LC/MS is rapidly becoming the technique of choice for high-throughput analysis of small volumes of biological fluid, and is an integral part of SurroMed's biological profiling platform. Existing software and algorithms for mass spectrometry data visualization and analysis are ill-equipped to deal with the the number and complexity of LC/MS spectra generated by high-throughput biomedical studies. This talk will describe a novel de-noising algorithm based on the noise distribution of LC/MS data, and a novel, general, multidimensional algorithm for distinguishing peaks from noise and artifacts that can incorporate existing knowledge and methods for identifying peaks in individual mass chromatograms and mass spectra. Together or separately, these algorithms offer significantly improved performance over current methods. A new program for LC/MS data analysis and its application to LC/MS spectra of biological samples will be discussed.

MALDI-TOF-MS has become one of the most well established techniques for the analysis of biological samples. This has been mainly due to its ease of use and relative insensitivity to biological matrixes which are used in the preparation of most biological samples.  However, it has been previously demonstrated that removing these contaminants can significantly improve the quality of the resulting spectra. Furthermore, MALDI-TOF-MS is now a technique which is routinely automated for both the sample preparation and analysis of many biological samples, which include those resulting from a proteomics experiment. Clearly, any method of sample preparation developed for MALDI-TOF-MS applications must be amenable to full automation. Presented in this poster is a new plate design for sample preparation of biological samples (patent pending). The plate design allows for the concentration of very dilute samples and the removal of inorganic salt contamination.  The whole sample preparation procedure is performed in full upon the MALDI-TOF-MS sample stage.  Presented in the poster is the optimized plate design and preparation methods to significantly improve the quality of the resulting MS spectrum compared with conventional MALDI sample preparation. The MALDI sample preparation of protein digests resulting from in gel digestion of gel spots from 2D gel electrophoresis are evaluated.  It is shown in this poster that the sensitivity of the mass spectrometer is dramatically improved. The method is compared with alternative methods of sample preparation and its amenability for automation is demonstrated.