There are many situations where it is important to understand the chemical information of a sample and how it changes through a process or over a time period. This information can provide good insight about a system and is useful for addressing a variety of questions and analysis objectives. For example, it may reveal the chemical reactions and the kinetics of the process. It may also indicate when a target state has been achieved, when a system is deviating from a target state, or how parameter variations impact the process. These types of detailed investigations can be important for optimization and understanding a wide range of systems. In this work, we explore the process of food spoilage by tracking the degradation of tomatoes. While this is a specific look at a tomato, an understanding of general food deterioration is important as spoilage impacts the quality and safety of food products and has significant financial implications. Until a process like this is well understood, evaluating the chemical profile and the changes is generally a non-targeted discovery task. For food spoilage, many of the changes that occur will be reflected in the volatile and semi-volatile components of the sample. The aroma profile of the sample itself changes, and chemical markers of microbial activity are also likely to form. GC and TOFMS are well-established techniques for these types of non-targeted characterizations of volatile and semi-volatile analytes and are well-suited for this type of investigation. Individual analytes are separated by GC, and TOFMS often provides the identification for these isolated analytes. The analyte coverage and sample characterization can be improved further by extending the analytical separation to two dimensions with comprehensive two-dimensional gas chromatography (GCxGC). GCxGC enhances the peak capacity and allows for more thoroughly exploring complex samples by determining more individual analytes. One of the challenges of interpreting this rich data, however, is linking analyte information across the multiple samples in order to determine the trends and patterns. Thus, software tools that compare sets of GCxGC samples are also useful for this type of analysis. LECO’s ChromaTOF Sync 2D offers advanced data processing options for handling these types of data sets. The software facilitates non-targeted characterization and comparisons by combining information for multiple GCxGC samples to a single peak table with full peak finding and deconvolution. This allows for effectively comparing analytes across the data set to find similarities, differences, and trends. The combination of GCxGC-TOFMS and ChromaTOF Sync 2D helped to reveal useful information about the tomato samples. In this case, the tools are demonstrated for monitoring the spoilage of a tomato sample, but they have broad applicability for many other process types.