Reproducibility in Protein Profiling by MALDI-TOF Mass Spectrometry (Proteomics and Protein Markers‪)‬

Protein profiling with high-throughput sample preparation and MALDI-TOF MS analysis is a new potential tool for the diagnosis of human diseases (1). In MALDI protein profiling, biological fluids such as serum, urine, and tissue extracts are treated with a simple preparation step to capture proteins and remove lipids and salts. The protein solution is mixed with a so-called matrix solution that catalyzes the (co)crystallization of matrix molecules and proteins onto a target plate, and the target plate is then analyzed by MALDI-TOF MS. In MALDI-TOF MS the proteins are liberated in an ionized form from the target surface by firing a laser pulse at the crystallized proteins. The ionized proteins are accelerated through a vacuum tube by an electrical field and reach a detector. Smaller proteins are accelerated to higher velocities than heavier proteins, and the "time of flight" is proportional to m/z. The charge (z) of the ionized proteins is often 1, making the m/z value equal to the mass value. The spectral output produced by MALDI protein profiling consists of a number of protein peaks, which are described by an m/z value on the horizontal axis and by a peak-intensity value on the vertical axis, and is referred to as a "protein profile". Recently, MALDI protein profiling has been applied in proteomics biomarker research (1); however, several aspects of MALDI protein profiling need further evaluation and optimization before clinical use (2). First, high-throughput MALDI protein profiling is presently confined to the detection of highly abundant proteins (1). For example, with the MALDI protein-profiling platforms from Ciphergen Biosystems (the SELDI-TOF MS platform) and Bruker Daltonics, serum analyses primarily detect highly abundant plasma proteins and their fragments [e.g., (3)]. Sensitivity in clinical proteomics can be effectively improved with extensive prefractionation strategies, which still need critical evaluation before they can be used in high-throughput protein profiling. In one study, the use of reversed-phase HPLC and MALDI protein profiling to analyze plasma samples in a medium-throughput setup led to improved sensitivity (4).