.08E + 03", "8.88E + 03", "5.11E + 03", "5.29E + 03", "1.74E + 03"], ["XP_027275687.1", "Laminin subunit alpha-5", "413024.52", "6.49", "8.50E + 04", "1.33E + 03", "8.53E + 03", "2.29E + 03", "5.54E + 03", "3.87E + 03", "4.65E + 03", "1.58E + 03"], ["XP_027276427.1", "Nucleobindin-1 isoform x3", "50536.07", "5.14", "7.26E + 05", "8.60E + 03", "2.58E + 03", "9.22E + 02", "5.52E + 03", "2.30E + 03", "1.06E + 04", "6.58E + 03"], ["XP_027277053.1", "Protein-glutamine gamma-glutamyltransferase 2", "75859.39", "5.08", "1.08E + 05", "3.30E + 03", "1.76E + 03", "7.39E + 02", "1.03E + 03", "6.81E + 02", "4.04E + 03", "2.16E + 03"], ["XP_027278026.1", "Thrombospondin-1 isoform x2", "129381.17", "4.7", "1.12E + 06", "2.36E + 04", "9.32E + 03", "3.97E + 03", "6.71E + 03", "9.85E + 02", "7.11E + 03", "1.68E + 03"], ["XP_027278163.1", "Catalase isoform x1", "61373.12", "8.29", "7.38E + 04", "3.74E + 03", "2.23E + 03", "7.48E + 02", "2.00E + 03", "1.10E + 03", "7.40E + 03", "1.58E + 03"], ["XP_027278164.1", "Catalase isoform x2", "53742.95", "7.33", "7.48E + 04", "1.10E + 03", "2.48E + 03", "2.46E + 02", "2.36E + 03", "6.59E + 02", "7.45E + 03", "8.38E + 02"], ["XP_027279237.1", "Matrix metalloproteinase-9", "78513.36", "5.6", "4.31E + 04", "2.60E + 03", "4.31E + 03", "1.59E + 03", "1.05E + 04", "3.66E + 03", "5.71E + 03", "2.24E + 03"], ["XP_027279240.1", "Lysosomal protective protein", "54517.02", "5.64", "1.34E + 06", "0.00E + 00", "3.44E + 03", "1.21E + 03", "6.16E + 03", "1.66E + 03", "4.86E + 03", "3.13E + 03"], ["XP_027279242.1", "Phospholipid transfer protein isoform x2", "49761.99", "5.94", "3.95E + 05", "2.05E + 03", "7.01E + 03", "1.74E + 03", "2.75E + 03", "1.23E + 03", "5.27E + 03", "1.83E + 03"], ["XP_027279907.1", "Insulin-like growth factor-binding protein 4", "28087.88", "6.78", "2.80E + 05", "4.71E + 03", "2.10E + 03", "1.78E + 03", "4.60E + 02", "1.44E + 02", "4.72E + 02", "7.07E + 01"], ["XP_027280118.1", "Nucleoside diphosphate kinase b", "16808.49", "7.78", "8.71E + 05", "8.65E + 03", "2.13E + 03", "4.30E + 02", "5.08E + 03", "3.38E + 03", "3.93E + 03", "7.21E + 02"], ["XP_027280121.1", "Nucleoside diphosphate kinase a isoform x1", "16808.49", "5.96", "4.03E + 05", "1.02E + 04", "1.60E + 04", "7.06E + 03", "2.90E + 04", "1.91E + 04", "1.83E + 04", "2.18E + 04"], ["XP_027280122.1", "Nucleoside diphosphate kinase a isoform x2", "12274.62", "5", "7.94E + 05", "4.24E + 03", "9.15E + 03", "1.12E + 03", "5.37E + 03", "7.92E + 02", "5.05E + 03", "1.53E + 03"], ["XP_027280299.1", "Emilin-1 isoform x1", "112462.1", "5.24", "1.37E + 05", "6.18E + 03", "2.13E + 03", "6.39E + 02", "3.16E + 03", "5.94E + 02", "9.26E + 03", "2.71E + 03"], ["XP_027280300.1", "Emilin-1 isoform x2", "101625.04", "5.09", "1.22E + 05", "1.25E + 03", "5.39E + 03", "8.94E + 02", "2.52E + 03", "6.40E + 02", "3.39E + 03", "2.41E + 03"], ["XP_027281003.1", "Nucleophosmin isoform x2", "32290", "4.61", "9.43E + 05", "1.05E + 04", "9.38E + 03", "7.51E + 03", "4.03E + 03", "1.60E + 03", "5.94E + 03", "2.13E + 03"], ["XP_027281136.1", "Fatty acid synthase isoform x2", "276787.25", "5.95", "9.64E + 04", "2.36E + 03", "7.46E + 03", "6.20E + 03", "7.63E + 03", "9.34E + 02", "6.81E + 03", "3.24E + 03"], ["XP_027281297.1", "Lysosomal alpha-glucosidase", "104942.51", "5.65", "6.10E + 05", "2.82E + 04", "1.64E + 04", "9.02E + 03", "1.80E + 04", "2.88E + 03", "4.56E + 03", "1.55E + 03"], ["XP_027281318.1", "Galectin-3-binding protein", "63474.18", "5.06", "9.51E + 05", "2.46E + 04", "1.26E + 04", "5.04E + 03", "8.36E + 03", "5.68E + 03", "6.46E + 03", "3.00E + 03"], ["XP_027281357.1", "Septin-9 isoform x4", "65464.66", "7.16", "7.81E + 04", "9.63E + 02", "1.28E + 04", "3.83E + 03", "3.51E + 03", "2.62E + 03", "3.64E + 03", "1.17E + 