Liquid chromatography-mass spectrometry: a tool for proteome analysis and biomarker discovery and validation.

Background: Mass spectrometry (MS) coupled to liquid chromatography (LC) represents a widely used analytical tool for studying proteins, and discovering various diseases biomarkers.

Objectives/methods: To enable interested readers to grasp fundamental and experimental concepts of liquid chromatography separation for protein analytes and their accurate detection when interfaced with the powerful technique of mass spectrometry. Methods for enhancing LC separation, the utility of an atmospheric pressure soft ionization method, particularly electrospray ionization, as well as the interphase of improved chromatographic columns with the various modes of mass spectrometry, and the characteristics of the various mass analyzers, will be elucidated in order to achieve sensitive and specific detection of protein markers.

Conclusions: With a coherent biomarker pipeline, the successful throughput from a discovery phase to a robust validation method has nevertheless been disappointing. The development of faster, cost-effective and sensitive multidimensional MS methods, improvements in sample preparation and processing procedures such as high abundance protein depletion and faster chromatographic columns and modes, in addition to optimization of MS-based detection methods, are expected to improve further the analytical performance of proteomic techniques for biomarker discovery in complicated, but convenient, non- or minimally invasive clinical samples such as blood and urine, and ultimately to improve the biomarker validation process.