A dynamic noise level algorithm for spectral screening of peptide MS/MS spectra.
A dynamic noise level algorithm for spectral screening of peptide MS/MS spectra.
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DOI：
10.1186/1471-2105-11-436
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发表时间：
2010-08-23
影响因子：
3
通讯作者：
Freitas MA
中科院分区：
文献类型：
--
作者：
Xu H;Freitas MA
高通量霰弹枪蛋白质组学数据包含大量来自非肽离子的光谱或质量太差而无法获得高度自信的肽鉴定的光谱。这些光谱在某些数据库搜索程序中不能与任何阳性肽匹配识别，或者在其他数据库搜索程序中被识别为假阳性。去除这些谱可以改善数据库搜索结果，降低计算开销。提出了一种新的算法来过滤散弹枪蛋白质组学实验中质量较差的串联质谱。该算法动态地、独立地确定串联质谱数据集中各谱的噪声级。光谱根据所需信号峰值的最小数量进行滤波，信噪比为2。该算法在23个样本数据集上进行了测试，其中包含62,117个总光谱。当使用MassMatrix数据库搜索软件搜索时，光谱筛选去除了89.0%没有产生肽匹配的串联质谱。只有6.0%的串联质谱产生的肽匹配被认为是真正的阳性匹配在光谱筛选后丢失。该算法在Mascot、OMSSA、X!等数据库搜索程序中均能有效去除未识别光谱。串联（75.93% ~ 91.00%），真阳性匹配损失较小（3.59% ~ 9.40%）。
High-throughput shotgun proteomics data contain a significant number of spectra from non-peptide ions or spectra of too poor quality to obtain highly confident peptide identifications. These spectra cannot be identified with any positive peptide matches in some database search programs or are identified with false positives in others. Removing these spectra can improve the database search results and lower computational expense. A new algorithm has been developed to filter tandem mass spectra of poor quality from shotgun proteomic experiments. The algorithm determines the noise level dynamically and independently for each spectrum in a tandem mass spectrometric data set. Spectra are filtered based on a minimum number of required signal peaks with a signal-to-noise ratio of 2. The algorithm was tested with 23 sample data sets containing 62,117 total spectra. The spectral screening removed 89.0% of the tandem mass spectra that did not yield a peptide match when searched with the MassMatrix database search software. Only 6.0% of tandem mass spectra that yielded peptide matches considered to be true positive matches were lost after spectral screening. The algorithm was found to be very effective at removal of unidentified spectra in other database search programs including Mascot, OMSSA, and X!Tandem (75.93%-91.00%) with a small loss (3.59%-9.40%) of true positive matches.
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影响因子：
3.3
作者：
Purvine, S;Kolker, N;Kolker, E
通讯作者：
Kolker, E
影响因子：
4.4
作者：
Craig, R;Cortens, JP;Beavis, RC
通讯作者：
Beavis, RC
DOI：
10.1016/s1044-0305(00)00097-0
发表时间：
2000-05-01
影响因子：
3.2
作者：
Moore, RE;Young, MK;Lee, TD
通讯作者：
Lee, TD
影响因子：
3
作者：
Wong, Jason W. H.;Sullivan, Matthew J.;Cartwright, Hugh M.;Cagney, Gerard
通讯作者：
Cagney, Gerard
影响因子：
5.8
作者：
Bern, Marshall;Goldberg, David;Yates, John R., III
通讯作者：
Yates, John R., III