SimPhospho: a software tool enabling confident phosphosite assignment
| العنوان: | SimPhospho: a software tool enabling confident phosphosite assignment |
|---|---|
| المؤلفون: | Tomoya Tsubosaka, Tomi Suomi, Garry L. Corthals, Susumu Y. Imanishi, Veronika Suni, Laura L. Elo |
| المساهمون: | Supramolecular Separations (HIMS, FNWI) |
| المصدر: | Bioinformatics Bioinformatics, 34(15), 2690-2692. Oxford University Press |
| بيانات النشر: | Oxford University Press (OUP), 2018. |
| سنة النشر: | 2018 |
| مصطلحات موضوعية: | Phosphopeptides, Proteomics, 0301 basic medicine, Statistics and Probability, Computer science, Mass spectrometry, computer.software_genre, Biochemistry, Tandem mass spectrum, 03 medical and health sciences, Tandem Mass Spectrometry, ta318, Phosphorylation, Databases, Protein, Molecular Biology, Phosphopeptide, Phosphoproteomics, Applications Notes, Pipeline (software), Computer Science Applications, Computational Mathematics, Identification (information), 030104 developmental biology, Computational Theory and Mathematics, Data mining, Data and Text Mining, Protein Processing, Post-Translational, computer, Software, Test data |
| الوصف: | Motivation 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. Results 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. Availability and implementation SimPhospho is open source and it is available for Windows, Linux and Mac operating systems. The software and its user’s manual with detailed description of data analysis as well as test data can be found at https://sourceforge.net/projects/simphospho/. Supplementary information Supplementary data are available at Bioinformatics online. |
| وصف الملف: | application/pdf |
| تدمد: | 1367-4811 1367-4803 |
| DOI: | 10.1093/bioinformatics/bty151 |
| URL الوصول: | https://explore.openaire.eu/search/publication?articleId=doi_dedup___::03571e5ef0a63cdc1e0afcf3afe9b710 https://doi.org/10.1093/bioinformatics/bty151 |
| Rights: | OPEN |
| رقم الانضمام: | edsair.doi.dedup.....03571e5ef0a63cdc1e0afcf3afe9b710 |
| قاعدة البيانات: | OpenAIRE |
| تدمد: | 13674811 13674803 |
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| DOI: | 10.1093/bioinformatics/bty151 |