Integrated Analysis Of Hepatic Carcinoma Proteomics Data Based On Spectral Library Identification Strategy

Hepatocellular carcinoma is one of the most common malignancies and its mortality ranks second among all the malignancies in the world.Its etiology and specific molecular mechanisms of action have not been well studied.Proteomics study on liver cancer inis one of the hot and important areas of current life sciences.With its high sensitivity and fast speed,the spectral library searching has become a mature strategy for tandem mass spectra based proteins identification in proteomics recently.Many continuously updated spectral library construction and search tools have been developed.But their principles and characteristics are different and there is no standard on how to choose a suitable tool for data analysis.Therefore,it is very important to comprehensively evaluate the spectral library identification tools and establish a standardized workflow for the study of liver cancer.We implement a comprehensive evaluation of three spectral library building tools and four spectral library search engines is implemented in this paper.Firstly,in this study a comprehensive evaluation of spectral library search strategy is implemented and a complete pipeline of spectra library search strategy is built.Secondly,five liver cancer proteomics datasets are used to construct a liver cancer specific spectra library which contains a total of 93,951 peptides.Finally,the spectra library is applied to liver cancer analysis.The results show that the spectrum identification rate is increased by 18.06%,and the number of identified proteins is increased by 51.98%,compared with MaxQuant.Compared with the expression data of proteins identified before,fifty-five proteins are found significantly differently expressed in hepatocellular carcinoma and cirrhosis.There are 16 proteins that showed significant difference in both of the two data sets from Tanta University(TU dataset)and Georgetown University(GU dataset).Among these proteins,COMP,VWF and APOC1 have not been reported to be involved in liver cancer before.This study shows that the spectra library search strategy with a self-buillt specific spectral library can significantly improve the spectrum identification rate and increase the number of identified proteins.New potential liver cancer markers can by discovered by integrating proteome data analysis.It lays a foundation for further study of liver cancer,and provides a reference for the analysis of other critical diseases.