The use of hyphenated Fourier transform mass spectrometry (FTMS) methods affords additional information about complex chemical mixtures. Coeluted components can be resolved thanks to the ultrahigh resolving power, which also allows extracted ion chromatograms (EICs) to be used for the observation of isomers. As such data sets can be large and data analyses laborious, improved tools are needed for data analyses and extraction of key information. The typical workflow for this type of data is based upon manually dividing the total ion chromatogram (TIC) into several windows of usually equal retention time, averaging the signal of each window to create a single mass spectrum, extracting a peak list, performing the compositional assignments, visualizing the results, and repeating the process for each window. Through removal of the need to manually divide a data set into many time windows and analyze each one, a time-consuming workflow has been significantly simplified. An environmental sample from the oil sands region of Alberta, Canada, and dissolved organic matter samples from the Suwannee River Fulvic Acid (SRFA) and marine waters (Marine DOM) were used as a test bed for the new method. A complete solution named KairosMS was developed in the R language utilizing the Tidyverse packages and Shiny for the user interface. KairosMS imports raw data from common file types, processes it, and exports a mass list for compositional assignments. KairosMS then incorporates those assignments for analysis and visualization. The present method increases the computational speed while reducing the manual work of the analysis when compared to other current methods. The algorithm subsequently incorporates the assignments into the processed data set, generating a series of interactive plots, EICs for individual components or entire compound classes, and can export raw data or graphics for off-line use. Using the example of petroleum related data, it is then visualized according to heteroatom class, carbon number, double bond equivalents, and retention time. The algorithm also gives the ability to screen for isomeric contributions and to follow homologous series or compound classes, instead of individual components, as a function of time.