Reducing the haystack to find the needle: improved protein identification after fast elimination of non-interpretable peptide MS/MS spectra and noise reduction.
Reducing the haystack to find the needle: improved protein identification after fast elimination of non-interpretable peptide MS/MS spectra and noise reduction.
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DOI：
10.1186/1471-2164-11-s1-s13
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发表时间：
2010-02-10
期刊：
影响因子：
4.4
通讯作者：
Eisenhaber F
中科院分区：
文献类型：
--
作者：
Mujezinovic N;Schneider G;Wildpaner M;Mechtler K;Eisenhaber F
串联质谱仪(MS/MS)已成为鉴定生物样品中蛋白质的标准方法，但MS/MS谱图的庞大数量和噪声污染阻碍了快速、可靠的计算机辅助解释。通常，如果蛋白质识别根本不受噪声的阻碍，每个样本的一小部分光谱(最常见的是只有几个%)和大约10%的峰对最终结果有贡献。两个快速的前处理屏幕可以大大减少MS/MS数据的海量。(1)简单的序列梯形规则去除了多肽序列中无法解释的光谱。(2)改进的傅立叶变换判据清除了剩余数据中的背景。平均而言，只有35%的MS/MS谱(每个谱的大小减小约四分之一)的剩余部分必须移交给解释软件，以进行可靠的蛋白质鉴定，基本上不会丢失信息，趋势是提高序列覆盖范围，并按比例减少计算机资源消耗。在串联MS/MS谱中寻找序列阶梯并随后抑制噪声是一种有希望的策略，可以减少电喷雾MS/MS谱的数量，提高蛋白质匹配的可靠性。补充材料和软件可从附带的网址为http://mendel.bii.a-star.edu.sg/mass-spectrometry/MSCleaner-2.0/.的万维网站点获得
Tandem mass spectrometry (MS/MS) has become a standard method for identification of proteins extracted from biological samples but the huge number and the noise contamination of MS/MS spectra obstruct swift and reliable computer-aided interpretation. Typically, a minor fraction of the spectra per sample (most often, only a few %) and about 10% of the peaks per spectrum contribute to the final result if protein identification is not prevented by the noise at all. Two fast preprocessing screens can substantially reduce the haystack of MS/MS data. (1) Simple sequence ladder rules remove spectra non-interpretable in peptide sequences. (2) Modified Fourier-transform-based criteria clear background in the remaining data. In average, only a remainder of 35% of the MS/MS spectra (each reduced in size by about one quarter) has to be handed over to the interpretation software for reliable protein identification essentially without loss of information, with a trend to improved sequence coverage and with proportional decrease of computer resource consumption. The search for sequence ladders in tandem MS/MS spectra with subsequent noise suppression is a promising strategy to reduce the number of MS/MS spectra from electro-spray instruments and to enhance the reliability of protein matches. Supplementary material and the software are available from an accompanying WWW-site with the URL http://mendel.bii.a-star.edu.sg/mass-spectrometry/MSCleaner-2.0/.