Degroeve Sven, Maddelein Davy, Martens Lennart
Department of Medical Protein Research, VIB, A. Baertsoenkaai 3, B-9000 Ghent, Belgium Department of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, A. Baertsoenkaai 3, B-9000 Ghent, Belgium
Department of Medical Protein Research, VIB, A. Baertsoenkaai 3, B-9000 Ghent, Belgium Department of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, A. Baertsoenkaai 3, B-9000 Ghent, Belgium.
Nucleic Acids Res. 2015 Jul 1;43(W1):W326-30. doi: 10.1093/nar/gkv542. Epub 2015 May 18.
We present an MS(2) peak intensity prediction server that computes MS(2) charge 2+ and 3+ spectra from peptide sequences for the most common fragment ions. The server integrates the Unimod public domain post-translational modification database for modified peptides. The prediction model is an improvement of the previously published MS(2)PIP model for Orbitrap-LTQ CID spectra. Predicted MS(2) spectra can be downloaded as a spectrum file and can be visualized in the browser for comparisons with observations. In addition, we added prediction models for HCD fragmentation (Q-Exactive Orbitrap) and show that these models compute accurate intensity predictions on par with CID performance. We also show that training prediction models for CID and HCD separately improves the accuracy for each fragmentation method. The MS(2)PIP prediction server is accessible from http://iomics.ugent.be/ms2pip.
我们展示了一个MS(2)峰强度预测服务器，它可根据肽序列计算最常见碎片离子的MS(2) 2+和3+电荷谱。该服务器整合了用于修饰肽的Unimod公共领域翻译后修饰数据库。预测模型是对先前发表的用于Orbitrap-LTQ CID谱的MS(2)PIP模型的改进。预测的MS(2)谱可作为谱文件下载，并可在浏览器中可视化以与观测结果进行比较。此外，我们添加了用于HCD碎裂（Q-Exactive Orbitrap）的预测模型，并表明这些模型能计算出与CID性能相当的准确强度预测。我们还表明，分别针对CID和HCD训练预测模型可提高每种碎裂方法的准确性。可通过http://iomics.ugent.be/ms2pip访问MS(2)PIP预测服务器。
