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DeCyder™ MS is a novel software program for fully automated differential expression analysis based on LC-MS/MS data including detection, quantitation, sample to sample comparison and statistical data evaluation. Results can be interactively confirmed against original raw data through 2D and 3D data visualizations.

This work demonstrates the development and validation of a novel clinical proteomics approach in which specific protein targets can be expeditiously and selectively isolated from acomplex biological fluid for MS characterization.

By using the detection, matching, and visualization approach ofDeCyder™ MS were retention time, precursor mass, and the topology of the intensity profile is utilized in combination with the matching of tandem mass spectra, it is possible to achieve repeat analysis with a very high reproducibility.