03"], ["XP_027281359.1", "Septin-9 isoform x5", "37045.04", "7.1", "7.81E + 04", "3.14E + 03", "8.26E + 02", "3.54E + 02", "4.29E + 02", "1.56E + 02", "6.13E + 02", "3.17E + 02"], ["XP_027282087.1", "Retinoid-inducible serine carboxypeptidase", "50314.9", "5.39", "4.82E + 05", "1.41E + 03", "3.12E + 03", "1.43E + 03", "2.39E + 03", "1.85E + 03", "2.59E + 03", "9.03E + 02"], ["XP_027282154.1", "Clathrin heavy chain 1 isoform x3", "185225.19", "5.48", "1.29E + 05", "3.56E + 03", "3.61E + 04", "3.82E + 04", "6.45E + 03", "2.07E + 03", "2.04E + 03", "7.87E + 02"], ["XP_027282301.1", "C-c motif chemokine 2", "15813.25", "9.32", "3.12E + 06", "2.16E + 04", "2.03E + 03", "4.27E + 02", "1.22E + 03", "3.98E + 02", "4.94E + 03", "2.68E + 03"], ["XP_027282549.1", "Pigment epithelium-derived factor isoform x2", "46223.36", "6.43", "3.52E + 05", "3.74E + 03", "7.57E + 03", "4.32E + 03", "4.18E + 03", "1.21E + 03", "1.60E + 04", "1.49E + 04"], ["XP_027282819.1", "Eukaryotic initiation factor 4a-i", "44896.37", "5.32", "1.30E + 05", "6.13E + 03", "4.71E + 03", "1.77E + 03", "4.04E + 03", "1.25E + 03", "5.36E + 03", "1.55E + 03"], ["XP_027283255.1", "Sparc isoform x4", "33838.15", "4.75", "1.27E + 05", "4.71E + 02", "2.26E + 03", "1.06E + 03", "3.57E + 03", "8.75E + 02", "4.94E + 03", "9.27E + 02"], ["XP_027283783.1", "Granulins isoform x2", "65464.66", "5.97", "1.15E + 06", "2.05E + 04", "4.31E + 03", "3.70E + 03", "3.09E + 03", "5.03E + 02", "2.42E + 03", "3.59E + 02"], ["XP_027284007.1", "Keratin, type i cytoskeletal 10 isoform x3", "62700.11", "5.04", "1.14E + 06", "3.30E + 04", "1.34E + 04", "6.51E + 03", "1.34E + 04", "9.83E + 03", "6.90E + 03", "7.36E + 02"], ["XP_027284023.1", "Complement c1r subcomponent", "77960.45", "5.71", "4.54E + 05", "1.17E + 04", "1.28E + 04", "2.44E + 03", "9.64E + 03", "2.48E + 03", "7.56E + 03", "9.74E + 02"], ["XP_027284024.1", "Complement c1r subcomponent-like protein", "53742.95", "6.31", "1.27E + 05", "4.03E + 03", "1.73E + 04", "2.46E + 03", "1.04E + 04", "1.90E + 03", "7.97E + 03", "2.96E + 03"], ["XP_027284060.1", "Triosephosphate isomerase isoform x2", "27534.97", "6.13", "3.21E + 05", "4.50E + 03", "2.85E + 03", "1.18E + 03", "7.05E + 03", "5.43E + 02", "8.88E + 03", "1.57E + 03"], ["XP_027284552.1", "T-complex protein 1 subunit eta isoform x2", "60046.13", "7.07", "1.99E + 05", "9.43E + 02", "4.42E + 03", "1.16E + 03", "5.37E + 03", "4.88E + 02", "5.42E + 03", "1.24E + 03"], ["XP_027286043.1", "Transforming protein rhoa isoform x1", "21342.36", "7.51", "3.42E + 04", "2.87E + 03", "1.12E + 03", "1.66E + 02", "5.14E + 02", "2.04E + 02", "3.00E + 03", "1.36E + 03"], ["XP_027288083.1", "Metalloproteinase inhibitor 1", "22448.19", "8.84", "7.24E + 05", "1.45E + 04", "9.22E + 03", "4.82E + 03", "2.12E + 03", "4.14E + 02", "3.07E + 03", "1.06E + 03"], ["XP_027288193.1", "V-type proton atpase subunit s1 isoform x2", "51199.56", "5.52", "4.65E + 04", "1.42E + 03", "1.55E + 03", "1.39E + 02", "5.38E + 03", "2.56E + 03", "1.92E + 03", "1.26E + 03"], ["XP_027289308.1", "Alpha-enolase isoform x2", "47992.67", "5.85", "3.72E + 05", "2.87E + 03", "5.96E + 03", "1.49E + 03", "4.81E + 03", "1.64E + 03", "6.16E + 03", "3.51E + 03"]], "row_count": 153, "column_count": 12, "numeric_cells": 1762, "header_rows": 1, "locator": "section[18]/table-wrap[1]#Tab4"}}], "gaps": ["asset:data:geo:PXD016047 not downloaded", "asset:data:geo:PXD016047 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "correlation_analysis", "specific": "pearson", "label": "Correlation analysis", "dsl_operations": ["pearson_r"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["paired_numeric_columns"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "A Pearson correlation matrix was constructed using the intensities of all identified proteins."