Efficacy analysis of combining three comparative-omics profilings to screen candidate biological macromolecules

To evaluate the efficacy of integrated comparative omics in screening candidate biological macromolecules, three methods, namely, 2-DE + MALDI-TOF-MS, tumor-associated cDNA microarray and whole-transcriptome cDNA microarray were examined by three biotechnological companies to compare a stable transfected cell line with its control one. The results showed that the percentages of the up-regulate in three methods are largely consistent. 21.59 % of tumor-associated microarray results are the same with that of whole-transcriptome microarray. SOD2 is the unique intersection of three methods. Consulting the results of pI and Mw derived from microarray cannot increase the detection rate of target molecules during protein spot selection for mass spectrometry. Two protein spots with different regulating directions were identified to be the same protein. Conclusively, proteomic and genomic methods reveal the macromolecular changes from different aspects. Their detection ranges are complementary. The combination of different genomic methods can improve the validity and stability and reduce the noise changes. However, it is no sense to compare proteomics with genomics.