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We also discuss optimal parameters for different types of data and illustrate the new tool on a human skeletal muscle dataset for lysine-acetylation.<\/jats:p>\n               <jats:p>Availability and implementation: The software is freely available on the SourceForge website http:\/\/luciphor2.sourceforge.net.<\/jats:p>\n               <jats:p>Contact: \u00a0hyung_won_choi@nuhs.edu.sg, nesvi@med.umich.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu788","type":"journal-article","created":{"date-parts":[[2014,11,27]],"date-time":"2014-11-27T01:24:52Z","timestamp":1417051492000},"page":"1141-1143","source":"Crossref","is-referenced-by-count":29,"title":["LuciPHOr2: site localization of generic post-translational modifications from tandem mass spectrometry data"],"prefix":"10.1093","volume":"31","author":[{"given":"Damian","family":"Fermin","sequence":"first","affiliation":[{"name":"1 Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA, 2Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore and 3Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA"}]},{"given":"Dmitry","family":"Avtonomov","sequence":"additional","affiliation":[{"name":"1 Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA, 2Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore and 3Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA"}]},{"given":"Hyungwon","family":"Choi","sequence":"additional","affiliation":[{"name":"1 Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA, 2Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore and 3Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA"}]},{"given":"Alexey I.","family":"Nesvizhskii","sequence":"additional","affiliation":[{"name":"1 Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA, 2Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore and 3Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA"},{"name":"1 Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA, 2Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore and 3Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA"}]}],"member":"286","published-online":{"date-parts":[[2014,11,25]]},"reference":[{"key":"2023051309143664100_btu788-B1","doi-asserted-by":"crossref","first-page":"3753","DOI":"10.1021\/pr300229m","article-title":"Occurrence and detection of phosphopeptide isomers in large-scale phosphoproteomics experiments","volume":"6","author":"Courcelles","year":"2012","journal-title":"J. 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