{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,22]],"date-time":"2026-01-22T02:05:07Z","timestamp":1769047507569,"version":"3.49.0"},"reference-count":13,"publisher":"Oxford University Press (OUP)","issue":"19","license":[{"start":{"date-parts":[[2020,7,8]],"date-time":"2020-07-08T00:00:00Z","timestamp":1594166400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"NRF-VU Desmond Tutu Doctoral"},{"name":"TB Research and DST\/NRF Centre of Excellence for Biomedical Tuberculosis Research"},{"name":"South African Research Chairs Initiative of the Department of Science and Technology and National Research Foundation (NRF) of South Africa","award":["86539"],"award-info":[{"award-number":["86539"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,12,8]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Proteomics is a powerful tool for protein expression analysis and is becoming more readily available to researchers through core facilities or specialized collaborations. However, one major bottleneck for routine implementation and accessibility of this technology to the wider scientific community is the complexity of data analysis. To this end, we have created ProVision, a free open-source web-based analytics platform that allows users to analyze data from two common proteomics relative quantification workflows, namely label-free and tandem mass tag-based experiments. Furthermore, ProVision allows the freedom to interface with the data analysis pipeline while maintaining a user-friendly environment and providing default parameters for fast statistical and exploratory data analysis. Finally, multiple customizable quality control, differential expression plots as well as enrichments and protein\u2013protein interaction prediction can be generated online in one platform.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Quick start and step-by-step tutorials as well as tutorial data are fully incorporated in the web application. This application is available online at https:\/\/provision.shinyapps.io\/provision\/ for free use. The source code is available at https:\/\/github.com\/JamesGallant\/ProVision under the GPL version 3.0 license.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaa620","type":"journal-article","created":{"date-parts":[[2020,7,1]],"date-time":"2020-07-01T03:20:23Z","timestamp":1593573623000},"page":"4965-4967","source":"Crossref","is-referenced-by-count":35,"title":["ProVision: a web-based platform for rapid analysis of proteomics data processed by MaxQuant"],"prefix":"10.1093","volume":"36","author":[{"given":"James Luke","family":"Gallant","sequence":"first","affiliation":[{"name":"Division of Molecular Biology and Human Genetics, Department of Biomedical Science, DST\/NRF Centre of Excellence in Biomedical TB Research, SA MRC Centre for Tuberculosis Research, Faculty of Medicine and Health Science, Stellenbosch University , Tygerberg, Cape Town 7505, South Africa"},{"name":"Section Molecular Microbiology, Amsterdam Institute for Molecules, Medicines and Systems, Vrije Universiteit Amsterdam , Amsterdam 1081 HZ, The Netherlands"}]},{"given":"Tiaan","family":"Heunis","sequence":"additional","affiliation":[{"name":"Division of Molecular Biology and Human Genetics, Department of Biomedical Science, DST\/NRF Centre of Excellence in Biomedical TB Research, SA MRC Centre for Tuberculosis Research, Faculty of Medicine and Health Science, Stellenbosch University , Tygerberg, Cape Town 7505, South Africa"},{"name":"Biosciences Institute, Faculty of Medical Sciences, Newcastle University , Newcastle upon Tyne NE2 4HH, UK"}]},{"given":"Samantha Leigh","family":"Sampson","sequence":"additional","affiliation":[{"name":"Division of Molecular Biology and Human Genetics, Department of Biomedical Science, DST\/NRF Centre of Excellence in Biomedical TB Research, SA MRC Centre for Tuberculosis Research, Faculty of Medicine and Health Science, Stellenbosch University , Tygerberg, Cape Town 7505, South Africa"}]},{"given":"Wilbert","family":"Bitter","sequence":"additional","affiliation":[{"name":"Section Molecular Microbiology, Amsterdam Institute for Molecules, Medicines and Systems, Vrije Universiteit Amsterdam , Amsterdam 1081 HZ, The Netherlands"},{"name":"Department of Medical Microbiology and Infection Control , Amsterdam UMC, location VUmc, Amsterdam 1081 HZ, The Netherlands"}]}],"member":"286","published-online":{"date-parts":[[2020,7,8]]},"reference":[{"key":"2023062408050778700_btaa620-B1","doi-asserted-by":"crossref","first-page":"2524","DOI":"10.1093\/bioinformatics\/btu305","article-title":"MSstats: an R package for statistical analysis of quantitative mass spectrometry-based proteomic experiments","volume":"30","author":"Choi","year":"2014","journal-title":"Bioinformatics"},{"key":"2023062408050778700_btaa620-B2","doi-asserted-by":"crossref","first-page":"2513","DOI":"10.1074\/mcp.M113.031591","article-title":"Accurate proteome-wide label-free quantification by delayed normalization and maximal peptide ratio extraction, termed MaxLFQ","volume":"13","author":"Cox","year":"2014","journal-title":"Mol. 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