{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:33555887", "kind": "science-record", "revision": 6, "content_hash": "sha256:d2e1e6e5c13ed832ca5d2e058709b5c56dc5aea3d87e9a4da6e6432595f03e2f", "created_at": "2026-11-01T15:41:24Z", "updated_at": "2026-11-01T21:24:37Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Comprehensive Analysis of Tryptic Peptides Arising from Disulfide Linkages in NISTmAb and Their Use for Developing a Mass Spectral Library.", "doi": "10.1021/acs.jproteome.0c00823", "pmid": "33555887", "authors": ["Qian Dong", "Xinjian Yan", "Yuxue Liang", "Sanford P Markey", "Sergey L Sheetlin", "Concepcion A Remoroza", "William E Wallace", "Stephen E Stein"], "journal": "Journal of proteome research", "year": 2021, "abstract": "This work presents methods for identifying and then creating a mass spectral library for disulfide-linked peptides originating from the NISTmAb, a reference material of the humanized IgG1k monoclonal antibody (RM 8671). Analyses involved both partially reduced and non-reduced samples under neutral and weakly basic conditions followed by nanoflow liquid chromatography tandem mass spectrometry (LC-MS/MS). Spectra of peptides containing disulfide bonds are identified by both MS1 ion and MS2 fragment ion data in order to completely map all the disulfide linkages in the NISTmAb. This led to the detection of 383 distinct disulfide-linked peptide ions, arising from fully tryptic cleavage, missed cleavage, irregular cleavage, complex Met/Trp oxidation mixtures, and metal adducts. Fragmentation features of disulfide bonds under low-energy collision dissociation were examined. These include (1) peptide bond cleavage leaving disulfide bonds intact; (2) disulfide bond cleavage, often leading to extensive fragmentation; and (3) double cleavage products resulting from breakages of two peptide bonds or both peptide and disulfide bonds. Automated annotation of various complex MS/MS fragments enabled the identification of disulfide-linked peptides with high confidence. Peptides containing each of the nine native disulfide bonds were identified along with 86 additional disulfide linkages arising from disulfide bond shuffling. The presence of shuffled disulfides was nearly completely abrogated by refining digest conditions. A curated spectral library of 702 disulfide-linked peptide spectra was created from this analysis and is publicly available for free download. Since all IgG1 antibodies have the same constant regions, the resulting library can be used as a tool for facile identification of \"hard-to-find\" disulfide-bonded peptides. Moreover, we show that one may identify such peptides originating from IgG1 proteins in human serum, thereby serving as a means of monitoring the completeness of protein reduction in proteomics studies. Data are available via ProteomeXchange with identifier PXD023358.", "claims": [{"id": "claim-method", "statement": "In this study, the median value of RT range for specific experiments is used in a discriminant filter to remove unrelated identifications.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33555887", "locator": "sections[11] \"Estimation of the Median RT Range\" paragraph 2", "quote": "In this study, the median value of RT range for specific experiments is used in a discriminant filter to remove unrelated identifications."