Spectral quality assessment for high-throughput tandem mass spectrometry proteomics
Spectral quality assessment for high-throughput tandem mass spectrometry proteomics
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DOI：
10.1089/omi.2004.8.255
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发表时间：
2004-09-01
影响因子：
3.3
通讯作者：
Kolker, E
中科院分区：
文献类型：
--
作者：
Purvine, S;Kolker, N;Kolker, E
目前细胞蛋白含量的串联质谱分析技术每次实验通常会产生数千到数万个谱图。本研究引入了一种名为 SPEQUAL 的新算法，旨在自动进行串联质谱质量评估。给定光谱的质量可以从三个基本组成部分进行评估：(i) 电荷状态区分，(ii) 总信号强度，以及 (iii) 信噪比估计。单个和多个前体电荷状态 (i) 之间的区别为给定光谱提供了二进制分数。部分（ii）和（iii）提供部分分数，随后将其汇总并乘以第一个分数。 SPEQUAL 应用于源自近 3,000 个串联质谱的 10,000 多个数据文件，并对结果（最终累积分数）进行手动验证。 SPEQUAL 的性能被确定为对于一般光谱质量估计和特别是前体电荷状态区分具有高灵敏度和特异性以及低错误率。每个部分分数均由可调节阈值控制，以针对不同的分析流程和仪器微调 SPEQUAL 的性能。该光谱质量评估工具旨在为研究人员发挥咨询作用，帮助过滤通常由高通量串联质谱蛋白质组分析产生的数千个光谱。最后，SPEQUAL 被实现为基于 Java GUI 和基于命令行的界面，可供学术和工业研究人员免费使用。
Current techniques in tandem mass spectrometric analyses of cellular protein contents often produce thousands to tens of thousands of spectra per experiment. This study introduces a new algorithm, named SPEQUAL, which is aimed at automated tandem mass spectral quality assessment. The quality of a given spectrum can be evaluated from three basic components: (i) charge state differentiation, (ii) total signal intensity, and (iii) signal-to-noise estimates. The differentiation between single and multiple precursor charge states (i) provides a binary score for a given spectrum. Components (ii) and (iii) provide partial scores which are subsequently summarized and multiplied by the first score. SPEQUAL was applied to over 10,000 data files derived from almost 3,000 tandem mass spectra, and the results (final cumulative scores) were manually verified. SPEQUAL's performance was determined to have high sensitivity and specificity and low error rates for both spectral quality estimates in general and precursor charge state differentiation in particular. Each of the partial scores is controlled by adjustable thresholds to fine-tune SPEQUAL's performance for different analysis pipelines and instrumentation. This spectral quality assessment tool is intended to act in an advisory role to the researcher, assisting in filtration of thousands of spectra typically produced by high throughput tandem mass spectrometric proteome analyses. Lastly, SPEQUAL was implemented as Java GUI-based and command-line-based interfaces freely available for both academic and industrial researchers.