{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:33:57Z","timestamp":1772138037412,"version":"3.50.1"},"reference-count":64,"publisher":"Oxford University Press (OUP)","issue":"14","license":[{"start":{"date-parts":[[2020,5,5]],"date-time":"2020-05-05T00:00:00Z","timestamp":1588636800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100000038","name":"Natural Sciences and Engineering Research Council of Canada","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000038","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000038","name":"NSERC","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000038","id-type":"DOI","asserted-by":"publisher"}]},{"name":"CREATE TECHNOMISE program"},{"DOI":"10.13039\/100008762","name":"Genome Canada","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100008762","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000092","name":"Ontario Genomics Institute","doi-asserted-by":"publisher","award":["OGI-156"],"award-info":[{"award-number":["OGI-156"]}],"id":[{"id":"10.13039\/501100000092","id-type":"DOI","asserted-by":"publisher"}]},{"name":"NSERC CREATE in Technologies for Microbiome Science and Engineering (TECHNOMISE) Program"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,7,30]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Enzymatic digestion of proteins before mass spectrometry analysis is a key process in metaproteomic workflows. Canonical metaproteomic data processing pipelines typically involve matching spectra produced by the mass spectrometer to a theoretical spectra database, followed by matching the identified peptides back to parent-proteins. However, the nature of enzymatic digestion produces peptides that can be found in multiple proteins due to conservation or chance, presenting difficulties with protein and functional assignment.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>To combat this challenge, we developed pepFunk, a peptide-centric metaproteomic workflow focused on the analysis of human gut microbiome samples. Our workflow includes a curated peptide database annotated with Kyoto Encyclopedia of Genes and Genomes (KEGG) terms and a gene set variation analysis-inspired pathway enrichment adapted for peptide-level data. Analysis using our peptide-centric workflow is fast and highly correlated to a protein-centric analysis, and can identify more enriched KEGG pathways than analysis using protein-level data. Our workflow is open source and available as a web application or source code to be run locally.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>pepFunk is available online as a web application at https:\/\/shiny.imetalab.ca\/pepFunk\/ with open-source code available from https:\/\/github.com\/northomics\/pepFunk.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Contact<\/jats:title>\n                    <jats:p>dfigeys@uottawa.ca<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaa289","type":"journal-article","created":{"date-parts":[[2020,4,27]],"date-time":"2020-04-27T15:38:42Z","timestamp":1588001922000},"page":"4171-4179","source":"Crossref","is-referenced-by-count":16,"title":["pepFunk: a tool for peptide-centric functional analysis of metaproteomic human gut microbiome studies"],"prefix":"10.1093","volume":"36","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9832-7797","authenticated-orcid":false,"given":"Caitlin M A","family":"Simopoulos","sequence":"first","affiliation":[{"name":"Department of Biochemistry , Microbiology and Immunology, Faculty of Medicine, Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1H 8M5, Canada"},{"name":"Faculty of Medicine , SIMM-University of Ottawa Joint Research Center in Systems and Personalized Pharmacology, University of Ottawa, Ottawa, ON K1H 8M5, Canada"}]},{"given":"Zhibin","family":"Ning","sequence":"additional","affiliation":[{"name":"Department of Biochemistry , Microbiology and Immunology, Faculty of Medicine, Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1H 8M5, Canada"},{"name":"Faculty of Medicine , SIMM-University of Ottawa Joint Research Center in Systems and Personalized Pharmacology, University of Ottawa, Ottawa, ON K1H 8M5, Canada"}]},{"given":"Xu","family":"Zhang","sequence":"additional","affiliation":[{"name":"Department of Biochemistry , Microbiology and Immunology, Faculty of Medicine, Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1H 8M5, Canada"},{"name":"Faculty of Medicine , SIMM-University of Ottawa Joint Research Center in Systems and Personalized Pharmacology, University of Ottawa, Ottawa, ON K1H 8M5, Canada"}]},{"given":"Leyuan","family":"Li","sequence":"additional","affiliation":[{"name":"Department of Biochemistry , Microbiology and Immunology, Faculty of Medicine, Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1H 8M5, Canada"},{"name":"Faculty of Medicine , SIMM-University of Ottawa Joint Research Center in Systems and Personalized Pharmacology, University of Ottawa, Ottawa, ON K1H 8M5, Canada"}]},{"given":"Krystal","family":"Walker","sequence":"additional","affiliation":[{"name":"Department of Biochemistry , Microbiology and Immunology, Faculty of Medicine, Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1H 8M5, Canada"},{"name":"Faculty of Medicine , SIMM-University of Ottawa Joint Research Center in Systems and Personalized Pharmacology, University of Ottawa, Ottawa, ON K1H 8M5, Canada"}]},{"given":"Mathieu","family":"Lavall\u00e9e-Adam","sequence":"additional","affiliation":[{"name":"Department of Biochemistry , Microbiology and Immunology, Faculty of Medicine, Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1H 8M5, Canada"}]},{"given":"Daniel","family":"Figeys","sequence":"additional","affiliation":[{"name":"Department of Biochemistry , Microbiology and Immunology, Faculty of Medicine, Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1H 8M5, Canada"},{"name":"Faculty of Medicine , SIMM-University of Ottawa Joint Research Center in Systems and Personalized Pharmacology, University of Ottawa, Ottawa, ON K1H 8M5, Canada"},{"name":"Canadian Institute for Advanced Research , Toronto, ON M5G 1M1, Canada"}]}],"member":"286","published-online":{"date-parts":[[2020,5,5]]},"reference":[{"key":"2023062213545187600_btaa289-B1","doi-asserted-by":"crossref","first-page":"307ra152","DOI":"10.1126\/scitranslmed.aab2271","article-title":"Early infancy microbial and metabolic alterations affect risk of childhood asthma","volume":"7","author":"Arrieta","year":"2015","journal-title":"Sci. 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