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Data are available via ProteomeXchange with identifier PXD023358.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33555887", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Data are available via ProteomeXchange with identifier PXD023358."}], "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:33555887"], "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:PXD023358"], "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:PXD023358"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:33555887", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1021/acs.jproteome.0c00823", "sha256": "sha256:c5afe9b149bf7fc354209b723490f98ca8dcab23aef74081b9b307b23df92137", "bytes": 68125, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1021/acs.jproteome.0c00823", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9278810", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PXD023358", "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=PXD023358", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD023358", "version": null, "note": "Data are available via ProteomeXchange with identifier PXD023358.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data are available via ProteomeXchange with identifier PXD023358.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "Comprehensive Analysis of Tryptic Peptides Arising from Disulfide Linkages in NISTmAb", "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:33555887:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:e3746fc58c9de09148bc41a9b3da2c8752f3fa9319758cc9deacf727302422d5", "bytes": 317, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[14]/table-wrap[1]#tbl1", "version": null, "note": "Classification of the Three Major Groups of Product Ions Observed in the Spectra of Disulfide Peptide Discussed in This Section, SGTASVVCLLNNFYPR_SS_VYACEVTHQGLSSPVTKa", "structure": {"pmcid": "PMC9278810", "section_index": 14, "section_title": "Classification of Product Ions", "row_count": 0, "column_count": 0}, "table": {"label": "Table 1", "caption": "Classification of the Three Major Groups of Product Ions Observed in the Spectra of Disulfide Peptide Discussed in This Section, SGTASVVCLLNNFYPR_SS_VYACEVTHQGLSSPVTKa", "rows": [], "row_count": 0, "column_count": 0, "numeric_cells": 0, "header_rows": 0, "locator": "section[14]/table-wrap[1]#tbl1"}}, {"id": "asset:table:pmid:33555887:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:b8fb84bbb05529e35ce14f37fff216f6267cef378e9fecc1e27f38b13a62d8d1", "bytes": 5189, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[19]/table-wrap[1]#tbl2", "version": null, "note": "Disulfide-Linked Peptides Detected for Each of the Nine Native Disulfide Linkages Obtained from the Triplicate LC–MS/MS Analyses of the 18 h NISTmAb Digest Partially Reduced with TCEP and Alkylated with IAMg,h", "structure": {"pmcid": "PMC9278810", "section_index": 19, "section_title": "Identification of Native (Expected) NISTmAb Disulfide Linkages", "row_count": 61, "column_count": 8}, "table": {"label": "Table 2", "caption": "Disulfide-Linked Peptides Detected for Each of the Nine Native Disulfide Linkages Obtained from the Triplicate LC–MS/MS