}}], "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": ["pearson_r"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: pearson."}, "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": ["PXD016047"], "resolved_accessions": ["PXD016047"], "statements": ["The raw DDA data files for library generation, the search result (group files), the CHO spectral library, and the SWATH-MS acquisition data applied in the current study have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org)34via the PRIDE partner repository35,36 with the data set identifier PXD01604728."], "basis": "The paper names PXD016047 in ProteomeXchange Consortium (via the PRIDE partner repository) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["pearson_r"], "assets": ["source:pmid:32782267", "data:geo:PXD016047", "asset:table:pmid:32782267:1", "asset:table:pmid:32782267:2", "asset:table:pmid:32782267:3", "asset:table:pmid:32782267:4"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:PXD016047"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:22:01Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 40872, "completion_tokens": 1303, "cached_tokens": 776}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:32782267", "type": "paper", "label": "pmid:32782267"}, {"id": "source:pmid:32782267", "type": "manuscript", "label": "PMID 32782267 full text"}, {"id": "data:geo:PXD016047", "type": "dataset", "label": "GEO PXD016047"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:32782267", "type": "paper", "label": "pmid:32782267"}, {"id": "source:pmid:32782267", "type": "manuscript", "label": "PMID 32782267 full text"}, {"id": "data:geo:PXD016047", "type": "dataset", "label": "GEO PXD016047"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-32782267", "type": "extraction", "used": ["source:pmid:32782267"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-PXD016047", "type": "accession_resolution", "used": ["data:geo:PXD016047"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}, {"id": "agent:minimax-reader", "type": "software", "label": "MiniMax literature reader"}], "source_run_id": "reading-sci-2026-11-01", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:32782267", "parent_hash": "sha256:5669f104c7990b21f3565d2ef079517960bcc9ce2aceebf5ebad44943818cb9c", "fork_of": null, "generation": 5}, "gaps": ["asset:data:geo:PXD016047 licence not read", "asset:data:geo:PXD016047 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "cell_culture", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["isting of 199,102 identified peptides from a CHO-K1 cell proteome. The robustness, accuracy and", "b-producing CHO-K1 (CCL-61, ATCC) cells were cultured in fully chemically-defined protein-free cultur", "Methods CHO cell cultures The mAb-producing CHO-K1 (CCL-61, ATCC) cells were cultured in fully", "culture fluid (HCCF, collected on day 14 of CHO-K1 fed-batch cell cultures), CHO-DG44 and CHO-S"], "order_basis": "paper_text_order:786", "id": "assay:1"}, {"role": "data_generation", "definition_id": "elisa", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["HCP content in DSP samples was determined by ELISA using a Generation III CHO HCP kit (Cygnus T", "digested and analyzed accordingly (Fig. 1). ELISA analysis of these samples showed that the to", "TH-MS results were not only in line with the ELISA result, but also provided critical informati"], "order_basis": "paper_text_order:5269", "id": "assay:2"}, {"role": "analysis", "definition_id": "correlation_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["pearson_r"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["A Pearson correlation matrix was constructed using the intensities of all identified