Similarity among Tandem Mass Spectra from Proteomic Experiments: Detection, Significance, and Utility
Similarity among Tandem Mass Spectra from Proteomic Experiments: Detection, Significance, and Utility
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DOI：
10.1021/ac026424o
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发表时间：
2003-05-15
影响因子：
7.4
通讯作者：
Yates, JR
中科院分区：
文献类型：
--
作者：
Tabb, DL;MacCoss, MJ;Yates, JR
液相色谱与串联质谱联用是从复杂蛋白质混合物中鉴定肽段的一种标准技术。通过这种技术获得的大多数碎片离子谱是独特的，但有些是重复的。通过点积算法计算了一维和二维液相色谱实验所得谱图之间的相似性。对相似的谱图进行分组，并计算每个样品的重复程度。在来自一维凝胶条带的一维液相色谱数据中，18%的碎片离子谱是重复的。对200多种蛋白质进行的六轮二维液相色谱分离产生了28%的重复谱图。通过12轮二维液相色谱分离分析的大鼠海马匀浆含有25%的重复谱图。然而，去除这些重复谱图会导致通过SEQUEST成功鉴定出的肽段减少。我们提出对肽段鉴定算法进行一种改进，通过明确识别并利用谱图相似性来提高其性能和准确性。
Liquid chromatography paired with tandem mass spectrometry is a standard technique for identifying peptides from complex protein mixtures. Most fragment ion spectra acquired by this technique are unique, but some are repeated. Similarities among the spectra from 1D and 2D liquid chromatography experiments were calculated by the dot product algorithm. Similar spectra were grouped, and the degree of duplication was calculated for each sample. In 1D liquid chromatography data from 1D gel bands, 18% of the fragment ion spectra were duplicates. A six-cycle 2D liquid chromatographic separation of more than 200 proteins produced 28% duplicate spectra. A rat hippocampal homogenate analyzed by a 12-cycle 2D liquid chromatographic separation contained 25% duplicate spectra. Removal of these duplicate spectra, however, resulted in fewer peptides being successfully identified by SEQUEST. We propose a modification for peptide identification algorithms that would improve their performance and accuracy by explicitly recognizing and making use of spectral similarity.