Analyses of the 18 h NISTmAb Digest Partially Reduced with TCEP and Alkylated with IAMg,h", "rows": [["bond name", "position in protein", "class", "missed cleaved sites", "peptide sequence", "mass", "charge", "absolute abund."], ["1a VH", "HC22-HC97", "tryptic 25%", "0", "eESGPALVKPTQTLTLTCTFSGFSLSTAGMSVGWIR_SS_VTNMDPADTATYYCAR", "5431.587", "4,5,6", "3.6 × 1010"], ["missed cleav.", "1", "eESGPALVKPTQTLTLTCTFSGFSLSTAGMSVGWIR_SS_VTNMDPADTATYYCARD", "8213.882", "5,6,7", "9.3 × 1010"], ["MIFNFYFDVWGQGTTVTVSSASTK"], ["2", "ESGPALVKPTQTLTLTCTFSGFSLSTAGMSVGWIR_SS_VTNMDPADTATYYCARDMI", "9381.511", "6,7", "8.6 × 1009"], ["FNFYFDVWGQGTTVTVSSASTKGPSVFPLAPSSK"], ["2", "ESGPALVKPTQTLTLTCTFSGFSLSTAGMSVGWIRQPPGK_SS_VTNMDPADTATYYC", "8721.163", "5,6,7,8", "3.2 × 1009"], ["ARDMIFNFYFDVWGQGTTVTVSSASTK"], ["3", "ESGPALVKPTQTLTLTCTFSGFSLSTAGMSVGWIR_SS_DTSKNQVVLKVTNMDPADT", "9326.501", "6,7,8", "2.3 × 1009"], ["ATYYCARDMIFNFYFDVWGQGTTVTVSSASTK"], ["3", "ESGPALVKPTQTLTLTCTFSGFSLSTAGMSVGWIRQPPGK_SS_VTNMDPADTATYYC", "9888.792", "7,8", "8.3 × 1008"], ["ARDMIFNFYFDVWGQGTTVTVSSASTKGPSVFPLAPSSK"], ["semi- tryptic", "0", "ESGPALVKPTQTLTLTCTFSGF_SS_VTNMDPADTATYYCAR", "4085.906", "4,5", "2.4 × 1009"], ["0", "ESGPALVKPTQTLTLTCTFSGFSL_SS_VTNMDPADTATYYCAR", "4286.022", "3", "3.4 × 1008"], ["", "", "", "", "", "", "", ""], ["2a CH1", "HC147-HC203", "tryptic 94%", "0", "eSTSGGTAALGCLVK_SS_DYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSV", "7916.919", "5,6,7,8", "1.8 × 1011"], ["VTVPSSSLGTQTYICNVNHKPSNTK"], ["missed cleav.", "1", "fSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSS", "7898.909", "5,6", "4.4 × 1009"], ["LGTQTYICNVNHKPSNTK"], ["1", "STSGGTAALGCLVK_SS_DYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTV", "8259.11", "6,7", "4.8 × 1008"], ["PSSSLGTQTYICNVNHKPSNTKVDK"], ["semi- tryptic", "0", "STSGGTAALGCLVK_SS_SWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQT", "6869.428", "5,6,7", "4.5 × 1009"], ["YICNVNHKPSNTK"], ["0", "STSGGTAALGCLVK_SS_TVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQ", "7069.544", "6", "1.8 × 1009"], ["TYICNVNHKPSNTK"], ["0", "STSGGTAALGCLVK_SS_SLSSVVTVPSSSLGTQTYICNVNHKPSNTK", "4409.221", "5,6", "3.3 × 1008"], ["0", "STSGGTAALGCLVK_SS_SVVTVPSSSLGTQTYICNVNHKPSNTK", "4122.073", "4,5,6", "2.2 × 1008"], ["0", "STSGGTAALGCLVK_SS_SSVVTVPSSSLGTQTYICNVNHKPSNTK", "4209.105", "4,5", "1.4 × 1008"], ["0", "STSGGTAALGCLVK_SS_TVPSSSLGTQTYICNVNHKPSNTK", "3836.904", "4,5", "9.3 × 1007"], ["", "", "", "", "", "", "", ""], ["3a CH2", "HC264-HC324", "tryptic 96%", "0", "eTPEVTCVVVDVSHEDPEVK_SS_CK", "2328.098", "2,3,4,5", "2.5 × 1011"], ["missed cleav.", "2", "TPEVTCVVVDVSHEDPEVK_SS_VVSVLTVLHQDWLNGKEYKCK", "4537.287", "4,5,6,7", "6.6 × 1009"], ["3", "TPEVTCVVVDVSHEDPEVK_SS_VVSVLTVLHQDWLNGKEYKCKVSNK", "4965.526", "5,6", "1.5 × 1009"], ["1", "TPEVTCVVVDVSHEDPEVK_SS_EYKCK", "2748.299", "4,5", "9.4 × 1008"], ["1", "TPEVTCVVVDVSHEDPEVK_SS_CKVSNK", "2756.336", "4,5", "2.8 × 1008"], ["semi- tryptic", "0", "TPEVTCVVVDVSHED_SS_CK", "1874.839", "4", "5.1 × 1008"], ["0", "TPEVTCVVVDVSH_SS_CK", "1630.77", "2", "4.7 × 1008"], ["0", "TPEVTCVVVD_SS_CK", "1307.61", "2,3", "3.4 × 1008"], ["", "", "", "", "", "", "", ""], ["4a CH3", "HC370-HC428", "tryptic 99%", "0", "eNQVSLTCLVK_SS_WQQGNVFSCSVMHEALHNHYTQK", "3844.824", "3,4,5,6,7", "9.9 × 1010"], ["semi- tryptic", "0", "NQVSLTCLVK_SS_VFSCSVMHEALHNHYTQK", "3231.563", "4,5", "7.6 × 1007"], ["", "", "", "", "", "", "", ""], ["5b VL", "LC23- LC87", "tryptic 92%", "0", "VTITCSASSR_SS_FSGSGSGTEFTLTISSLQPDDFATYYCFQGSGYPFTFGGGTK", "5446.46", "4,5", "1.4 × 1010"], ["missed cleav.", "1", "DIQMTQSPSTLSASVGDRVTITCSASSR_SS_FSGSGSGTEFTLTISSLQPDDFATYYCFQ", "7320.344", "5", "1.0 × 1009"], ["GSGYPFTFGGGTK"], ["2", "VTITCSASSR_SS_FSGSGSGTEFTLTISSLQPDDFATYYCFQGSGYPFTFGGGTKVEIKR", "6071.851", "5,6", "2.0 × 1008"], ["", "", "", "", "", "", "", ""], ["6b CL", "LC133-LC193", "tryptic 66%", "0", "SGTASVVCLLNNFYPR_SS_VYACEVTHQGLSSPVTK", "3555.749", "3,4,5", "1.2 × 1011"], ["missed cleav.", "1", "SGTASVVCLLNNFYPR_SS_HKVYACEVTHQGLSSPVTK", "3820.903", "3,4,5,6,7", "6.2 × 1010"], ["2", "SGTASVVCLLNNFYPR_SS_ADYEKHKVYACEVTHQGLSSPVTK", "4427.168", "5,6", "6.0 × 1008"], ["semi- tryptic", "0", "SGTASVVCLLNNFYPR_SS_VYACEVTH", "2658.257", "4", "4.5 × 1007"], ["", "", "", "", "", "", "", ""], ["7c H-L", "HC223-LC213", "missed cleav.", "1", "SCDKTHTC(CAM)PPC(CAM)PAPELLGGPSVFLFPPKPK_SS_GEC", "3467.639", "3,4,5,6,7", "2.6 × 1010"], ["2", "SCDKTHTC(CAM)PPC(CAM)PAPELLGGPSVFLFPPKPK_SS_SFNRGEC", "3971.883", "4,5,6,7", "3.3 × 1009"], ["3", "SCDKTHTC(CAM)PPC(CAM)PAPELLGGPSVFLFPPKPKDTLMISR_SS_SFNRGEC", "4788.299", "4,5,6", "2.7 × 1009"], ["1", "SCDK_SS_SFNRGEC", "1260.486", "2,3,4", "7.8 × 1008"], ["", "", "", "", "", "", "", ""], ["8 and 9d Hinge", "HC229-HC229 and HC232-HC232", "tryptic 82%", "0", "THTCPPCPAPELLGGPSVFLFPPKPK_2(SS)_THTCPPCPAPELLGGPSVFLFPPKPK", "5456.799", "4,5,6,7,8", "6.7 × 1010"], ["missed cleav.", "1", "THTCPPCPAPELLGGPSVFLFPPKPK_2(SS)_SC(CAM)DKTHTCPPCPAPELLGGPSVFLFPPKPK", "5889.962", "5,6,7,8,9", "1.2 × 1010"], ["2", "SC(CAM)DKTHTCPPCPAPELLGGPSVFLFPPKPK_2(SS)_SC(CAM)DKTHTCPPCPAPELLGGPSVFLFPPKPK", "6323.125", "4,5,6,7,8,9", "2.2 × 1009"], ["semi- tryptic", "0", "THTCPPCPAPELLGGPSVFLFPPKPK_2(SS)_THTCPPCPAPELLGGPSVF", "4649.298", "5", "5.4 × 1008"]], "row_count": 61, "column_count": 8, "numeric_cells": 195, "header_rows": 1, "locator": "section[19]/table-wrap[1]#tbl2"}}, {"id": "asset:table:pmid:33555887:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:b8f57dd0117bb89ef964e64562c30a7bb84a727aef246577e8e27d9d207560aa", "bytes": 1300, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[22]/table-wrap[1]#tbl4", "version": null, "note": "Selected Disulfide-Linked Peptide Ions with Varied Amino Acid Compositions and Charge States that Were Studied for Fragmentation Patterns under HCD and FT-CID", "structure": {"pmcid": "PMC9278810", "section_index": 22, "section_title": "Irregular Cleavage Products", "row_count": 16, "column_count": 9}, "table": {"label": "Table 4", "caption": "Selected Disulfide-Linked Peptide Ions with Varied Amino Acid Compositions and Charge States that Were Studied for Fragmentation Patterns under HCD and FT-CID", "rows": [["# bond", "bond name", "Cys position in protein", "disulfide-linked peptide sequence", "peptide class", "# ion", "charge", "precursor m/z", "replicate