In recent analyses of phospholipids, the application of mass spectrometry (MS) has become increasingly popular. To elucidate the function of phospholipids, it is necessary to analyze not only their classes and subclasses, but also their molecular species. In choosing analytical methods for lipidomics, we selected several different approaches in the identification of phospholipid molecular species. The first approach, global and shotgun liquid chromatographic tandem MS (LC-MS/MS) analysis, uses data-dependent MS/MS scanning, whereas the second approach is structure related, focusing on methods using precursor ion scanning or neutral loss scanning. The third approach uses theoretically expanded multiple reaction monitoring for the analysis of targeted molecules in extremely small amounts. Data from the first and second types of analyses can be obtained with the use of our search engine, Lipid Search (http://lipidsearch.jp), and most probable molecular species can be obtained with their compensated ion intensities. Identified individual molecular species can be automatically profiled according to their compensated ion intensities. Profiled data can be visualized in the state of relative increase or decrease. These data are available via the Lipid Bank (http://lipidbank.jp) and the MassBank (http://www.massbank.jp).