In the past dozen years, many new strategies for mass-spectrometry-based analyses of lipids have been developed. Lipidomics has emerged as a comprehensive approach to analysis of lipids from biological systems, and the most-utilized lipidomics methodologies involve electrospray ionization (ESI) sources and triple quadrupole analyzers. While mass spectral techniques for lipid profiling have advanced, challenges in developing uniform data acquisition methods and in handling, storing, and analyzing mass spectral data remain. Investigation of other ionization methods, including matrix-assisted laser desorption/ionization (MALDI) and atmospheric pressure chemical ionization (APCI), has demonstrated that these are useful in specific applications. APCI is particularly amenable to analysis of less polar lipids, and MALDI provides a rapid technology with application for tissue imaging. Time-of-flight secondary ion mass spectrometry (TOF-SIMS) is particularly suited for imaging of tissues and cells.