Fractionation of phosphopeptides on strong anion-exchange capillary trap column for large-scale phosphoproteome analysis of microgram samples.

It is one of the key issues to develop powerful fractionating method to increase the identification of the low-abundance phosphopeptides. In this study, a semi-online 2-D LC separation strategy based on three-step fractionation of the enriched peptides on strong anion-exchange trap column was developed. It was demonstrated that the sensitivity and phosphoproteome coverage obtained by this fractionating method with strong anion-exchange trap column is much higher than those by the conventional methods based on C18 trap column. In addition, when the same amount of sample was loaded, the number of identified phosphopeptides had increased 108%. Combination of this three-step fractionation method with RPLC-MS/MS analysis by 300 min RP-gradient separation was applied to phosphoproteome analysis of human liver proteins, and 853 unique phosphopeptides was positively identified from 500 microg tryptic digest of human liver proteins. After three cycles' consecutive analyses, 1554 unique phosphopeptides and 1566 phosphorylated sites were totally identified from 735 phosphorylated proteins at a false discovery rate of <1% in about 54 h of analysis time.