A Catalog of Proteins Expressed in the AG Secreted Fluid during the Mature Phase of the Chinese Mitten Crabs (Eriocheir sinensis).

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:26305468", "kind": "science-record", "revision": 3, "content_hash": "sha256:02bbf78875a734b332e76cb601cca6781b770948170d4d71602c41cbdd8505b3", "created_at": "2026-11-01T15:40:10Z", "updated_at": "2026-11-01T18:47:30Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "A Catalog of Proteins Expressed in the AG Secreted Fluid during the Mature Phase of the Chinese Mitten Crabs (Eriocheir sinensis).", "doi": "10.1371/journal.pone.0136266", "pmid": "26305468", "authors": ["Lin He", "Qing Li", "Lihua Liu", "Yuanli Wang", "Jing Xie", "Hongdan Yang", "Qun Wang"], "journal": "PloS one", "year": 2015, "abstract": "The accessory gland (AG) is an important component of the male reproductive system of arthropods, its secretions enhance fertility, some AG proteins bind to the spermatozoa and affect its function and properties. Here we report the first comprehensive catalog of the AG secreted fluid during the mature phase of the Chinese mitten crab (Eriocheir sinensis). AG proteins were separated by one-dimensional gel electrophoresis and analyzed by reverse phase high-performance liquid chromatography coupled with tandem mass spectrometry (HPLC-MS/MS). Altogether, the mass spectra of 1173 peptides were detected (1067 without decoy and contaminants) which allowed for the identification of 486 different proteins annotated upon the NCBI database (http://www.ncbi.nlm.nih.gov/) and our transcritptome dataset. The mass spectrometry proteomics data have been deposited at the ProteomeXchange with identifier PXD000700. An extensive description of the AG proteome will help provide the basis for a better understanding of a number of reproductive mechanisms, including potentially spermatophore breakdown, dynamic functional and morphological changes in sperm cells and sperm acrosin enzyme vitality. Thus, the comprehensive catalog of proteins presented here can serve as a valuable reference for future studies of sperm maturation and regulatory mechanisms involved in crustacean reproduction.", "claims": [{"id": "claim-data-access", "statement": "The mass spectrometry proteomics data have been deposited at the ProteomeXchange with identifier PXD000700.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26305468", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The mass spectrometry proteomics data have been deposited at the ProteomeXchange with identifier PXD000700."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study used Mascot target–decoy database searching with peptide identifications accepted at a false-positive rate below 1% and p<0.05, identified 486 accessory-gland proteins from 1,067 peptides after excluding decoys and contaminants, and deposited the mass-spectrometry proteomics data in ProteomeXchange under identifier PXD000700.", "kind": "quantitative", "target": {"value": 1.0, "unit": "per cent", "tolerance": null, "source": "Protein searches were performed with Mascot 2.2.07 software (www.matrixscience.com) against the constructed database. The acceptance criterion for peptide identifications was a false positive identification rate of less than 1%."}, "evidence": [{"asset": "source:pmid:26305468", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Altogether, the mass spectra of 1173 peptides were detected (1067 without decoy and contaminants) which allowed for the identification of 486 different proteins annotated upon the NCBI database (http://www.ncbi.nlm.nih.gov/) and our transcritptome dataset."}, {"asset": "source:pmid:26305468", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The mass spectrometry proteomics data have been deposited at the ProteomeXchange with identifier PXD000700."}, {"asset": "source:pmid:26305468", "locator": "sections[6] \"Protein database construction and searches\" paragraph 2", "quote": "Protein searches were performed with Mascot 2.2.07 software (www.matrixscience.com) against the constructed database. The acceptance criterion for peptide identifications was a false positive identification rate of less than 1%."}, {"asset": "source:pmid:26305468", "locator": "sections[6] \"Protein database construction and searches\" paragraph 2", "quote": "Peptide identifications with a minimum peptide length of 6 amino acids, Mascot peptide identification score ≥60 and significant for peptide mass fingerprint with a p<0.05 were considered valid."