spectra"], ["2", "CH1", "147–203", "STSGGTAALGCLVK_SS_DYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYS", "tryptic", "1", "6", "1320.494", "42"], ["LSSVVTVPSSSLGTQTYICNVNHKPSNTK", "2", "7", "1131.996", "157"], ["3", "CH2", "264–324", "TPEVTCVVVDVSHEDPEVK_SS_CK", "tryptic", "3", "3", "777.04", "424"], ["4", "4", "583.032", "955"], ["*EVTCVVVDVSHEDPEVK_SS_CK", "semi-tryptic", "5", "3", "711.006", "18"], ["*TPEVTCVVVDVSHED_SS_CK", "6", "3", "625.854", "20"], ["7", "4", "469.717", "14"], ["4", "CH3", "370–428", "NQVSLTCLVK_SS_WQQGNVFSCSVMHEALHNHYTQK", "tryptic", "8", "4", "962.213", "149"], ["9", "5", "769.972", "582"], ["10", "6", "641.811", "41"], ["11", "7", "550.268", "29"], ["6", "CL", "133–193", "SGTASVVCLLNNFYPR_SS_VYACEVTHQGLSSPVTK", "tryptic", "12", "3", "1186.257", "17"], ["13", "4", "889.945", "277"], ["14", "5", "712.157", "475"], ["7", "H-L", "223–213", "SCDK_SS_SFNRGEC", "missed cleavage", "15", "3", "421.169", "30"]], "row_count": 16, "column_count": 9, "numeric_cells": 70, "header_rows": 1, "locator": "section[22]/table-wrap[1]#tbl4"}}, {"id": "asset:table:pmid:33555887:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:1089f8a516002a20d6de9172744614f95ebcb24c4a1a17fa9f33f9732f4a84bc", "bytes": 4346, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[27]/table-wrap[1]#tbl3", "version": null, "note": "Fragment Ion Annotation in an FT-CID MS/MS Spectrum of the Charge 3+ Disulfide-Linked Peptide, SGTASVVCLLNNFYPR_SS_VYACEVTHQGLSSPVTKa", "structure": {"pmcid": "PMC9278810", "section_index": 27, "section_title": "Overview of Different Types of Fragments Observed", "row_count": 56, "column_count": 9}, "table": {"label": "Table 3", "caption": "Fragment Ion Annotation in an FT-CID MS/MS Spectrum of the Charge 3+ Disulfide-Linked Peptide, SGTASVVCLLNNFYPR_SS_VYACEVTHQGLSSPVTKa", "rows": [["class", "group", "cleavage site", "m/z", "mass error in ppm", "assignment of fragment", "charge", "sequence", "percent abundance"], ["intact disulfide bond fragment", "1a", "single C-N cleavage in either peptide", "985.8223", "1.1", "y9", "3", "CLLNNFYPR_SS_VYACEVTHQGLSSPVTK", "5.5"], ["1075.204", "1.9", "y12-NH3", "3", "SVVCLLNNFYPR_SS_VYACEVTHQGLSSPVTK", "18.5"], ["1080.879", "1.4", "y12", "3", "SVVCLLNNFYPR_SS_VYACEVTHQGLSSPVTK", "25.4"], ["1131.5491", "2.2", "b(2)16-H2O", "3", "SGTASVVCLLNNFYPR_SS_VYACEVTHQGLSSPVT", "10.2"], ["1308.6421", "1", "b9-H2O", "2", "SGTASVVCL_SS_VYACEVTHQGLSSPVTK", "6.4"], ["1312.1265", "1", "b(2)8-H2O", "2", "SGTASVVCLLNNFYPR_SS_VYACEVTH", "19.5"], ["1321.1309", "0.3", "b(2)8", "2", "SGTASVVCLLNNFYPR_SS_ YACEVTH", "32.8"], ["1385.1595", "0.2", "b(2)9", "2", "SGTASVVCLLNNFYPR_SS_VYACEVTHQ", "47"], ["1413.6871", "4.6", "b11-H5NO", "2", "SGTASVVCLLN_SS_VYACEVTHQGLSSPVTK", "19.9"], ["1431.2117", "0.4", "b11", "2", "SGTASVVCLLN_SS_VYACEVTHQGLSSPVTK", "26.5"], ["1478.229", "0.5", "y9", "2", "CLLNNFYPR_SS_VYACEVTHQGLSSPVTK", "100"], ["1488.2318", "1.3", "b12", "2", "SGTASVVCLLNN_SS_VYACEVTHQGLSSPVTK", "17.7"], ["1504.7283", "3.3", "b(2)12-H2O", "2", "SGTASVVCLLNNFYPR_SS_VYACEVTHQGLS", "30"], ["1513.7325", "2.6", "b(2)12", "2", "SGTASVVCLLNNFYPR_SS_VYACEVTHQGLS", "27.7"], ["1527.7645", "1.4", "y10", "2", "VCLLNNFYPR_SS_VYACEVTHQGLSSPVTK", "98.5"], ["1539.2399", "3.8", "b(2)13-2H2O", "2", "SGTASVVCLLNNFYPR_SS_VYACEVTHQGLSS", "38.4"], ["1553.2588", "2.7", "b13-NH3", "2", "SGTASVVCLLNNF_SS_VYACEVTHQGLSSPVTK", "7.2"], ["1557.2498", "3.3", "b(2)13", "2", "SGTASVVCLLNNFYPR_SS_VYACEVTHQGLSS", "48.7"], ["1561.7668", "0.7", "b13", "2", "SGTASVVCLLNNF_SS_VYACEVTHQGLSSPVTK", "26"], ["1577.3018", "3.3", "y11", "2", "VVCLLNNFYPR_SS_VYACEVTHQGLSSPVTK", "22.8"], ["1612.3059", "4.1", "y12-NH3", "2", "SVVCLLNNFYPR_SS_VYACEVTHQGLSSPVTK", "18.7"], ["1625.7781", "1.8", "b14-H5NO", "2", "SGTASVVCLLNNFY_SS_VYACEVTHQGLSSPVTK", "6.9"], ["1629.3011", "0.6", "a14", "2", "SGTASVVCLLNNFY_SS_VYACEVTHQGLSSPVTK", "6.6"], ["1634.7865", "0.1", "b14-NH3", "2", "SGTASVVCLLNNFY_SS_VYACEVTHQGLSSPVTK", "15.6"], ["1641.3032", "2.8", "a(2)15", "2", "SGTASVVCLLNNFYPR_SS_VYACEVTHQGLSSPV", "18.2"], ["1643.2998", "0.1", "b14", "2", "SGTASVVCLLNNFY_SS_VYACEVTHQGLSSPVTK", "55.1"], ["1646.7877", "2.6", "b(2)15-NH3", "2", "SGTASVVCLLNNFYPR_SS_VYACEVTHQGLSSPV", "30.1"], ["1655.3022", "1.8", "b(2)15", "2", "SGTASVVCLLNNFYPR_SS_VYACEVTHQGLSSPV", "86.6"], ["1696.8263", "1.5", "b(2)16-H2O", "2", "SGTASVVCLLNNFYPR_SS_VYACEVTHQGLSSPVT", "22.1"], ["1705.8307", "1", "b(2)16", "2", "SGTASVVCLLNNFYPR_SS_VYACEVTHQGLSSPVT", "31.8"], ["1b", "double C-N cleavage in one peptide", "1533.7521", "3.1", "int5-15", "2", "SVVCLLNNFYP_SS_VYACEVTHQGLSSPVTK", "13.1"], ["1c", "double C-N cleavage in both peptides", "1306.1199", "4.1", "[b(2)13-y10]", "2", "VYACEVTHQGLSS_SS_VCLLNNFYPR", "8.1"], ["1329.6398", "1.2", "[a14:b(2)11]", "2", "SGTASVVCLLNNFY_SS_VYACEVTHQGL", "7"], ["1373.158", "2.8", "[a14:b(2)12]", "2", "SGTASVVCLLNNFY_SS_VYACEVTHQGLS", "44.1"], ["1404.179", "4.9", "[b(2)14:y11]", "2", "VYACEVTHQGLSSP_SS_VVCLLNNFYPR", "11"], ["cleaved disulfide bond fragments", "2a", "C-S cleavage", "892.9614", "1.2", "y(2)17-H2S", "2", "VYACEVTHQGLSSPVTK", "3.5"], ["925.9394", "3.3", "y(2)17 + S", "2", "VYACEVTHQGLSSPVTK", "11.2"], ["1456.7136", "4.1", "y12 + S", "1", "SVVCLLNNFYPR", "8.2"], ["1772.8417", "2.3", "y16 + S", "1", "SGTASVVCLLNNFYPR", "17.1"], ["1850.8861", "4.6", "y(2)17 + S", "1", "VYACEVTHQGLSSPVTK", "10.1"], ["fragments without disulfide bond", "3a", "single C-N cleavage in both peptides", "435.2348", "0.6", "y3", "1", "YPR", "7.5"], ["444.2815", "0.4", "y(2)4", "1", "PVTK", "12.8"], ["531.3135", "0.4", "y(2)5", "1", "SPVTK", "7.3"], ["582.3021", "2.3", "y4", "1", "FYPR", "10"], ["618.3459", "0.3", "y(2)6", "1", "SSPVTK", "8.8"], ["696.3465", "0.2", "y5", "1", "NFYPR", "18.5"], ["788.4503", "1.2", "y(2)8", "1", "GLSSPVTK", "21.2"], ["810.3889", "0.5", "y6", "1", "NNFYPR", "51.8"], ["899.4845", "1.4", "y(2)9-NH3", "1", "QGLSSPVTK", "13.5"], ["916.511", "1.3", "y(2)9", "1", "QGLSSPVTK", "12"], ["923.4728", "0.6", "y7", "1", "LNNFYPR", "40.9"], ["1036.5577", "0.3", "y8", "1", "LLNNFYPR", "29.9"], ["1053.5677", "1", "y(2)10", "1", "HQGLSSPVTK", "23"], ["1154.6155", "0.8", "y(2)11", "1", "THQGLSSPVTK", "44.5"], ["1382.7231", "3.1", "y(2)13", "1", "EVTHQGLSSPVTK", "11.5"]], "row_count": 56, "column_count": 9, "numeric_cells": 271, "header_rows": 1, "locator": "section[27]/table-wrap[1]#tbl3"}}], "gaps": ["asset:data:geo:PXD023358 not downloaded", "asset:data:geo:PXD023358 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": null, "specific": null, "label": "Median value of RT range", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "In this study, the median value of RT range for specific experiments is used in a discriminant filter to remove unrelated identifications."