Analysis of serum proteins by LC-MS/MS

Serum contains a vast array of proteins, some of which are specific to blood whilst others are secreted into blood from tissues and organs. The so-called tissue leakage factors reveal information about the tissue from which they originate and are therefore of great potential importance as disease biomarkers. There are already a number of blood-borne biomarkers in routine clinical use that aid in the diagnosis or management of cancer. However, there is a pressing need for additional markers, and new methods to find them are under development. Here we provide a protocol for serum protein profiling using liquid chromatography tandem mass spectrometry (LC-MS/MS). Included in this procedure, we detail the pre-processing steps of lipid and high-abundance protein removal. These procedures can also be employed up-stream of quantification methods such as isobaric tags for relative and absolute quantification (iTRAQ). Chapter 12 is devoted to the iTRAQ approach for quantifying proteins, and it is therefore not described in this chapter.