Department of Chemistry and Biology, Ryerson University, Toronto, Ontario, Canada.
Anal Biochem. 2011 Feb 15;409(2):189-94. doi: 10.1016/j.ab.2010.10.027. Epub 2010 Oct 25.
Proteomics uses tandem mass spectrometers and correlation algorithms to match peptides and their fragment spectra to amino acid sequences. The replication of multiple liquid chromatography experiments with electrospray ionization of peptides and tandem mass spectrometry (LC-ESI-MS/MS) produces large sets of MS/MS spectra. There is a need to assess the quality of large sets of experimental results by statistical comparison with that of random expectation. Classical frequency-based statistics such as goodness-of-fit tests for peptide-to-protein distributions could be used to calculate the probability that an entire set of experimental results has arisen by random chance. The frequency distributions of authentic MS/MS spectra from human blood were compared with those of false positive MS/MS spectra generated by a computer, or instrument noise, using the chi-square test. Here the mechanics of the chi-square test to compare the results in toto from a set of LC-ESI-MS/MS experiments with those of random expectation is detailed. The chi-square analysis of authentic spectra demonstrates unambiguously that the analysis of blood proteins separated by partition chromatography prior to tryptic digestions has a low probability that the cumulative peptide-to-protein distribution is the same as that of random or noise false positive spectra.
蛋白质组学使用串联质谱仪和相关算法将肽及其片段图谱与氨基酸序列进行匹配。通过对肽的液相色谱-电喷雾电离和串联质谱（LC-ESI-MS/MS）进行多次复制实验，会产生大量的 MS/MS 图谱。需要通过与随机预期的统计比较来评估大量实验结果的质量。经典的基于频率的统计方法，如肽-蛋白分布的拟合优度检验，可以用于计算整个实验结果是随机产生的概率。使用卡方检验比较来自人血液的真实 MS/MS 图谱与计算机生成的假阳性 MS/MS 图谱或仪器噪声的频率分布。这里详细介绍了将一组 LC-ESI-MS/MS 实验的结果与随机预期结果进行整体比较的卡方检验的原理。真实图谱的卡方分析明确表明，在胰蛋白酶消化之前通过分配色谱分离血液蛋白质的分析，其累积的肽-蛋白分布与随机或噪声假阳性图谱相同的可能性很低。
