There is intense interest in comprehensive proteomic approaches for analyzing integral membrane proteins and lipoproteins. Key features of mass spectrometric analysis center on enriching biological material for proteins of interest, efficiently digesting them, extracting the resulting peptides, and using fractionation methods to comprehensively sample proteins or peptides by tandem mass spectrometry. However, lipid-associated proteins are generally rich in hydrophobic domains and are often low in abundance. These features, together with the associated lipid, make their mass spectrometric analysis technically challenging. In this article, we review analytical strategies for successful proteomic analysis of lipid-associated proteins. Now that the genomes of humans and many model organisms have been fully sequenced, scientists must determine the molecular and cellular functions of the hundreds of thousands of proteins encoded by those genomes. They would also like to explain how the proteins cooperate or otherwise interact in complex physiological systems and how inappropriate interactions trigger human disease. These important biological problems are the central focus of the rapidly emerging field of proteomics, the study of protein expression, structure, and function.Mass spectrometry (MS) is a powerful tool for proteomics because it can identify and quantify hundreds or even thousands of proteins in complex biological samples. To study peptides and proteins with MS, it is necessary to vaporize these normally involatile compounds. Therefore, a key element in the development of MS-based proteomics, recognized by the 2002 Nobel Prize in Chemistry, was the discovery of methods for introducing peptides and proteins into the gas phase (1, 2).The two most common ionization techniques are ESI and MALDI. ESI is typically applied to analytes in the liquid phase and is often used in concert with separation techniques, such as reverse-phase chromatography. Therefore, it is well suited to the analysis of complex mixtures. MALDI, which uses laser pulses to vaporize analytes embedded in a crystalline matrix, is generally applied to relatively simple mixtures of peptides or proteins.Although protein identification based on tandem mass spectrometric (MS/MS) analysis of intact proteins is an ideal approach, this so-called "top-down" proteomic method (3) is still being developed and is not amenable to largescale investigations. Most proteomic studies take a "bottomup" approach (4) by first digesting proteins with a protease (typically trypsin). The resulting small peptides are much more amenable to separation [typically by liquid chromatography (LC)] and MS/MS analysis.Two general approaches have evolved for protein analysis: gel-based proteomics and gel-free proteomics. The first methodology is widely used by biological investigators and involves various forms of electrophoretic gel-based separations, primarily one-dimensional (e.g., SDS-PAGE) or two-dimensional electrophoresis (2DE). Separated protein spots (or proteoly...