In-depth quantitative proteomics uncovers specie-specific metabolic programs in Leishmania (Viannia) species.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:32804927", "kind": "science-record", "revision": 4, "content_hash": "sha256:71b9c1537449fa08559d2d227f5bd2ca76fb7f61ad2fad519300d532ad2c6da2", "created_at": "2026-11-01T15:41:08Z", "updated_at": "2026-11-01T21:23:39Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "In-depth quantitative proteomics uncovers specie-specific metabolic programs in Leishmania (Viannia) species.", "doi": "10.1371/journal.pntd.0008509", "pmid": "32804927", "authors": ["Nathalia Pinho", "Jacek R Wiśniewski", "Geovane Dias-Lopes", "Leonardo Saboia-Vahia", "Ana Cristina Souza Bombaça", "Camila Mesquita-Rodrigues", "Rubem Menna-Barreto", "Elisa Cupolillo", "Jose Batista de Jesus", "Gabriel Padrón", "Patricia Cuervo"], "journal": "PLoS neglected tropical diseases", "year": 2020, "abstract": "Leishmania species are responsible for a broad spectrum of diseases, denominated Leishmaniasis, affecting over 12 million people worldwide. During the last decade, there have been impressive efforts for sequencing the genome of most of the pathogenic Leishmania spp. as well as hundreds of strains, but large-scale proteomics analyses did not follow these achievements and the Leishmania proteome remained mostly uncharacterized. Here, we report a comprehensive comparative study of the proteomes of strains representing L. braziliensis, L. panamensis and L. guyanensis species. Proteins extracted by SDS-mediated lysis were processed following the multi-enzyme digestion-filter aided sample preparation (FASP) procedure and analysed by high accuracy mass spectrometry. \"Total Protein Approach\" and \"Proteomic Ruler\" were applied for absolute quantification of proteins. Principal component analysis demonstrated very high reproducibility among biological replicates and a very clear differentiation of the three species. Our dataset comprises near 7000 proteins, representing the most complete Leishmania proteome yet known, and provides a comprehensive quantitative picture of the proteomes of the three species in terms of protein concentration and copy numbers. Analysis of the abundance of proteins from the major energy metabolic processes allow us to highlight remarkably differences among the species and suggest that these parasites depend on distinct energy substrates to obtain ATP. Whereas L. braziliensis relies the more on glycolysis, L. panamensis and L. guyanensis seem to depend mainly on mitochondrial respiration. These results were confirmed by biochemical assays showing opposite profiles for glucose uptake and O2 consumption in these species. In addition, we provide quantitative data about different membrane proteins, transporters, and lipids, all of which contribute for significant species-specific differences and provide rich substrate for explore new molecules for diagnosing purposes. Data are available via ProteomeXchange with identifier PXD017696.", "claims": [{"id": "claim-method", "statement": "Significances were calculated using the t-test with a threshold of false discovery rate (FDR) of 1%.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32804927", "locator": "sections[6] \"Proteomic data analysis\" paragraph 2", "quote": "Significances were calculated using the t-test with a threshold of false discovery rate (FDR) of 1%."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All relevant data are within the manuscript and its Supporting Information files. Mass spectrometry data are available via ProteomeXchange with identifier PXD017696.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32804927", "locator": "sections[20] \"Data Availability\" paragraph 2", "quote": "All relevant data are within the manuscript and its Supporting Information files. Mass spectrometry data are available via ProteomeXchange with identifier PXD017696."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "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:32804927"], "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:PXD017696"], "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:PXD017696"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:32804927", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1371/journal.pntd.0008509", "sha256": "sha256:5741caef730057c8a0cabe83e34f526ba9334db5cffad767e6916afe3bee1e17", "bytes": 69487, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1371/journal.pntd.0008509", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7451982", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PXD017696", "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=PXD017696", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD017696", "version": null, "note": "All relevant data are within the manuscript and its Supporting Information files. Mass spectrometry data are available via ProteomeXchange with identifier PXD017696.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "All relevant data are within the manuscript and its Supporting Information files. Mass spectrometry data are available via ProteomeXchange with identifier PXD017696.