Two modes of separation coupled with MS enable researchers to study complicated biological structures.Proteins are the molecular products of genes and play a central role in many biological processes. Protein expression occurs as a function of cellular and environmental conditions, and consequently proteins are expressed at different times and under different conditions. Insight is thus garnered by determining how protein expression has changed in a biological context.Over the past two decades, MS has become an important tool for the analysis of proteins. 1,2 One current method for the analysis of protein mixtures is proteolytic digestion followed by LC/MS/ MS. Once hard-to-handle proteins are converted into chemically well-behaved peptides, the approach overcomes many difficulties associated with protein mixture analysis. 3 Tandem MS has been particularly effective because the data can be directly used to identify peptides and subsequently infer which proteins (digested or undigested) are in the mixture. 4 This type of approach for the analysis of protein mixtures is often referred to as "shotgun" proteomics ( Figure 1).Because increasingly complicated biological structures are studied by tandem MS, the need for more powerful and highly resolving separation methods has grown. Consequently, the development and use of multidimensional LC (MDLC) in proteomics has thrived over the past few years. MDLC combines two or more forms of LC to increase the peak capacity, and thus the resolving power, of separations to better fractionate peptides prior to entering the mass spectrometer.High-resolution separation serves two functions in combination with MS. It better resolves peptides differing in charge and hydrophobicity to minimize ion suppression and improve ionization efficiency, and it simplifies the complexity of peptide ions entering the mass spectrometer to minimize undersampling. This last aspect is important because the tandem MS process is driven by data-dependent data acquisition and has a finite cycle time. A higher peak capacity and better resolving power improve the acquisition of data and can lead to a better representation of the proteins in the mixture. Improved resolution also results in a larger dynamic range.Although MDLC is by no means a new concept and has a long history, it has been enjoying a renaissance in proteomics. 5 In this article, we will provide an overview of the background, important applications, and future prospects for MDLC; in particular, we will focus on applications involving peptides. (To listen to a podcast about this feature, please go to the Analytical Chemistry website at pubs.acs.org/ac.)