proteins."], "order_basis": "consumes_earlier_output", "id": "assay:3"}]},"meta":{"api_version":"v1","automation_ladder_snapshot":"ba34b49490d9bfaf","automation_ladder_caveats":["Method extraction is rule-based and has no hand-judged accuracy sample. Evidence bands order textual support; method agreement intervals are null (n=0), never probabilities. Work-type validation does not validate methods.","Operation coverage describes only explicitly named methods. It does not prove a complete protocol, compatible parameters, successful compilation or re-execution. Unrecognised or ambiguous methods require review.","Data reachability is a textual accession or public-data statement. No dataset was downloaded or checked for access, completeness or licence.","Capabilities are planning states seeded from the dated equipment register. No bench ownership, completed quote or partner booking is inferred. Procurement counts are dependencies, not guaranteed replications or financial returns.","Tier and blocker counts are deterministic assessments of this corpus, not measured agreement. R3 is reserved for procurement; unresolved methods and data require human work (R4). The most restrictive axis wins, with capability, method, data as tie-breaks. Resolving one blocker can leave another at the same tier."],"engine":"corpus_engine","engine_provider":"rule_based_v1+lex99e1195c7d6f","run_id":"run-20261023T122449232913","source":"esearch","source_detail":"PubMed mirror biomed_pubmed (read-only)","run_status":"complete","imported_at":"2026-11-03T20:16:52+00:00","generated_at":"2026-11-04T02:45:49+00:00","total_papers":5529,"total_assays_tracked":29,"automatable_assay_families":6,"validated":true,"caveat_count":9,"blocking_caveats":5,"caveats":[{"code":"low_evidence_dominates","basis":["4,152 of 5,529 classifications (75.1%) matched no cue evidence and sit at the 0.05 floor.","34 of 230 data_only calls (14.8%) are in that group."],"claim":"Work type and confidence bands","gloss":"Most records were classified from their title and framing alone, with assay-cue coverage at zero.","detail":"Most classifications in this run rest on no matched evidence at all. At the evidence floor the work type comes from title framing and a fixed prior, not from anything in the paper, so the published work-type split should be read as a rough triage signal rather than a measured distribution. The impact is bounded but not removed: since 2026-10-23 the engine excludes floor-confidence records from the shortlist entirely and publishes them separately as held out, so the recommendation is unaffected even though the census is.","status":"unverified","severity":"high"},{"code":"runtime_is_modelled","basis":["Runtime is summed from published per-assay hour figures. Timing awaits the first executed replication.","4,407 of 5,529 records (79.7%) model to 0.00 hours because no assay was matched, which the ranking then reads as \"cheapest\".","0 of 10 shortlisted records carry a 0.00-hour estimate."],"claim":"Estimated replication runtime","gloss":"The hour figures are estimates built from assay mentions; timing awaits the first executed replication.","detail":"The hour figures are a cost model derived from the bench steps implied by each matched assay family. The first executed replication will supply measured timing. Records without an assay match currently receive a zero-hour model value.","status":"unverified","severity":"high"},{"code":"signal_score_without_citations","basis":["5,529 of 5,529 records (100.0%) have no citation count from the source metadata."],"claim":"Signal score","gloss":"The signal score uses publication-type weight because the mirror supplied zero citation counts.","detail":"The source supplied no citation counts for any record in this run, so