Dataset for the proteomic and transcriptomic analyses of perivitelline fluid proteins in Pomacea snail eggs.

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The data are related to a research article titled 'An integrated proteomic and transcriptomic analysis of perivitelline fluid proteins in a freshwater gastropod laying aerial eggs' (Mu et al., 2017) [1]. RNA was extracted from the albumen gland and other tissues and sequenced on an Illumina Hiseq. 2000. The assembled transcriptome was translated into protein sequences and then used for protein identification. Proteins from the perivitelline fluid of P. maculata were separated in SDS-PAGE and analyzed by LTQ-Orbitrap Elite coupled to an Easy-nLC. The translated transcriptome data are provided in this article. Proteomic data (.raw file format) are available via ProteomeXchange with the identifier PXD006718.", "claims": [{"id": "claim-method", "statement": "Peptides which had more than nine amino acids were retained and 1% of false discovery rate threshold was adopted in the protein identification.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29021998", "locator": "sections[10] \"Protein identification\" paragraph 2", "quote": "Peptides which had more than nine amino acids were retained and 1% of false discovery rate threshold was adopted in the protein identification."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Proteomic data (.raw file format) are available via ProteomeXchange with the identifier PXD006718.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29021998", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Proteomic data (.raw file format) are available via ProteomeXchange with the identifier PXD006718."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Protein identification used Mascot with peptide acceptance at an ion score ≥22 and a 1% false discovery rate, retaining proteins with at least three matched peptides detected in at least two replicates; the raw MS/MS files are available through ProteomeXchange under identifier PXD006718.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:29021998", "locator": "sections[10] \"Protein identification\" paragraph 2", "quote": "The raw MS/MS files were converted into.mgf files (Raw data are available via ProteomeXchange with identifier PXD006718) using Proteome Discovery 1.3.0.339, and searched against the P. maculata database with 77584 protein sequences containing both ‘decoy’ and ‘target’ sequences using Mascot version 2.3.2."}, {"asset": "source:pmid:29021998", "locator": "sections[10] \"Protein identification\" paragraph 2", "quote": "Peptides having an ion score ≥22 (corresponding to 95% confidence) were kept. Peptides which had more than nine amino acids were retained and 1% of false discovery rate threshold was adopted in the protein identification. Proteins which had at least three matched peptides and were detected in at least two replicates were kept."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Protein identification used Mascot with peptide acceptance at an ion score ≥22 and a 1% false discovery rate, retaining proteins with at least three matched peptides detected in at least two replicates; the raw MS/MS files are available through ProteomeXchange under identifier PXD006718.", "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:29021998"], "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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