Proteomic characterization of fresh spermatozoa and supernatant after cryopreservation in relation to freezability of carp (Cyprinus carpio L) semen.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:29565997", "kind": "science-record", "revision": 7, "content_hash": "sha256:fa67ce51c03a2abfdef4d44721c8dea9831057fde1947f410c66f009396f6ac7", "created_at": "2026-11-01T15:40:32Z", "updated_at": "2026-11-01T21:59:46Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Proteomic characterization of fresh spermatozoa and supernatant after cryopreservation in relation to freezability of carp (Cyprinus carpio L) semen.", "doi": "10.1371/journal.pone.0192972", "pmid": "29565997", "authors": ["Mariola A Dietrich", "Andrzej Ciereszko"], "journal": "PloS one", "year": 2018, "abstract": "Our recent studies suggested that the freezability of carp semen is related to seminal plasma protein profiles. Here, we aimed to compare the spermatozoa proteomes of good (GF) and poor (PF) freezability semen of carp. To achieve this, we used two-dimensional difference in gel electrophoresis followed by MALDI-TOF/TOF mass spectrometry. The semen was classified as GF or PF based on sperm motility after freeze/thawing. We identified proteins enriched in spermatozoa of GF (22 proteins) and PF (18 proteins) semen. We also identified 12 proteins enriched in the supernatant after cryopreservation of PF semen. Good freezability is related to high concentrations of proteins involved in the maintenance of flagella structure, membrane fluidity, efficient control of Ca2+ and sperm motility, energy production, and antioxidative protection, which likely reflects the full maturation status of spermatozoa of GF semen. On the other hand poor freezability seems to be related to the presence of proteins identified as released in high quantities from cryopreserved sperm of PF. Thus, the identified proteins might be useful bioindicators of freezing resilience and could be used to screen carp males before cryopreservation, thus improve long-term sperm preservation in carp. Data are available via ProteomeXchange with identifier PXD008187.", "claims": [{"id": "claim-method", "statement": "Fisher’s exact test and Benjamini-Hochberg multiple testing corrections were used to calculate the significance (p ≤ 0.05) of functional and canonical pathways of proteins involved in sperm motility.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29565997", "locator": "sections[8] \"Ingenuity pathway and STRING analyses\" paragraph 2", "quote": "Fisher’s exact test and Benjamini-Hochberg multiple testing corrections were used to calculate the significance (p ≤ 0.05) of functional and canonical pathways of proteins involved in sperm motility."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Data are available via ProteomeXchange with identifier PXD008187.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29565997", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Data are available via ProteomeXchange with identifier PXD008187."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Using 2D-DIGE followed by MALDI-TOF/TOF mass spectrometry with a significance criterion of p<0.05, the study identified 22 proteins enriched in spermatozoa of good-freezability semen, 18 enriched in spermatozoa of poor-freezability semen, and 12 enriched in the supernatant after cryopreservation of poor-freezability semen; the source proteomics data are available through ProteomeXchange under PXD008187.", "kind": "quantitative", "target": {"value": 1.1, "unit": "fold change", "tolerance": null, "source": "The analysis of spermatozoa proteins from good and poor freezability semen using quantitative 2D-DIGE technology led to the detection of 1,555 matched spots, of which 54 spots had significantly difference abundances (>1.1-fold change, p<0.05) between GF and PF (Fig 1A and 1B)."}, "evidence": [{"asset": "source:pmid:29565997", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "To achieve this, we used two-dimensional difference in gel electrophoresis followed by MALDI-TOF/TOF mass spectrometry."}, {"asset": "source:pmid:29565997", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "We identified proteins enriched in spermatozoa of GF (22 proteins) and PF (18 proteins) semen. We also identified 12 proteins enriched in the supernatant after cryopreservation of PF semen."}, {"asset": "source:pmid:29565997", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Data are available via ProteomeXchange with identifier PXD008187."}, {"asset": "source:pmid:29565997", "locator": "sections[11] \"Comparison of fresh spermatozoa proteome of good and poor freezability semen\" paragraph 2", "quote": "The analysis of spermatozoa proteins from good and poor freezability semen using quantitative 2D-DIGE technology led to the detection of 1,555 matched spots, of which 54 spots had significantly difference abundances (>1.1-fold change, p<0.05) between GF and PF (Fig 1A and 1B)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Using 2D-DIGE followed by MALDI-TOF/TOF mass spectrometry with a significance criterion of p<0.05, the study identified 22 proteins enriched in spermatozoa of good-freezability semen, 18 enriched in spermatozoa of poor-freezability semen, and 12 enriched in the supernatant after cryopreservation of poor-freezability semen; the source proteomics data are available through ProteomeXchange under PXD008187.", "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:29565997"], "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:PXD008187"], "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:PXD008187"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:29565997", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1371/journal.pone.0192972", "sha256": "sha256:fe7d1bd21f125a84aaeaa47da8373b0c46e6ef6db85d57b10d5c9f8d2e9ec2e7", "bytes": 44341, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1371/journal.pone.0192972", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC5863941", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PXD008187", "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=PXD008187", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD008187", "version": null, "note": "Data are available via ProteomeXchange with identifier PXD008187.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data are available via ProteomeXchange with identifier PXD008187.