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Liquid chromatography coupled to tandem mass spectrometry (LC-MS\/MS) is the most widely used analytical approach. Although unmodified peptides are automatically identified by consolidated algorithms, phosphopeptides still require automated tools to avoid time-consuming manual interpretation. To improve phosphopeptide identification efficiency, a novel procedure was developed and implemented in a Perl\/C tool called PhosphoHunter, here proposed and evaluated. It includes a preliminary heuristic step for filtering out the MS\/MS spectra produced by nonphosphorylated peptides before sequence identification. A method to assess the statistical significance of identified phosphopeptides was also formulated. PhosphoHunter performance was tested on a dataset of 1500\u2009MS\/MS spectra and it was compared with two other tools: Mascot and Inspect. Comparisons demonstrated that a strong point of PhosphoHunter is sensitivity, suggesting that it is able to identify real phosphopeptides with superior performance. Performance indexes depend on a single parameter (intensity threshold) that users can tune according to the study aim. All the three tools localized &gt;90% of phosphosites.<\/jats:p>","DOI":"10.1155\/2015\/382869","type":"journal-article","created":{"date-parts":[[2015,1,12]],"date-time":"2015-01-12T22:28:08Z","timestamp":1421101688000},"page":"1-12","source":"Crossref","is-referenced-by-count":2,"title":["PhosphoHunter: An Efficient Software Tool for Phosphopeptide Identification"],"prefix":"10.1155","volume":"2015","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6309-0996","authenticated-orcid":true,"given":"Alessandra","family":"Tiengo","sequence":"first","affiliation":[{"name":"Dipartimento di Ingegneria Industriale e dell\u2019Informazione, Universit\u00e0 degli Studi di Pavia, Via Ferrata 5, 27100 Pavia, Italy"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5431-3083","authenticated-orcid":true,"given":"Lorenzo","family":"Pasotti","sequence":"additional","affiliation":[{"name":"Dipartimento di Ingegneria Industriale e dell\u2019Informazione, Universit\u00e0 degli Studi di Pavia, Via Ferrata 5, 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