Separating the wheat from the chaff: unbiased filtering of background tandem mass spectra improves protein identification
Separating the wheat from the chaff: unbiased filtering of background tandem mass spectra improves protein identification
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DOI：
10.1021/pr800140v
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发表时间：
2008-08-01
影响因子：
4.4
通讯作者：
Shevchenko, Andrej
中科院分区：
文献类型：
--
作者：
Junqueira, Magno;Spirin, Victor;Shevchenko, Andrej
在数据库搜索时，LC-MS/MS运行中获得的光谱中只有一小部分与靶蛋白的肽相匹配。其余的，操作上称为背景，光谱来自各种控制不佳的来源，影响数据库搜索的吞吐量和信心。在这里，我们报告了一种算法及其软件实现，可以快速去除背景光谱，而不管它们的精确来源。该方法估计了筛选的MS/MS光谱与来自部分冗余背景库的未注释光谱之间的相异性距离，该背景库由几个对照和空白运行汇编而成。过滤MS/MS查询增强了蛋白质鉴定能力时，搜索缺乏光谱序列匹配的特异性。在序列相似性搜索中，它平均减少了30倍的孤儿命中数，这些孤儿命中数与背景蛋白质污染物没有明确相关，需要手动验证。去除高质量的背景MS/MS光谱，同时保留数据集中来自靶蛋白的真实光谱，降低了严格数据库搜索的假阳性率，并提高了低丰度蛋白的鉴定。
Only a small fraction of spectra acquired in LC-MS/MS runs matches peptides from target proteins upon database searches. The remaining, operationally termed background, spectra originate from a variety of poorly controlled sources and affect the throughput and confidence of database searches. Here, we report an algorithm and its software implementation that rapidly removes background spectra, regardless of their precise origin. The method estimates the dissimilarity distance between screened MS/MS spectra and unannotated spectra from a partially redundant background library compiled from several control and blank runs. Filtering MS/MS queries enhanced the protein identification capacity when searches lacked spectrum to sequence matching specificity. In sequence-similarity searches it reduced by, on average, 30-fold the number of orphan hits, which were not explicitly related to background protein contaminants and required manual validation. Removing high quality background MS/MS spectra, while preserving in the data set the genuine spectra from target proteins, decreased the false positive rate of stringent database searches and improved the identification of low-abundance proteins.