The SELDI-TOF mass spectroscopy platform was designed for high-throughput protein profiling and biomarker discovery. The resolution of SELDI-TOF has been improved by incorporating fractionation and a variety of affinity capture techniques [1,2]. Still there are sources of technical and biologic variation which make reproducing and validating potential biomarkers challenging [3-6]. Further refinements to the technique are necessary to ensure that the variability in mass spectra is due to biology and to minimize systematic biases from non-disease associated factors [7-9].
Validation of disease biomarkers relies on optimized and reproducible laboratory methods. The automation of the SELDI-TOF platform and the standardization of parameters for analysis have resulted in good intra- and inter-laboratory correlation and relatively reproducible results [2,3,8]. However, there is still a need to identify the sources of variation and determine how to reduce the variation to make the SELDI-TOF platform reliable and reproducible. We examined some the front-end steps, including sample handling and preparation that occur during SELDI-TOF. Fine-tune adjustments of laser intensity and detector sensitivity for each chip type and each fraction coupled with spot-to-spot correction increased peak detection and significantly decreased the intensity coefficient of variation (CV). These further refinements to the SELDI-TOF platform will enhance biomarker identification and validation efforts.
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