Identification and characterization of disulfide bonds in proteins and peptides from tandem MS data by use of the MassMatrix MS/MS search engine
Identification and characterization of disulfide bonds in proteins and peptides from tandem MS data by use of the MassMatrix MS/MS search engine
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DOI：
10.1021/pr070363z
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发表时间：
2008-01-01
影响因子：
4.4
通讯作者：
Freitas, Michael A.
中科院分区：
文献类型：
--
作者：
Xu, Hua;Zhang, Liwen;Freitas, Michael A.
开发了一种新的数据库搜索算法来识别串联 MS 数据集中的二硫键连接的肽。该算法包含在新开发的串联 MS 数据库搜索程序 MassMatrix 中。该算法利用MassMatrix中的概率评分模型来实现蛋白质和肽中二硫键的识别。无需化学还原或其他衍生化即可高置信度地鉴定具有二硫键的蛋白质和肽。该方法在具有已知二硫键的肽和蛋白质标准品上进行了测试。标准组中的所有二硫键均由 MassMatrix 鉴定。该算法在牛胰腺核糖核酸酶 A (RNaseA) 上进行了进一步测试。 MassMatrix 检测到 RNaseA 中的 4 个天然二硫键，每个二硫键具有多个经过验证的肽匹配，具有高统计得分。由于二硫键互换，在碱性条件（pH = 8.0）下的蛋白质消化物中还观察到 15 个非天然二硫键。在消化过程中最大限度地减少二硫键交换（pH = 6.0）后，仅观察到一个非天然二硫键。 MassMatrix 算法提供了另一种从串联质谱数据中发现二硫键的方法。
A new database search algorithm has been developed to identify disulfide-linked peptides in tandem MS data sets. The algorithm is included in the newly developed tandem MS database search program, MassMatrix. The algorithm exploits the probabilistic scoring model in MassMatrix to achieve identification of disulfide bonds in proteins and peptides. Proteins and peptides with disulfide bonds can be identified with high confidence without chemical reduction or other derivatization. The approach was tested on peptide and protein standards with known disulfide bonds. All disulfide bonds in the standard set were identified by MassMatrix. The algorithm was further tested on bovine pancreatic ribonuclease A (RNaseA). The 4 native disulfide bonds in RNaseA were detected by MassMatrix with multiple validated peptide matches for each disulfide bond with high statistical scores. Fifteen nonnative disulfide bonds were also observed in the protein digest under basic conditions (pH = 8.0) due to disulfide bond interchange. After minimizing the disulfide bond interchange (pH = 6.0) during digestion, only one nonnative disulfide bond was observed. The MassMatrix algorithm offers an additional approach for the discovery of disulfide bond from tandem mass spectrometry data.