Proteomics Analysis of Human Renal Clear Cell Carcinoma by Two MS2-based Label-free Approaches

Advanced renal cancer is not sensitive to chemotherapy or radiotherapy, and its effective treatment is very limited. At present, the recognition of specific and effective molecular targets for advanced renal cancer is far from enough. In this work, 2046 proteins were identified from the renal clear cell carcinoma and its adjacent normal tissues by using label-free quantitative proteomics approaches based on MS2 data. Two kinds of data processing methods, i. e. spectral counting and MS2 total ion current (MS2 TIC), were used to analyze the data derived from proteomics identification. The results showed that 144 differential proteins and 120 differential proteins were screened by MS2 TIC method and spectral counting method, respectively. A total of 147 differential proteins were screened by the two methods. Among them, there were 46 up-regulated proteins in tumor tissue, including annexin A4, laminin alpha-4 subunit, pyruvate kinase, ATP citrate synthetase and histone H1.5, carbonic anhydrase 9, etc.; there were 101 down-regulated proteins in tumor tissue , including beta subunit of electron transfer flavin, 3-ketoalkyl COA thiolase, villin-1, f subunit of V-type proton ATP synthetase, mitochondrial phosphate carrier protein, 8 subunit of cytochrome b-cl complex, multidrug resistance protein 1, retinol dehydrogenase 2, uromodulin, etc. The results of some differential protein analyses were validated by using MS1-based quantitative method. The label-free quantification using MS2 data was used to analyze the proteome in renal clear cell carcinoma and its adjacent normal tissues. The differential proteins could be used as candidate biomarkers for diagnosis, treatment and prognosis of renal clear cell carcinoma, which could used to find the potential targets for effective treatment of advanced renal clear cell carcinoma.