{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,29]],"date-time":"2025-10-29T13:31:27Z","timestamp":1761744687617,"version":"3.37.3"},"reference-count":16,"publisher":"Oxford University Press (OUP)","issue":"15","license":[{"start":{"date-parts":[[2018,3,27]],"date-time":"2018-03-27T00:00:00Z","timestamp":1522108800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001691","name":"Japan Society for the Promotion of Science","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001691","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001691","name":"KAKENHI","doi-asserted-by":"crossref","award":["JP16K08206"],"award-info":[{"award-number":["JP16K08206"]}],"id":[{"id":"10.13039\/501100001691","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100002341","name":"Academy of Finland","doi-asserted-by":"publisher","award":["128712","304995","310561"],"award-info":[{"award-number":["128712","304995","310561"]}],"id":[{"id":"10.13039\/501100002341","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004785","name":"Nordforsk","doi-asserted-by":"crossref","award":["070325"],"award-info":[{"award-number":["070325"]}],"id":[{"id":"10.13039\/501100004785","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,8,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Mass spectrometry combined with enrichment strategies for phosphorylated peptides has been successfully employed for two decades to identify sites of phosphorylation. However, unambiguous phosphosite assignment is considered challenging. Given that site-specific phosphorylation events function as different molecular switches, validation of phosphorylation sites is of utmost importance. In our earlier study we developed a method based on simulated phosphopeptide spectral libraries, which enables highly sensitive and accurate phosphosite assignments. To promote more widespread use of this method, we here introduce a software implementation with improved usability and performance.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We present SimPhospho, a fast and user-friendly tool for accurate simulation of phosphopeptide tandem mass spectra. Simulated phosphopeptide spectral libraries are used to validate and supplement database search results, with a goal to improve reliable phosphoproteome identification and reporting. The presented program can be easily used together with the Trans-Proteomic Pipeline and integrated in a phosphoproteomics data analysis workflow.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>SimPhospho is open source and it is available for Windows, Linux and Mac operating systems. The software and its user\u2019s manual with detailed description of data analysis as well as test data can be found at https:\/\/sourceforge.net\/projects\/simphospho\/.<\/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\/bty151","type":"journal-article","created":{"date-parts":[[2018,3,26]],"date-time":"2018-03-26T19:12:05Z","timestamp":1522091525000},"page":"2690-2692","source":"Crossref","is-referenced-by-count":9,"title":["SimPhospho: a software tool enabling confident phosphosite assignment"],"prefix":"10.1093","volume":"34","author":[{"given":"Veronika","family":"Suni","sequence":"first","affiliation":[{"name":"TUCS \u2013 Turku Centre for Computer Science, FI-20500 Turku, Finland"},{"name":"Bioinformatics Unit, Turku Centre for Biotechnology, University of Turku and \u00c5bo Akademi University, Tykist\u00f6katu 6, FI-20520 Turku, Finland"}]},{"given":"Tomi","family":"Suomi","sequence":"additional","affiliation":[{"name":"Bioinformatics Unit, Turku Centre for Biotechnology, University of Turku and \u00c5bo Akademi University, Tykist\u00f6katu 6, FI-20520 Turku, Finland"}]},{"given":"Tomoya","family":"Tsubosaka","sequence":"additional","affiliation":[{"name":"Faculty of Pharmacy, Meijo University, Nagoya, Japan"}]},{"given":"Susumu Y","family":"Imanishi","sequence":"additional","affiliation":[{"name":"Faculty of Pharmacy, Meijo University, Nagoya, Japan"}]},{"given":"Laura L","family":"Elo","sequence":"additional","affiliation":[{"name":"Bioinformatics Unit, Turku Centre for Biotechnology, University of Turku and \u00c5bo Akademi University, Tykist\u00f6katu 6, FI-20520 Turku, Finland"}]},{"given":"Garry L","family":"Corthals","sequence":"additional","affiliation":[{"name":"Van't Hoff Institute of Molecular Sciences, 1090 GS Amsterdam, The Netherlands"}]}],"member":"286","published-online":{"date-parts":[[2018,3,27]]},"reference":[{"key":"2023012713054641900_bty151-B1","doi-asserted-by":"crossref","first-page":"1285","DOI":"10.1038\/nbt1240","article-title":"A probability-based approach for high-throughput protein phosphorylation analysis and site localization","volume":"24","author":"Beausoleil","year":"2006","journal-title":"Nat. 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