Peptidome profiling dataset of ovarian cancer and non-cancer proximal fluids: Ascites and blood sera.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:30627607", "kind": "science-record", "revision": 3, "content_hash": "sha256:a905257cfcd345501cc7872e8fe9b819ba51b40a74bf54d06074e8a89ed8ca0f", "created_at": "2026-11-01T15:40:40Z", "updated_at": "2026-11-01T18:50:13Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Peptidome profiling dataset of ovarian cancer and non-cancer proximal fluids: Ascites and blood sera.", "doi": "10.1016/j.dib.2018.12.056", "pmid": "30627607", "authors": ["Victoria Shender", "Georgij Arapidi", "Ivan Butenko", "Nikolay Anikanov", "Olga Ivanova", "Vadim Govorun"], "journal": "Data in brief", "year": 2019, "abstract": "Despite a large number of proteomic studies of biological fluids from ovarian cancer patients, there is a lack of sensitive screening methods in clinical practice (Kim et al., 2016) (DOI:https://doi.org/10.1111/cas.12987[1]). Low molecular weight endogenous peptides more easily diffuse across endothelial barriers than proteins and can be more relevant biomarker candidates (Meo et al., 2016) (DOI:https://doi.org/10.18632/oncotarget.8931[2], (Bery et al., 2014) DOI:https://doi.org/10.1186/1559-0275-11-13[3], (Huang et al., 2018) DOI:https://doi.org/10.1097/IGC.0000000000001166[4]). Detailed peptidomic analysis of 26 ovarian cancer and 15 non-cancer samples of biological fluids (ascites and sera) were performed using TripleTOF 5600+ mass-spectrometer. Prior to LC-MS/MS analysis, peptides were extracted from biological fluids using anion exchange sorbent with subsequent peptide desorption from the surface of highly abundant proteins. In total, we identified 4874 peptides; 3123 peptides were specific for the ovarian cancer samples. The mass-spectrometry peptidomics data presented in this data article have been deposited to the ProteomeXchange Consortium (Deutsch et al., 2017) (DOI:https://doi.org/10.1093/nar/gkw936[5]) via the PRIDE partner repository with the dataset identifier PXD009382 and https://doi.org/10.6019/PXD009382, http://www.ebi.ac.uk/pride/archive/projects/PXD009382.", "claims": [{"id": "claim-data-access", "statement": "Data accessibilityData are with this article. The LC-MS/MS data have been deposited to the ProteomeXchange Consortium via the PRIDE [6] partner repository with the dataset identifier PXD009382 and 10.6019/PXD009382.Direct download link: http://www.ebi.ac.uk/pride/archive/projects/PXD009382", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30627607", "locator": "sections[1] \"p\" paragraph 1", "quote": "Data accessibilityData are with this article. 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The LC-MS/MS data have been deposited to the ProteomeXchange Consortium via the PRIDE [6] partner repository with the dataset identifier PXD009382 and 10.6019/PXD009382.Direct download link: http://www.ebi.ac.uk/pride/archive/projects/PXD009382", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "Peptidome profiling of ovarian cancer and non-cancer proximal fluids: ascites and blood sera", "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:30627607:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:b8b05f98f447da1700ad74dd4f6a45e80e50ccffa0504dfcc56893821ca37671", "bytes": 1509, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[1]/table-wrap[1]#t0015", "version": null, "note": null, "structure": {"pmcid": "PMC6321966", "section_index": 1, "section_title": "p", "row_count": 12, "column_count": 2}, "table": {"label": null, "caption": null, "rows": [["Subject area", "Biochemistry"], ["More specific subject area", "Peptidomics, Ovarian Cancer Biomarkers"], ["Type of data", "Table, LC-MS/MS data and identification data"], ["How data were acquired", "Peptides were analyzed on a TripleTOF 5600+ mass spectrometer with a NanoSpray III ion source (Sciex, Canada) coupled with a NanoLC Ultra 2D+ nano-HPLC system (Eksigent, USA)"], ["Data format", "Raw and analyzed data"], ["Experimental factors", "6 ovarian cancer and 5 cirrhosis ascites samples;"], ["Serum samples from 20 ovarian cancer patients;"], ["Serum samples from 10 healthy donors."], ["Experimental features", "Pools of 6 ovarian cancer ascites, 5 cirrhosis ascites, 10 serum samples from healthy donors and two pools of 10 ovarian cancer sera were fractionated using anion exchange QAE Sephadex A-25 sorbent and analyzed by LC-MS/MS."], ["Data source location", "Federal Research and Clinical Center of Physical Chemical Medicine of the Federal Medical and Biological Agency of the Russian Federation, Malaya Pirogovskaya 1a, Moscow 119435, Russian Federation."], ["Data accessibility", "Data are with this article. The LC-MS/MS data have been deposited to the ProteomeXchange Consortium via the PRIDE [6] partner repository