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "Comprehensive quantitative analysis of the proteome of Leishmania (Viannia) species", "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:32804927:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:4a9bbf6b583235ace9d80f1b9326846675f3c3bbfc3ca03500cd15b5951f9969", "bytes": 757, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[1]#pntd.0008509.t001", "version": null, "note": "Summary of general information about the proteomes of Leishmania braziliensis, L. panamensis and L. guyanensis promastigotes.", "structure": {"pmcid": "PMC7451982", "section_index": 12, "section_title": "The Leishmania (Viannia) proteome is distributed in about six orders of magnitude and L. braziliensis, L. panamensis and L. guyanensis are clearly separated by differences in their protein concentrations", "row_count": 7, "column_count": 4}, "table": {"label": "Table 1", "caption": "Summary of general information about the proteomes of Leishmania braziliensis, L. panamensis and L. guyanensis promastigotes.", "rows": [["", "L. braziliensis", "L. panamensis", "L. guyanensis"], ["International code", "MHOM/BR/2000/LTCP 13396", "MHOM/CO/2009/6634", "MHOM/BR/1997/NMT-MAO 292P"], ["Biological replicates", "5", "5", "4"], ["Peptides identified", "78398", "77940", "62018"], ["Protein groups identified", "6779", "6783", "6764"], ["Total protein per cell", "3.86 ± 0.1 pg", "3.89 ± 0.08 pg", "3.55 ± 0.2 pg"], ["Total protein molecules per parasite", "6.4 ± 0.20 x 107", "6.3 ± 0.13 x 107", "5.9 ± 0.35 x 107"]], "row_count": 7, "column_count": 4, "numeric_cells": 18, "header_rows": 1, "locator": "section[12]/table-wrap[1]#pntd.0008509.t001"}}, {"id": "asset:table:pmid:32804927:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:52cc2ba0536684773006f1600bc595ff984afd7572653d64bc93aa7a41c95baa", "bytes": 2267, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[2]#pntd.0008509.t002", "version": null, "note": "Top 20 most abundant protein groups in Leishmania (Viannia) proteomes in terms of protein copy number.Protein IDs according to UniProt. Detailed information in S2 Table. Lb: L. braziliensis; Lp: L. panamensis; Lg: L. guyanensis.", "structure": {"pmcid": "PMC7451982", "section_index": 12, "section_title": "The Leishmania (Viannia) proteome is distributed in about six orders of magnitude and L. braziliensis, L. panamensis and L. guyanensis are clearly separated by differences in their protein concentrations", "row_count": 21, "column_count": 8}, "table": {"label": "Table 2", "caption": "Top 20 most abundant protein groups in Leishmania (Viannia) proteomes in terms of protein copy number.Protein IDs according to UniProt. Detailed information in S2 Table. Lb: L. braziliensis; Lp: L. panamensis; Lg: L. guyanensis.", "rows": [["Majority protein ID", "Protein names", "Number of proteins", "Peptides", "Mol. weight [kDa]", "Lb Average copy number", "Lp Average copy number", "Lg Average copy number"], ["A4H675", "Histone H3", "1", "19", "14.76", "683514", "781749", "797009"], ["A4H7X1", "Histone H4", "5", "17", "11.36", "632678", "518407", "591973"], ["A4H9W2", "Histone H2B", "2", "16", "12.40", "615245", "701910", "721757"], ["A4HLC9", "Tubulin beta chain", "4", "38", "49.76", "596408", "564945", "516207"], ["A4H727", "Tubulin alpha chain", "3", "52", "49.68", "566849", "561107", "507227"], ["A4H8V4", "Elongation factor 1-alpha", "1", "51", "49.07", "550167", "489947", "554094"], ["A4HBV1", "Histone H2A", "3", "16", "14.13", "520962", "354314", "320116"], ["A4HMP3", "Kinetoplastid membrane protein-11", "1", "17", "11.17", "501495", "545944", "420273"], ["A4HER9", "Putative 10 kDa heat shock protein", "1", "12", "10.75", "477486", "294995", "301477"], ["A4HGY1", "Putative heat-shock protein hsp70", "3", "70", "71.28", "429433", "353265", "400574"], ["A4H5R9", "Putative calmodulin", "1", "17", "16.82", "392799", "434208", "399249"], ["A4HGV8", "Putative 40S ribosomal protein S17", "1", "21", "16.56", "350644", "286853", "297001"], ["A4H7N9", "Putative calpain-like cysteine peptidase", "1", "15", "13.06", "339950", "295024", "232822"], ["A4HKT8", "Nucleoside diphosphate kinase (EC 2.7.4.6)", "2", "16", "16.69", "336687", "301436", "167969"], ["A4HL70", "Heat shock protein 83–1", "1", "80", "80.66", "327133", "281794", "260786"], ["A4H8H2", "Putative 60S ribosomal protein L21", "2", "24", "18.03", "326347", "292275", "307616"], ["A4HD62", "Putative 60S ribosomal protein L17", "1", "15", "19.01", "316904", "296723", "301417"], ["A4HMZ5", "Putative 60S ribosomal subunit protein L31", "1", "21", "21.38", "301492", "254432", "243122"], ["A4HAF8", "Contig, possible fusion of chromosomes 20 and 34", "1", "12", "13.07", "299331", "231468", "250427"], ["A4HGE0", "40S ribosomal protein S14", "1", "15", "15.67", "294401", "248622", "256815"]], "row_count": 21, "column_count": 8, "numeric_cells": 136, "header_rows": 1, "locator": "section[12]/table-wrap[2]#pntd.0008509.t002"}}], "gaps": ["asset:data:geo:PXD017696 not downloaded", "asset:data:geo:PXD017696 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "principal_component_analysis", "specific": "pca", "label": "Principal component analysis", "dsl_operations": ["pca_fit"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["wide_numeric_matrix"], "evidence": {"score": 0.7, "band": "medium", "quote": "Principal component analysis"}}, {"id": "method-2", "family": null, "specific": null, "label": "t-test", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Significances were calculated using the t-test with a threshold of false discovery rate (FDR) of 1%."}}], "targets": [], "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": ["pca_fit"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: pca."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. 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