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "Proteomic characterization of fresh spermatozoa and supernatant after cryopreservation in relation to freezability of carp (Cyprinus carpio) semen", "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:29565997:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:bf56053e38846335c1fe37210e303be6b95d7bb47d99f47c709d830739cc6ae1", "bytes": 258, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[11]/table-wrap[1]#pone.0192972.t001", "version": null, "note": "Proteins of carp spermatozoa differentially expressed between good and poor freezability semen.", "structure": {"pmcid": "PMC5863941", "section_index": 11, "section_title": "Comparison of fresh spermatozoa proteome of good and poor freezability semen", "row_count": 0, "column_count": 0}, "table": {"label": "Table 1", "caption": "Proteins of carp spermatozoa differentially expressed between good and poor freezability semen.", "rows": [], "row_count": 0, "column_count": 0, "numeric_cells": 0, "header_rows": 0, "locator": "section[11]/table-wrap[1]#pone.0192972.t001"}}, {"id": "asset:table:pmid:29565997:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:3204101ceca61deaf1eb6b69a1ec0968bd30acf676fc04dc6755148c5b37d478", "bytes": 255, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[1]#pone.0192972.t002", "version": null, "note": "Proteins more abundant in the supernatant after cryopreservation of poor freezability semen.", "structure": {"pmcid": "PMC5863941", "section_index": 12, "section_title": "Comparison of supernatant after cryopreservation of good and poor freezability semen", "row_count": 0, "column_count": 0}, "table": {"label": "Table 2", "caption": "Proteins more abundant in the supernatant after cryopreservation of poor freezability semen.", "rows": [], "row_count": 0, "column_count": 0, "numeric_cells": 0, "header_rows": 0, "locator": "section[12]/table-wrap[1]#pone.0192972.t002"}}, {"id": "asset:table:pmid:29565997:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:2762ff5766df478f2d86bb291718a8db06e69cb36abb2145d21905a47beae744", "bytes": 244, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[13]/table-wrap[1]#pone.0192972.t003", "version": null, "note": "IPA analysis overview of differentially abundant sperm proteins of good and poor.", "structure": {"pmcid": "PMC5863941", "section_index": 13, "section_title": "Ingenuity pathway analysis of the differentially abundant proteins", "row_count": 0, "column_count": 0}, "table": {"label": "Table 3", "caption": "IPA analysis overview of differentially abundant sperm proteins of good and poor.", "rows": [], "row_count": 0, "column_count": 0, "numeric_cells": 0, "header_rows": 0, "locator": "section[13]/table-wrap[1]#pone.0192972.t003"}}], "gaps": ["asset:data:geo:PXD008187 not downloaded", "asset:data:geo:PXD008187 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "network_analysis", "specific": "ppi_network", "label": "Network / pathway analysis", "dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.8, "band": "high", "quote": "Protein-protein interaction"}}, {"id": "method-2", "family": null, "specific": null, "label": "Fisher’s exact test with Benjamini–Hochberg multiple-testing correction", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Fisher’s exact test and Benjamini-Hochberg multiple testing corrections were used to calculate the significance (p ≤ 0.05) of functional and canonical pathways of proteins involved in sperm motility."}}], "targets": [{"id": "target-published-estimate", "claim_id": "claim-target-result", "operation": "build_graph", "expected_value": 1.1, "unit": "fold change", "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": "build_graph", "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.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": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: ppi_network."}, "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": ["PXD008187"], "resolved_accessions": ["PXD008187"], "statements": ["Data are available via ProteomeXchange with identifier PXD008187."], "basis": "The paper names PXD008187 in ProteomeXchange Consortium and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "assets": ["source:pmid:29565997", "data:geo:PXD008187", "asset:table:pmid:29565997:1", "asset:table:pmid:29565997:2", "asset:table:pmid:29565997:3"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:PXD008187"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:34:02Z", "independence": "same_provider"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 8, "usage": {"prompt_tokens": 84309, "completion_tokens": 4672, "cached_tokens": 21792}}, "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:29565997", "type": "paper", "label": "pmid:29565997"}, {"id": "source:pmid:29565997", "type": "manuscript", "label": "PMID 29565997 full text"}, {"id": "data:geo:PXD008187", "type": "dataset", "label": "GEO PXD008187"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:29565997", "type": "paper", "label": "pmid:29565997"}, {"id": "source:pmid:29565997", "type": "manuscript", "label": "PMID 29565997 full text"}, {"id": "data:geo:PXD008187", "type": "dataset", "label": "GEO PXD008187"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-29565997", "type": "extraction", "used": ["source:pmid:29565997"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-PXD008187", "type": "accession_resolution", "used": ["data:geo:PXD008187"], "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:29565997", "parent_hash": "sha256:e8fbb49121736c9b77ca4c0f87b008cb0fcd167123d2f5fafd68f258c8bc5ae7", "fork_of": null, "generation": 6}, "gaps": ["asset:data:geo:PXD008187 licence not read", "asset:data:geo:PXD008187 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": ["Proteomic characterization of fresh spermatozoa and su", "teoforms) of Pv (Fig 4A and 4B). As with the proteomic data, an increase (p ≤ 0.05) in the relative", "el electrophoresis followed by MALDI-TOF/TOF mass spectrometry. The semen was classified as GF or PF based"], "order_basis": "paper_text_order:0", "id": "assay:1"}, {"role": "data_generation", "definition_id": "western_blot", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["c reticulum stress. Validation of 2D-DIGE by Western blot analysis of parvalbumin Polyclonal antibodie", "entative Pv protein spot pattern of from the Western blot analysis. Validation of 2D-DIGE results by W", "t analysis. Validation of 2D-DIGE results by Western blotting using anti-parvalbumin (Pv) antibodies.Repre", "i-parvalbumin (Pv) antibodies.Representative Western blot of spermatozoa of good freezability (GF) sem"], "order_basis": "paper_text_order:8075", "id": "assay:2"}, {"role": "analysis", "definition_id": "network_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.8, "evidence": ["Protein-protein interaction"], "order_basis": "consumes_earlier_output", "id": "assay:3"}]}