with the dataset identifier PXD009382 and 10.6019/PXD009382."], ["Direct download link: http://www.ebi.ac.uk/pride/archive/projects/PXD009382"]], "row_count": 12, "column_count": 2, "numeric_cells": 8, "header_rows": 0, "locator": "section[1]/table-wrap[1]#t0015"}}, {"id": "asset:table:pmid:30627607:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:b8b05f98f447da1700ad74dd4f6a45e80e50ccffa0504dfcc56893821ca37671", "bytes": 1509, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[1]/table-wrap[1]#t0015", "version": null, "note": null, "structure": {"pmcid": "PMC6321966", "section_index": 2, "section_title": "p", "row_count": 12, "column_count": 2}, "table": {"label": null, "caption": null, "rows": [["Subject area", "Biochemistry"], ["More specific subject area", "Peptidomics, Ovarian Cancer Biomarkers"], ["Type of data", "Table, LC-MS/MS data and identification data"], ["How data were acquired", "Peptides were analyzed on a TripleTOF 5600+ mass spectrometer with a NanoSpray III ion source (Sciex, Canada) coupled with a NanoLC Ultra 2D+ nano-HPLC system (Eksigent, USA)"], ["Data format", "Raw and analyzed data"], ["Experimental factors", "6 ovarian cancer and 5 cirrhosis ascites samples;"], ["Serum samples from 20 ovarian cancer patients;"], ["Serum samples from 10 healthy donors."], ["Experimental features", "Pools of 6 ovarian cancer ascites, 5 cirrhosis ascites, 10 serum samples from healthy donors and two pools of 10 ovarian cancer sera were fractionated using anion exchange QAE Sephadex A-25 sorbent and analyzed by LC-MS/MS."], ["Data source location", "Federal Research and Clinical Center of Physical Chemical Medicine of the Federal Medical and Biological Agency of the Russian Federation, Malaya Pirogovskaya 1a, Moscow 119435, Russian Federation."], ["Data accessibility", "Data are with this article. The LC-MS/MS data have been deposited to the ProteomeXchange Consortium via the PRIDE [6] partner repository with the dataset identifier PXD009382 and 10.6019/PXD009382."], ["Direct download link: http://www.ebi.ac.uk/pride/archive/projects/PXD009382"]], "row_count": 12, "column_count": 2, "numeric_cells": 8, "header_rows": 0, "locator": "section[1]/table-wrap[1]#t0015"}}, {"id": "asset:table:pmid:30627607:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:89df85b2aa6e8e9bbba728f9736f9776d728db280dc68cdd65ba57e90e4c61c3", "bytes": 788, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[3]/table-wrap[1]#t0005", "version": null, "note": "Characteristics of analyzed samples in each group.", "structure": {"pmcid": "PMC6321966", "section_index": 3, "section_title": "Data", "row_count": 7, "column_count": 4}, "table": {"label": "Table 1", "caption": "Characteristics of analyzed samples in each group.", "rows": [["Biomaterial type", "Pools", "Number of samples", "Number of replicates"], ["Ovarian Cancer Ascites", "Pool 1", "3 Ovarian Cancer patients after chemotherapy", "2 replicates"], ["Pool 2", "3 Ovarian Cancer patients after chemotherapy", "2 replicates"], ["Cirrhosis Ascites", "Pool 1", "5 female patients with Portal Alcoholic Cirrhosis", "2 replicates"], ["Ovarian Cancer Sera", "Pool 1", "10 Ovarian Cancer patients after chemotherapy", "1 replicate"], ["Pool 2", "10 Ovarian Cancer patients after chemotherapy", "2 replicates"], ["Healthy Donors’ Sera", "Pool 1", "10 female healthy donors", "2 replicates"]], "row_count": 7, "column_count": 4, "numeric_cells": 18, "header_rows": 1, "locator": "section[3]/table-wrap[1]#t0005"}}, {"id": "asset:table:pmid:30627607:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:7b106d4194f44ee073b61fc2c5e885066104059177aea90a72d8c07659de79c5", "bytes": 463, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[3]/table-wrap[2]#t0010", "version": null, "note": "Number of identified peptides and precursor proteins.", "structure": {"pmcid": "PMC6321966", "section_index": 3, "section_title": "Data", "row_count": 6, "column_count": 3}, "table": {"label": "Table 2", "caption": "Number of identified peptides and precursor proteins.", "rows": [["Sample group", "Number of identified peptides", "Number of precursor proteins"], ["Ovarian Cancer Ascites", "2876", "330"], ["Cirrhosis Ascites", "513", "125"], ["Ovarian Cancer Sera", "2082", "229"], ["Healthy Donors׳ Sera", "1452", "285"], ["Total Number", "4874", "597"]], "row_count": 6, "column_count": 3, "numeric_cells": 10, "header_rows": 1, "locator": "section[3]/table-wrap[2]#t0010"}}], "gaps": ["asset:data:geo:PXD009382 not downloaded", "asset:data:geo:PXD009382 licence not read"]}, "analysis": {"state": "absent", "methods": [], "targets": [], "gaps": ["method", "operations"]}, "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 (not named), 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. 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