Quantitative proteome analysis of proteins of K562 cell line by 18 O- labeling and LC-MS/MS technology

Aim Quantitative analysis of global protein levels, termed 'quantitative proteomics', is important for the system-based understanding of the molecular function of each protein component and is expected to provide insights into molecular mechanisms of various biological processes and systems. This study is to establish the quantitative proteomics of K562 cell line. Methods The protein quantitation of K562 cell line by 18 O labeling and LC-MS/MS technology. Results The identified proteins were performed by Bioworks version 3.1 (Thermo Finnigan) Protein Prophet of SEQUEST and Trans-Proteomic Pipeline systems. Under the protein probability > 0.5, peptide sequence was filtered, and obtained 186 peptide sequences. When probability >0.5, the false-positive rates were 14.8%, and the sensitivity was 73.2%. When protein probability > 0.4, it obtained 94 identified proteins and the sensitivity was 89.9%. It is showed that the condition for protein identification was accepted. The comparing test of 18 O- and 16 O-labeling proteins showed that the 18 O-labeling efficiency was affectied by LC-MS/MS analysis, SCX ion-exchanges, RP-LC separation and ion suppression of ESI. The accepted range of protein quantification was 0.5-2.0. In this range, the error rate was 12.6 %. Conclusion The study presented identifition and quantitation of proteins in K562 cell line, that has not been reported before, and employed a quantitative proteomic method will be useful for the protein difference in cancer sample versus normal.