S2P: A software tool to quickly carry out reproducible biomedical research projects involving 2D-gel and MALDI-TOF MS protein data

•S2P, a multiplatform application for the integrated analysis of 2D-gel and MALDI-based mass spectrometry protein data is presented.•Our software provides different functionalities to process 2D-gel and MALDI-mass spectrometry protein identification-based data in a computer-aided, reproducible manner.•S2P incorporates a user-friendly, intuitive graphical user interface (GUI), designed for biomedical researchers without advanced bioinformatics skills.•S2P reduces the time that researchers need to invest in order to prepare data for subsequent analysis, such as discovering potential biomarkers.•Different case studies demonstrate the usefulness of S2P.