Introduction:
The volume of spectral data to be processed has increased enormously with highthroughput peptide analysis techniques offered by developments of LC and MS instrumentation, a trend that has accelerated with the emergence of two dimensional LC-MS/MS configurations. The large number of spectra that are generated during the analysis of complex mixtures can lead to higher numbers of false positive identifications of proteins. It is essential to incorporate tools in the analysis that can measure the real confidence of protein identification results, not just a probabilistic score or empirical criteria. The following question was addressed for this study: What is the probability to have the observed a given SEQUEST output by chance? This is what we call misidentification probability. Here we outline the strategy we have followed to answer this question.

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