}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "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": "blocked", "tier": "R4", "blocking_axis": "method", "blocked_on": "method:not_determinable", "axes": {"method": {"tier": "R4", "expressible": false, "required_operations": [], "missing_operations": [], "basis": "The reader quoted the method the paper names (Median value of RT range), but the corpus's method extractor could not map it onto a DSL operation, so the method is published but not expressible."}, "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": ["PXD023358"], "resolved_accessions": ["PXD023358"], "statements": ["Data are available via ProteomeXchange with identifier PXD023358."], "basis": "The paper names PXD023358 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": [], "assets": ["source:pmid:33555887", "data:geo:PXD023358", "asset:table:pmid:33555887:1", "asset:table:pmid:33555887:2", "asset:table:pmid:33555887:3", "asset:table:pmid:33555887:4"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:PXD023358"]}, "gaps": ["method:not_determinable"]}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:26:52Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 51096, "completion_tokens": 1465, "cached_tokens": 792}}, "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:33555887", "type": "paper", "label": "pmid:33555887"}, {"id": "source:pmid:33555887", "type": "manuscript", "label": "PMID 33555887 full text"}, {"id": "data:geo:PXD023358", "type": "dataset", "label": "GEO PXD023358"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:33555887", "type": "paper", "label": "pmid:33555887"}, {"id": "source:pmid:33555887", "type": "manuscript", "label": "PMID 33555887 full text"}, {"id": "data:geo:PXD023358", "type": "dataset", "label": "GEO PXD023358"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-33555887", "type": "extraction", "used": ["source:pmid:33555887"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-PXD023358", "type": "accession_resolution", "used": ["data:geo:PXD023358"], "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:33555887", "parent_hash": "sha256:12712e996c7704f388a88b002294ace58c91a88ea986377d6802046322e800ab", "fork_of": null, "generation": 5}, "gaps": ["asset:data:geo:PXD023358 licence not read", "asset:data:geo:PXD023358 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "mass_spectrometry", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["wed by nanoflow liquid chromatography tandem mass spectrometry (LC-MS/MS). Spectra of peptides containing d", "uid chromatography tandem mass spectrometry (LC-MS/MS). Spectra of peptides containing disulfide b", "ing the completeness of protein reduction in proteomics studies. Data are available via ProteomeXcha"], "order_basis": "paper_text_order:472", "id": "assay:1"}, {"role": "data_generation", "definition_id": "animal_model", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["production lot of NISTmAb 8671 expressed in murine suspension culture.4 It was obtained from th", "ate production lot of NISTmAb 8671 expressed in murine suspension culture.4 It was obtained from th"], "order_basis": "paper_text_order:2416", "id": "assay:2"}]},"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":"2026-11-04T02:37:21+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}}}