The Plantain Proteome, a Focus on Allele Specific Proteins Obtained from Plantain Fruits.

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Plantains are a kind of cooking bananas that are economically very important in Africa, India, and Latin America. The aim of this work was to characterize the fruit proteome of common dessert bananas and plantains and to identify proteins that are only encoded by the plantain genome. We present the first plantain fruit proteome. All data are available via ProteomeXchange with identifier PXD005589. Using our in-house workflow, we found 37 alleles to be unique for plantain covered by 59 peptides. Although we do not have access (yet) to whole-genome sequencing data from triploid banana cultivars, we show that proteomics is an easily accessible complementary alternative to detect different allele specific SNPs/SAAPs. These unique alleles might contribute toward the differences in the metabolism between dessert bananas and plantains. This dataset will stimulate further analysis by the scientific community, boost plantain research, and facilitate plantain breeding.", "claims": [{"id": "claim-method", "statement": "In Scaffold, the threshold was set to minimum one peptide identified with 95% confidence and the false discovery rate (FDR) was automatically calculated based on default parameters from the software.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29333696", "locator": "sections[3] \"p\" paragraph 1", "quote": "In Scaffold, the threshold was set to minimum one peptide identified with 95% confidence and the false discovery rate (FDR) was automatically calculated based on default parameters from the software."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All data are available via ProteomeXchange with identifier PXD005589.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29333696", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "All data are available via ProteomeXchange with identifier PXD005589."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The paper presents the first plantain fruit proteome and reports 37 plantain-specific alleles covered by 59 peptides using spectral counting, with the mass-spectrometry data available through ProteomeXchange/PRIDE under identifier PXD005589.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:29333696", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "We present the first plantain fruit proteome."}, {"asset": "source:pmid:29333696", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Using our in‐house workflow, we found 37 alleles to be unique for plantain covered by 59 peptides."}, {"asset": "source:pmid:29333696", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "All data are available via ProteomeXchange with identifier PXD005589."}, {"asset": "source:pmid:29333696", "locator": "sections[4] \"p\" paragraph 1", "quote": "To find allele specific peptides in plantain fruits, we used a basic but very useful principle: spectral counting (Scaffold)."}, {"asset": "source:pmid:29333696", "locator": "sections[1] \"p\" paragraph 1", "quote": "The mass spectrometry proteomics data have been deposited at the ProteomeXchange Consortium Partner Repository10 via PRIDE11 with the dataset identifier PXD005589."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The paper presents the first plantain fruit proteome and reports 37 plantain-specific alleles covered by 59 peptides using spectral counting, with the mass-spectrometry data available through ProteomeXchange/PRIDE under identifier PXD005589.", "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:29333696"], "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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