Quality control of the secretary protein sample and identification of secretary proteins by proteomic data analysis

Abstract

Secretary proteins samples are usually polluted by cellular proteins from lysed cells in the culture. Here we set up a method for quality control of the sample and identification of secretary proteins by proteomic data analysis. Secretary protein samples from cultured cells and the soluble cell lysate were analyzed separately by SCX-RP-MS/MS. Several high abundant secretary proteins, which were annotated as secretary in swissprot and predicted as secretary by signal peptide prediction, were used as secretary protein markers. The ratios of positively identified spectra numbers of these marker proteins to total positive spectra in secretary protein sample or soluble cell lysate were defined as RSP or RSCL respectively. The enrichment multiple (EM) of secretary protein was estimated as RSP/RSCL. Secretary proteins were identified based on the ratio of positive spectra weight of each protein in secretary proteins sample and its weight in soluble cell lysate sample. We analyzed the secretary proteins of mouse dendritic cell sarcoma cell line cultured in protein-free medium. The sample EM is 39.144 proteins were identified, of which 99 proteins were known to be secreted, 33 proteins were both swiss-prot annotated and signal peptide predicted as secretary. 22 proteins were identified by either signal peptide prediction or swiss-prot annotation, 44 proteins were previously unidentified as secretary proteins. This work was supported by grants from National Natural Science Fundation of China (30370301)