TracMass 2--a modular suite of tools for processing chromatography-full scan mass spectrometry data.

In untargeted proteomics and metabolomics, raw data obtained with an LC/MS instrument are processed into a format that can be used for statistical analysis. Full scan MS data from chromatographic separation of biological samples are complex and analyte concentrations need to be extracted and aligned so that they can be compared across the samples. Several computer programs and methods have been developed for this purpose. There is still a need to improve the ease of use and feedback to the user because of the advanced multiparametric algorithms used. Here, we present and make publicly available, TracMass 2, a suite of computer programs that gives immediate graphical feedback to the data analyst on parameter settings and processing results, as well as producing state-of-the-art results. The main advantage of TracMass 2 is that the feedback and transparency of the processing steps generate confidence in the end result, which is a table of peak intensities. The data analyst can easily validate every step of the processing pipeline. Because the user receives feedback on how all parameter values affect the result before starting a lengthy computation, the user's learning curve is enhanced and the total time used for data processing can be reduced. TracMass 2 has been released as open source and is included in the Supporting Information . We anticipate that TracMass 2 will set a new standard for how chemometrical algorithms are implemented in computer programs.