MRMPROBS is launched as a universal program for targeted metabolomics using not only multiple reaction monitoring (MRM)- or selected reaction monitoring (SRM) but also SCAN and data independent MS/MS acquisition (DIA) data. Our objective is to develop a data processing tool for widely targeted metabolomics by means of mass spectrometers such as QqQ-MS, DIA-MS, and just single Q-MS. Although the strategy became increasingly popular for the simultaneous analysis of up to several hundred metabolites at high sensitivity, selectivity, and quantitative capability, software development for the data analysis of MRM transitions lags behind in metabolomics: data assessment usually relies on manual evaluation due to the lack of automated probabilistic measures. Here, we developed a software program, MRMPROBS (Multiple Reaction Monitoring based PROBabilistic System for widely targeted metabolomics), written in C# language for widely targeted metabolomics. It evaluates the metabolite peaks by posterior probability, defined as the odds ratio by means of a newly optimized multivariate logistic regression model, and visualizes large-scale MS data sets with user-friendly graphical user interfaces to allow data curation and statistical analyses.