the signal score is publication-type weight only. The citation term of the ranking is inert here, and the shortlist is ordered by publication type alone.","status":"unverified","severity":"high"},{"code":"abstract_absent","basis":["1,667 of 5,529 records (30.2%) carry no abstract at all."],"claim":"Evidence base for classification","gloss":"Some records contain a title and publication type only, defining the available classification evidence.","detail":"Where the mirror contains a title and publication types only, those fields define the classifier evidence. A methods section is required for fuller automated and human review.","status":"unverified","severity":"medium"},{"code":"classifier_agreement_measured","basis":["Published two-way decision agreement 77.7% (310 of 399 decidable records) from a stratified hand-check of 438 real records.","Three-way diagnostic agreement 73.9% (288 of 390 decidable records).","data_only agreement 75.2% (100 of 133 decidable).","48 record(s) could not be decided from title and abstract and were excluded from the denominator.","56 analysis-only records were published under another work type, so the data_only share is not an upper bound."],"claim":"Published automatable decision","gloss":"This figure has been checked against a human reading the same papers, so we know how often it is right.","detail":"The published automatable / not-automatable distribution comes from a rule-based classifier that was hand-checked against a fixed ground-truth definition. The agreement rates below are measured, not estimated. The three-way work type remains a diagnostic and is reported separately.","status":"measured","severity":"high"},{"code":"llm_comparison_not_measured","basis":["rule_based_v1+lex99e1195c7d6f produced 5,529 of 5,529 classifications.","Measured on 438 labelled records; these are RULE-BASED figures, not model results."],"claim":"Rule-based versus LLM agreement","gloss":"Every number here is the rule engine’s own. Model comparison begins when a working API credential is connected and measured.","detail":"The published two-way decision agreed with a human reading on 310 of 399 decidable records (77.7%). The diagnostic three-way label agreed on 288 of 390 decidable records (73.9%). Every percentage in this run belongs to the rule engine. Model comparison begins when a working API credential is connected and measured.","status":"not_measured","severity":"high"},{"code":"confidence_is_a_band","basis":["low band: 135 of 210 hand-judged records were correct, 64.3% [57.6, 70.5] (95% CI).","medium band: 80 of 104 hand-judged records were correct, 76.9% [68.0, 84.0] (95% CI).","high band: 73 of 76 hand-judged records were correct, 96.0% [89.0, 98.7] (95% CI).","A fitted calibrated probability was built, measured and withdrawn: it overstated held-out accuracy and reorders nothing."],"claim":"Confidence band and evidence score","gloss":"The confidence band carries a measured accuracy interval; 0.85 represents relative rank strength.","detail":"Confidence on this run is a BAND plus its measured accuracy interval. The number stored alongside each record is a monotone evidence score that orders records; 0.85 represents relative rank strength. A fitted probability was withdrawn after it overstated held-out accuracy. Threshold on the band.","status":"measured","severity":"medium"},{"code":"three_way_split_is_diagnostic","basis":["The corpus is published at the two-way decision: automatable or not-automatable. The three-way split (data_only / physical / mixed) is published as a diagnostic with its measured reliability attached, not as a claim, because the rule engine's `mixed` call cannot be defended.","The engine called 22 record(s) mixed; 10 matched the human judgement (45.5%, 95% CI 26.9-65.3).","The engine's `mixed` call is right on 10/22 hand-judged records (45.5%, 95% CI 26.9%-65.3%); a constant `physical` guess scores 36.4%.","The engine's `mixed` call does not reliably beat a constant `physical` guess on the hand-judged records it labels mixed.","The sign of that difference flips between two independent samples, so the three-way refinement is not demonstrably informative.","The mixed stratum contributes a disproportionate share of errors relative to its size.","At title-only depth the physical/mixed split collapses: a title says that work was done, not whether it was also analysed."],"claim":"The published decision is two-way","gloss":"The three-way split is shown for diagnosis only. The published split is two ways.","detail":"Count and filter the corpus on automatable versus not-automatable. The data_only / physical / mixed split remains an internal engine diagnostic because the mixed call has lower measured reliability.","status":"measured","severity":"medium"},{"code":"automatable_flag_unproven","basis":["6 of 29 assay families are marked automatable now: meta_analysis, machine_learning, survival_analysis, pca, molecular_docking, differential_expression.","The flag is a rule over assay family and work type; validation begins with the first executed replication.","It inherits the 75.2% data_only agreement rate, because the flag requires the record to be analysis-only."],"claim":"Automatable now","gloss":"This flag marks assay families the rules classify as data-only. The first executed replication will validate it.","detail":"This flag marks families the rules consider replicable from data alone. Its validity depends on the analysis-only classification and will be measured through an executed replication.","status":"unverified","severity":"medium"}],"confidence_policy":"band_with_measured_interval","confidence_contract":{"policy":"band_with_measured_interval","summary":"Confidence is reported as a BAND with a measured accuracy interval. The raw evidence score supplies monotone ordering. A fitted point estimate was withdrawn after it overstated held-out accuracy.","evidence_score":"A monotone evidence score in [0,1] built from cue mass, axis separation and text coverage. Use it to order records. Interpret 0.85 as relative rank strength.","confidence_band":"low | medium | high. Consumers threshold on this value.","band_accuracy":"Wilson 95% interval on the measured agreement of the hand-judged records in this band.","calibrated_confidence":"WITHDRAWN. Reintroduction requires held-out evidence demonstrating reliable estimates across every bin."},"band_accuracy":{"low":{"n":210,"low":0.576,"band":"low","high":0.7046,"agree":135,"accuracy":0.6429},"high":{"n":76,"low":0.8903,"band":"high","high":0.9865,"agree":73,"accuracy":0.9605},"medium":{"n":104,"low":0.6795,"band":"medium","high":0.8397,"agree":80,"accuracy":0.7692}},"provider":"rule_based_v1+lex99e1195c7d6f","lexicon_id":"99e1195c7d6f","contract_published_at":"2026-10-23T12:25:29.022232+00:00","confidence_is_band":true,"confidence_is_probability":false,"decision_taxonomy":"two_way","decidable_fraction_two_way":0.8854,"decidable_fraction_two_way_low":0.8565,"decidable_fraction_two_way_high":0.9143,"decidable_fraction_three_way":0.8586,"decidable_fraction_three_way_low":0.8287,"decidable_fraction_three_way_high":0.8884,"decidable_population":5529,"validation_sample_size":438,"three_way_cost_fraction":0.0268,"three_way_cost_records":148,"decision_counts":{"automatable":230,"not_automatable":5299},"decision_split":{"automatable":{"count":230,"share":0.04159884246699222},"not_automatable":{"count":5299,"share":0.9584011575330078}},"diagnostic_work_type_counts":{"mixed":24,"physical":5275,"data_only":230}}}