Preprocessing mass spectrometry (MS) data has been recognized as a crucial preliminary phase in order to perform data management and knowledge discovery tasks on mass spectra. The huge dimensionality and heterogeneity of MS data make mandatory the use of tools that are able to guide the user in the MS preprocessing task. However, most MS preprocessing tools are typically designed to perform only some preprocessing steps and are strictly coupled with MS data analysis modules. In this paper, we present Mass Spectra Preprocessing tool (MSPtool), a user-friendly versatile tool for preprocessing MS data. MSPtool provides the user with a wide set of MS preprocessing steps by means of an easy-to-use graphical interface. Also, this tool has been embedded in a time-series-based framework for MS data clustering.