SELYMATRA: Web Application for the analysis of mass spectra

Abstract

Surface Enhanced Laser Desorption/Ionization-Time Of Flight Mass Spectrometry (SELDI-TOF MS) is a variant of the MALDI. It is uses in many cases especially for the analysis of protein profiling and for preliminary screening tasks of complex sample aimed for the searching of biomarker. Unfortunately, these analysis are time consuming and strictly limited about the protein identification. Seldi analysis of mass spectra (SELYMATRA) is a Web Application (WA) developed with the aim of reduce these lacks automating the identification processes and introducing the possibility to predict the proteins present in complex mixtures from cells and tissues analysed by Mass Spectrometry. SELYMATRA has the following characteristics. The architectural pattern used to develop the WA is the Model-View-Controller (MVC), extremely used in the development of software system. The WA expects an user to upload data in a Microsoft Excel spreadsheet file format, usually generated by means of the proprietary Mass Spectrometry softwares. Several parameters can be set such as experiment conditions, range of isoelectric point, range of pH, relative errors and so on. The WA compare the mass value among two mass spectra (sample vs control) to extract differences, and according to the parameters set, it queries a local database for the prediction of the most likely proteins related to the masses differently expressed. The WA was validated in a cellular model overexpressing a tagged NURR1 receptor. SELYMATRA is available at http://140.164.61.23:8080/SELYMATRA.