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However, the complex datasets generated by MSP-MS pose significant analytical challenges and have limited accessibility for non-specialist users.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      We developed\n                      <jats:italic>mspms<\/jats:italic>\n                      , a Bioconductor R package with an accompanying graphical interface, to streamline the analysis of MSP-MS data.\n                      <jats:italic>Mspms<\/jats:italic>\n                      standardizes workflows for data preparation, processing, statistical analysis, and visualization. The tool is designed for accessibility, serving advanced users through the R package and broader audiences through a web-based interface. We validated\n                      <jats:italic>mspms<\/jats:italic>\n                      using data from four well-characterized cathepsins (A\u2013D), demonstrating that it reliably captures expected substrate specificities.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>mspms is the first publicly available, comprehensive platform for MSP-MS data analysis downstream of peptide identification and quantification. It integrates preprocessing, normalization, statistical testing, and visualization into a single, transparent, and user-friendly framework, making it a valuable resource for the protease research community. The package is distributed via Bioconductor, and a graphical interface is available online for interactive use.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1186\/s12859-026-06373-8","type":"journal-article","created":{"date-parts":[[2026,1,24]],"date-time":"2026-01-24T16:34:43Z","timestamp":1769272483000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["mspms: an R package and GUI for multiplex substrate profiling by mass spectrometry"],"prefix":"10.1186","volume":"27","author":[{"given":"Charlie","family":"Bayne","sequence":"first","affiliation":[]},{"given":"Brianna","family":"Hurysz","sequence":"additional","affiliation":[]},{"given":"David J.","family":"Gonzalez","sequence":"additional","affiliation":[]},{"given":"Anthony","family":"O\u2019Donoghue","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2026,1,24]]},"reference":[{"key":"6373_CR1","doi-asserted-by":"publisher","first-page":"30433","DOI":"10.1074\/jbc.R800035200","volume":"283","author":"C L\u00f3pez-Ot\u00edn","year":"2008","unstructured":"L\u00f3pez-Ot\u00edn C, Bond JS. 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