In this work a systematic strategy integrating liquid chromatography/tandem mass spectrometry (LC/MS/MS) and online databases was developed to identify phosphocholines (PC) and lysophosphatidylcholines (LPC) in human red blood cells (RBCs). First of all, the neutral loss scan of 59 and the precursor ion scan of m/z 184 were performed to find out the possible lipids with phosphocholine head-group structure in RBCs. The acquired [M+H]+ and [M+Na]+ adduct ions were then identified online using the Human Metabolome Database (HMDB) and the LIPID MAPS, which were then further confirmed by their MS/MS fragmentation. Based on the comparison of chemical structures of the detected PC and LPC with their corresponding MS/MS fragmentation pathways, several new diagnostic fragments or fragmentation pathway were found. These include, (1) the neutral losses of 183 could be used as a diagnostic fragmentation to discriminate PC and LPC; (2) product ions at m/z 104 could be used to distinguish LPC and their sn-2 isomers; (3) fragment ions at m/z 184 are characteristic fragmentation that could be used for discrimination of sodiated ions [M+Na]+ and protonated ions [M+H]+, especially for co-eluted PC or LPC with a molecular weight difference of 22. The structures of the above-mentioned fragment ions were confirmed by quadrupole time-of-flight (Q-TOF) MS. Furthermore, a PC and LPC focused LC/MS semi-quantification approach was also developed and validated. This approach could be useful for future lipidomic study. Copyright © 2009 John Wiley & Sons, Ltd.