{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,9,8]],"date-time":"2025-09-08T06:17:01Z","timestamp":1757312221356,"version":"3.37.3"},"reference-count":21,"publisher":"Oxford University Press (OUP)","issue":"21","license":[{"start":{"date-parts":[[2022,9,14]],"date-time":"2022-09-14T00:00:00Z","timestamp":1663113600000},"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","award":["#RGPIN-2018-05645"],"award-info":[{"award-number":["#RGPIN-2018-05645"]}],"id":[{"id":"10.13039\/501100000038","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Michael Cuccione Foundation and the BC Children\u2019s Hospital Foundation"},{"name":"BC Children\u2019s Hospital Research Institute and Michael Cuccione Childhood Cancer Research Program"},{"DOI":"10.13039\/501100000245","name":"Michael Smith Foundation for Health Research Scholar","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100000245","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Michael Cuccione Foundation"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,10,31]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>The comprehensive analysis of the proteome and its modulation by post-translational modification (PTM) is increasingly used in biological and biomedical studies. As a result, proteomics data analysis is ever more carried out by scientists with limited expertise in this type of data. While excellent software solutions for comprehensive and rigorous analysis of quantitative proteomic data exist, most are complex and not well suited for non-proteomics scientists. Integrative analysis of multi-level proteomics data on protein and diverse PTMs, like phosphorylation or proteolytic processing, remains particularly challenging and inaccessible to most biologists. To fill this void, we developed SQuAPP, an R-Shiny web-based analysis pipeline for the quantitative analysis of proteomic data. SQuAPP uses a streamlined workflow model to guide expert and novice users through quality control, data pre-processing, statistical analysis and visualization steps. Processing the protein, peptide and PTM datasets in parallel and their quantitative integration enable rapid identification of protein-level-independent modulation of protein modifications and intuitive interpretation of dynamic dependencies between different protein modifications.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>SQuAPP is available at http:\/\/squapp.langelab.org\/. The source code and local setup instructions can be accessed from https:\/\/github.com\/LangeLab\/SQuAPP.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btac628","type":"journal-article","created":{"date-parts":[[2022,9,13]],"date-time":"2022-09-13T20:24:12Z","timestamp":1663100652000},"page":"4956-4958","source":"Crossref","is-referenced-by-count":5,"title":["SQuAPP\u2014simple quantitative analysis of proteins and PTMs"],"prefix":"10.1093","volume":"38","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9810-7399","authenticated-orcid":false,"given":"Enes K","family":"Ergin","sequence":"first","affiliation":[{"name":"Department of Pathology and Laboratory Medicine, University of British Columbia , Vancouver, BC V6T 1Z7, Canada"},{"name":"Michael Cuccione Childhood Cancer Research Program, BC Children\u2019s Hospital Research , Vancouver, BC V5Z 4H4, Canada"}]},{"given":"Anuli C","family":"Uzozie","sequence":"additional","affiliation":[{"name":"Department of Pathology and Laboratory Medicine, University of British Columbia , Vancouver, BC V6T 1Z7, Canada"},{"name":"Michael Cuccione Childhood Cancer Research Program, BC Children\u2019s Hospital Research , Vancouver, BC V5Z 4H4, Canada"}]},{"given":"Siyuan","family":"Chen","sequence":"additional","affiliation":[{"name":"Department of Pathology and Laboratory Medicine, University of British Columbia , Vancouver, BC V6T 1Z7, Canada"},{"name":"Michael Cuccione Childhood Cancer Research Program, BC Children\u2019s Hospital Research , Vancouver, BC V5Z 4H4, Canada"}]},{"given":"Ye","family":"Su","sequence":"additional","affiliation":[{"name":"Department of Pathology and Laboratory Medicine, University of British Columbia , Vancouver, BC V6T 1Z7, Canada"},{"name":"Michael Cuccione Childhood Cancer Research Program, BC Children\u2019s Hospital Research , Vancouver, BC V5Z 4H4, Canada"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1171-5864","authenticated-orcid":false,"given":"Philipp F","family":"Lange","sequence":"additional","affiliation":[{"name":"Department of Pathology and Laboratory Medicine, University of British Columbia , Vancouver, BC V6T 1Z7, Canada"},{"name":"Michael Cuccione Childhood Cancer Research Program, BC Children\u2019s Hospital Research , Vancouver, BC V5Z 4H4, Canada"}]}],"member":"286","published-online":{"date-parts":[[2022,9,14]]},"reference":[{"key":"2022103112490729100_btac628-B1","doi-asserted-by":"crossref","first-page":"1105","DOI":"10.12688\/f1000research.14541.1","article-title":"drawProteins: a bioconductor\/R package for reproducible and programmatic generation of protein schematics. 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