A Proteogenomic Approach to Unravel New Proteins Encoded in the Leishmania donovani (HU3) Genome.

{"sci_version": "1.0", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38927711", "kind": "science-record", "revision": 1, "content_hash": "sha256:d5478c62377ab175abe95b8ccfcb46bb54f8942c4b0386c771ea98c6a66b78d7", "created_at": "2026-11-01T20:29:00Z", "updated_at": "2026-11-01T20:29:00Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "A Proteogenomic Approach to Unravel New Proteins Encoded in the Leishmania donovani (HU3) Genome.", "doi": "10.3390/genes15060775", "pmid": "38927711", "authors": ["Javier Adán-Jiménez", "Alejandro Sánchez-Salvador", "Esperanza Morato", "Jose Carlos Solana", "Begoña Aguado", "Jose M Requena"], "journal": "Genes", "year": 2024, "abstract": "The high-throughput proteomics data generated by increasingly more sensible mass spectrometers greatly contribute to our better understanding of molecular and cellular mechanisms operating in live beings. Nevertheless, proteomics analyses are based on accurate genomic and protein annotations, and some information may be lost if these resources are incomplete. Here, we show that most proteomics data may be recovered by interconnecting genomics and proteomics approaches (i.e., following a proteogenomic strategy), resulting, in turn, in an improvement of gene/protein models. In this study, we generated proteomics data from Leishmania donovani (HU3 strain) promastigotes that allowed us to detect 1908 proteins in this developmental stage on the basis of the currently annotated proteins available in public databases. However, when the proteomics data were searched against all possible open reading frames existing in the L. donovani genome, twenty new protein-coding genes could be annotated. Additionally, 43 previously annotated proteins were extended at their N-terminal ends to accommodate peptides detected in the proteomics data. Also, different post-translational modifications (phosphorylation, acetylation, methylation, among others) were found to occur in a large number of Leishmania proteins. Finally, a detailed comparative analysis of the L. donovani and Leishmania major experimental proteomes served to illustrate how inaccurate conclusions can be raised if proteomes are compared solely on the basis of the listed proteins identified in each proteome. Finally, we have created data entries (based on freely available repositories) to provide and maintain updated gene/protein models. Raw data are available via ProteomeXchange with the identifier PXD051920.", "claims": [{"id": "claim-data-access", "statement": "The data presented in this study are openly available in the Proteo-meXchange Consortium via the PRIDE partner repository at the dataset identifier PXD051920 and DOI: 10.6019/PXD051920.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38927711", "locator": "sections[22] \"Data Availability Statement\" paragraph 2", "quote": "The data presented in this study are openly available in the Proteo-meXchange Consortium via the PRIDE partner repository at the dataset identifier PXD051920 and DOI: 10.6019/PXD051920."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Proteogenomic analysis of L. donovani promastigotes identified 1,908 proteins, annotated 20 new protein-coding genes, extended 43 existing gene models, and detected multiple post-translational modifications.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:38927711", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "In this study, we generated proteomics data from Leishmania donovani (HU3 strain) promastigotes that allowed us to detect 1908 proteins in this developmental stage on the basis of the currently annotated proteins available in public databases."}, {"asset": "source:pmid:38927711", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "However, when the proteomics data were searched against all possible open reading frames existing in the L. donovani genome, twenty new protein-coding genes could be annotated."}, {"asset": "source:pmid:38927711", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Additionally, 43 previously annotated proteins were extended at their N-terminal ends to accommodate peptides detected in the proteomics data."}, {"asset": "source:pmid:38927711", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Also, different post-translational modifications (phosphorylation, acetylation, methylation, among others) were found to occur in a large number of Leishmania proteins."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "Proteogenomic analysis of L. donovani promastigotes identified 1,908 proteins, annotated 20 new protein-coding genes, extended 43 existing gene models, and detected multiple post-translational modifications.", "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:38927711"], "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": "blocked", "blocked_on": "data:accession_absent", "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": [], "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": [], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:obtain_source_data blocked on data:accession_absent"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:38927711", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3390/genes15060775", "sha256": "sha256:59e16bd70e004ca12d335c8db6dcd65330d57da553ee5566c79b5e3f747cb834", "bytes": 66697, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3390/genes15060775", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC11203134", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}], "gaps": []}, "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": "data", "blocked_on": "data:accession_absent", "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": "R4", "reachable": false, "accessions": ["PXD051920 and 10.6019/PXD051920"], "resolved_accessions": [], "statements": ["The data presented in this study are openly available in the Proteo-meXchange Consortium via the PRIDE partner repository at the dataset identifier PXD051920 and DOI: 10.6019/PXD051920."], "basis": "The paper names PXD051920 and 10.6019/PXD051920, but the accession does not resolve in the repository (no reason recorded), so the data cannot be reached from here. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:38927711"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:None"]}, "gaps": ["data:accession_absent"]}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T19:22:29Z", "independence": "single_reader"}, "evidence_check": {"method": null, "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 19520, "completion_tokens": 2060, "cached_tokens": 128}}, "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:38927711", "type": "paper", "label": "pmid:38927711"}, {"id": "source:pmid:38927711", "type": "manuscript", "label": "PMID 38927711 full text"}, {"id": "data:geo:None", "type": "dataset", "label": "GEO None"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:38927711", "type": "paper", "label": "pmid:38927711"}, {"id": "source:pmid:38927711", "type": "manuscript", "label": "PMID 38927711 full text"}, {"id": "data:geo:None", "type": "dataset", "label": "GEO None"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-38927711", "type": "extraction", "used": ["source:pmid:38927711"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-None", "type": "accession_resolution", "used": ["data:geo:None"], "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": null, "parent_hash": null, "fork_of": null, "generation": 0}, "gaps": ["execution.not_run", "method", "operations", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:obtain_source_data blocked on data:accession_absent"]}