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The study used Mascot target–decoy database searching with peptide identifications accepted at a false-positive rate below 1% and p<0.05, identified 486 accessory-gland proteins from 1,067 peptides after excluding decoys and contaminants, and deposited the mass-spectrometry proteomics data in ProteomeXchange under identifier PXD000700.", "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:26305468"], "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:PXD000700"], "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:PXD000700"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:26305468", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1371/journal.pone.0136266", "sha256": "sha256:3d1701b684546bdaa2eb3713950a93c2b9583aa824a09472e9e6351c300ada8a", "bytes": 40432, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1371/journal.pone.0136266", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC4549300", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PXD000700", "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=PXD000700", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD000700", "version": null, "note": "The mass spectrometry proteomics data have been deposited at the ProteomeXchange with identifier PXD000700.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The mass spectrometry proteomics data have been deposited at the ProteomeXchange with identifier PXD000700.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "Proteomic analysis of accessory gland in sexually mature Eriocheir sinensis", "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:26305468:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:ce8a11e21d02512dd796440801014cf13e87a303279c645e129b3c382b7b2926", "bytes": 233, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[1]#pone.0136266.t001", "version": null, "note": "Important proteins function in reproduction in E. sinensis (selected).", "structure": {"pmcid": "PMC4549300", "section_index": 12, "section_title": "AG proteins related to reproductive processes", "row_count": 0, "column_count": 0}, "table": {"label": "Table 1", "caption": "Important proteins function in reproduction in E. sinensis (selected).", "rows": [], "row_count": 0, "column_count": 0, "numeric_cells": 0, "header_rows": 0, "locator": "section[12]/table-wrap[1]#pone.0136266.t001"}}], "gaps": ["asset:data:geo:PXD000700 not downloaded", "asset:data:geo:PXD000700 licence not read"]}, "analysis": {"state": "absent", "methods": [], "targets": [{"id": "target-published-estimate", "claim_id": "claim-target-result", "operation": null, "expected_value": 1.0, "unit": "per cent", "tolerance": null, "state": "complete", "note": "The published estimate as the reader quoted it from the paper. No tolerance is published because the paper states none."}, {"id": "target-published-estimate-p-value", "claim_id": "claim-target-result", "operation": null, "expected_value": 0.05, "unit": "p-value", "tolerance": null, "state": "complete", "note": "The threshold the paper applied to its own result, as the paper states it. A run that reproduces the effect is judged against this threshold."}], "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. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["PXD000700"], "resolved_accessions": ["PXD000700"], "statements": ["The mass spectrometry proteomics data have been deposited at the ProteomeXchange with identifier PXD000700."], "basis": "The paper names PXD000700 in ProteomeXchange and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:26305468", "data:geo:PXD000700", "asset:table:pmid:26305468:1"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:PXD000700"]}, "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": "2026-10-31T18:24:35Z", "independence": "same_provider"}, "evidence_check": {"method": null, "availability": "verbatim"}, "calls": 8, "usage": {"prompt_tokens": 73595, "completion_tokens": 3584, "cached_tokens": 19464}}, "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:26305468", "type": "paper", "label": "pmid:26305468"}, {"id": "source:pmid:26305468", "type": "manuscript", "label": "PMID 26305468 full text"}, {"id": "data:geo:PXD000700", "type": "dataset", "label": "GEO PXD000700"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:26305468", "type": "paper", "label": "pmid:26305468"}, {"id": "source:pmid:26305468", "type": "manuscript", "label": "PMID 26305468 full text"}, {"id": "data:geo:PXD000700", "type": "dataset", "label": "GEO PXD000700"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-26305468", "type": "extraction", "used": ["source:pmid:26305468"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-PXD000700", "type": "accession_resolution", "used": ["data:geo:PXD000700"], "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:26305468", "parent_hash": "sha256:01ec3ce7c420d9d9490905d9db22f71b9b34b7381d6cd6a4b8ad68033cde6f46", "fork_of": null, "generation": 2}, "gaps": ["asset:data:geo:PXD000700 licence not read", "asset:data:geo:PXD000700 not downloaded", "execution.not_run", "method", "operations", "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": ["ce liquid chromatography coupled with tandem mass spectrometry (HPLC-MS/MS). Altogether, the mass spectra o", "ih.gov/) and our transcritptome dataset. The mass spectrometry proteomics data have been deposited at the P", "ranscritptome dataset. The mass spectrometry proteomics data have been deposited at the ProteomeXcha"], "order_basis": "paper_text_order:599", "id": "assay:1"}]}