University of Victoria Genome British Columbia Protein Centre, Department of Biochemistry & Microbiology, University of Victoria, #3101-4464 Markham Street, Vancouver Island Technology Park, Victoria, BC, Canada.
BMC Bioinformatics. 2010 Jan 28;11:64. doi: 10.1186/1471-2105-11-64.
Successful application of crosslinking combined with mass spectrometry for studying proteins and protein complexes requires specifically-designed crosslinking reagents, experimental techniques, and data analysis software. Using isotopically-coded ("heavy and light") versions of the crosslinker and cleavable crosslinking reagents is analytically advantageous for mass spectrometric applications and provides a "handle" that can be used to distinguish crosslinked peptides of different types, and to increase the confidence of the identification of the crosslinks.
Here, we describe a program suite designed for the analysis of mass spectrometric data obtained with isotopically-coded cleavable crosslinkers. The suite contains three programs called: DX, DXDX, and DXMSMS. DX searches the mass spectra for the presence of ion signal doublets resulting from the light and heavy isotopic forms of the isotopically-coded crosslinking reagent used. DXDX searches for possible mass matches between cleaved and uncleaved isotopically-coded crosslinks based on the established chemistry of the cleavage reaction for a given crosslinking reagent. DXMSMS assigns the crosslinks to the known protein sequences, based on the isotopically-coded and un-coded MS/MS fragmentation data of uncleaved and cleaved peptide crosslinks.
The combination of these three programs, which are tailored to the analytical features of the specific isotopically-coded cleavable crosslinking reagents used, represents a powerful software tool for automated high-accuracy peptide crosslink identification. See: http://www.creativemolecules.com/CM_Software.htm.
成功应用交联结合质谱研究蛋白质和蛋白质复合物需要专门设计的交联试剂、实验技术和数据分析软件。使用同位素编码（“重”和“轻”）版本的交联剂和可裂解交联试剂在质谱应用中具有分析优势，并且提供了一个“处理”，可用于区分不同类型的交联肽，并提高交联识别的置信度。
在这里，我们描述了一个专为分析使用同位素编码可裂解交联剂获得的质谱数据而设计的程序套件。该套件包含三个程序，分别称为：DX、DXDX 和 DXMSMS。DX 搜索质谱中是否存在由使用的同位素编码交联试剂的轻和重同位素形式产生的离子信号双峰。DXDX 根据给定交联试剂的裂解反应的既定化学性质，在裂解和未裂解的同位素编码交联之间搜索可能的质量匹配。DXMSMS 根据未裂解和裂解肽交联的同位素编码和未编码的 MS/MS 碎裂数据，将交联分配给已知的蛋白质序列。
这三个程序的组合，专门针对使用的特定同位素编码可裂解交联试剂的分析特点，代表了一种用于自动进行高精度肽交联识别的强大软件工具。请访问：http://www.creativemolecules.com/CM_Software.htm。
