论文标题
XLMOD：交联和色谱衍生化试剂本体论
XLMOD: Cross-linking and chromatography derivatization reagents ontology
论文作者
论文摘要
自1980年代首次应用蛋白质分析以来，质谱法经历了快速发展。虽然质谱法对蛋白质分析的最常见用途是对肽上的识别和定量工作流（从其母体蛋白质上消化），但质谱法对结构蛋白质组学的质谱法也迅速增长。一个例子是对可以提供有价值的结构信息的交联蛋白的分析，并补充经典蛋白质结构确定方法获得的信息，对结构确定和建模的综合方法有用。对于交联质谱的广泛且可重复的应用，必须进行交联实验结果的标准化表示。本文介绍了Hupo-PSI的XLMOD本体论的发展和释放。 XLMOD包含用于描述交联实验和交联相关化学修饰的试剂的术语，以及与计划和执行交联实验有关的主要特性。我们还描述了如何在HUPO-PSI-S MZIDENDML数据标准的新版本中使用XLMOD，以报告使用的交联试剂并以一致的方式结果。另外，XLMOD还包含用于在即将到来的MZTAB-M和MZTAB-L格式中指定它们的GC-MS和LC-MS衍生化试剂。
Mass spectrometry has experienced a rapid development since its first application for protein analysis in the 1980s. While the most common use of mass spectrometry for protein analysis is identification and quantification workflows on peptides (digested from their parent protein), there is also a rapidly growing use of mass spectrometry for structural proteomics. One example is the analysis of cross-linked proteins that can give valuable structural information, complementing the information gained by classical protein structure determination methods, useful for integrated methods of structure determination and modeling. For a broad and reproducible application of cross-linking mass spectrometry a standardized representation of cross-linking experimental results is necessary. This paper describes the developing and release of the xlmod ontology from the HUPO-PSI. xlmod contains terms for the description of reagents used in cross-linking experiments and of cross-linker related chemical modifications together with their main properties relevant for planning and performing cross-linking experiments. We also describe how xlmod is used within the new release of HUPO-PSI-s mzIdentML data standard, for reporting the used cross-linking reagents and results in a consistent manner. In addition xlmod contains terms for GC-MS and LC-MS derivatization reagents for specifying them in the upcoming mzTab-M and mzTab-L formats.
