Department of Biomedical Engineering, The University of Texas, Austin, Texas 78712, USA.
OMICS. 2010 Feb;14(1):115-26. doi: 10.1089/omi.2009.0082.
Proteomic profiling by mass spectrometry has tremendous potential for identifying disease biomarkers. A key limitation of mass spectrometry is that the information provided on the abundance of the various peptides is only relative. Thus, normalization is typically employed. Several normalization methods have been proposed and implemented in the literature. However, it is not clear if there is any reason to prefer one method over another. The goal of this study was to investigate the effect of normalization strategy on the identification of putative biomarkers from MALDI-TOF and SELDI-TOF mass spectra. Our results demonstrate that many of the putative biomarkers identified by mass spectrometry will be the same regardless of which data normalization scheme is applied. However, there can be substantial differences in the m/z values identified as being most discriminatory based on choice of normalization method. As there is no consistent pattern as to which normalization method yields the most promising targets for follow up study, we recommend that investigators routinely repeat their analysis with multiple normalization methods and consider the top several candidates identified in each case.
蛋白质组学通过质谱分析具有巨大的潜力来识别疾病生物标志物。质谱分析的一个主要限制是，关于各种肽丰度的信息仅具有相对意义。因此，通常采用标准化。已经在文献中提出并实施了几种标准化方法。然而，目前尚不清楚是否有任何理由偏爱一种方法而不是另一种方法。本研究的目的是研究标准化策略对从 MALDI-TOF 和 SELDI-TOF 质谱中鉴定潜在生物标志物的影响。我们的结果表明，无论应用哪种数据标准化方案，通过质谱鉴定的许多潜在生物标志物都是相同的。然而，基于标准化方法的选择，被鉴定为最具区分性的 m/z 值可能会有很大差异。由于没有一致的模式表明哪种标准化方法产生最有希望的后续研究目标，因此我们建议研究人员定期使用多种标准化方法重复他们的分析，并考虑每种情况下鉴定出的前几个候选者。
