LuciPHOr2：从串联质谱数据中进行通用翻译后修饰的位点定位
LuciPHOr2: site localization of generic post-translational modifications from tandem mass spectrometry data.
作者信息
Fermin Damian, Avtonomov Dmitry, Choi Hyungwon, Nesvizhskii Alexey I
机构信息
Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA, Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore and Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.
Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA, Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore and Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA, Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore and Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.
出版信息
Bioinformatics. 2015 Apr 1;31(7):1141-3. doi: 10.1093/bioinformatics/btu788. Epub 2014 Nov 25.
UNLABELLED
We present LuciPHOr2, a site localization tool for generic post-translational modifications (PTMs) using tandem mass spectrometry data. As an extension of the original LuciPHOr (version 1) for phosphorylation site localization, the new software provides a site-level localization score for generic PTMs and associated false discovery rate called the false localization rate. We describe several novel features such as operating system independence and reduced computation time through multiple threading. We also discuss optimal parameters for different types of data and illustrate the new tool on a human skeletal muscle dataset for lysine-acetylation.
AVAILABILITY AND IMPLEMENTATION
The software is freely available on the SourceForge website http://luciphor2.sourceforge.net.
SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.
未标注
我们展示了LuciPHOr2，这是一种利用串联质谱数据进行通用翻译后修饰（PTM）位点定位的工具。作为用于磷酸化位点定位的原始LuciPHOr（版本1）的扩展，新软件为通用PTM提供了位点级定位分数以及称为错误定位率的相关错误发现率。我们描述了几个新特性，如操作系统独立性和通过多线程减少计算时间。我们还讨论了不同类型数据的最佳参数，并在一个用于赖氨酸乙酰化的人类骨骼肌数据集中展示了这个新工具。
可用性和实现方式
该软件可在SourceForge网站http://luciphor2.sourceforge.net上免费获取。
补充信息
补充数据可在《生物信息学》在线版获取。
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