Schymanski's first research publications were from her undergraduate work when she worked on developing new metal-containing polymers which resulted in three lead author publications.
As a graduate student, Schymanski started using information on the fragmentation pattern of organic compounds as a means to expand the identification of unknown compounds. Schymanski applied these novel methods to the identification of unknown organic compounds found in wastewater, and used data collectively gathered by the NORMAN Association to define barriers to the identification of unknown organic compounds in water. Identifying and tracking unknown organic compounds continues to be an avenue of research pursued by Schymanski and she is a co-author on a 2014 textbook describing these methods.
In 2012, Schymanski and Steffen Neumann started the Critical Assessment of Small Molecule Identification (CASMI) contest that provided researchers with information about unknown organic compounds and challenged them to use automated computational tools identify the unknown compounds. The Metabolomics Society highlighted the 2012 contest in their newsletter. There have been multiple iterations of the contest, and Schymanski examined the results of the 2016 contest.
Schymanski's research focuses on characterizing organic compounds found in wastewater and exposomics, or the science of compounds that people are exposed to over their lifetimes. Schymanski has developed a subset of PubChem for exposomics, PubChemLite, which can be annotated to increase ability of researchers to identify unknown environmental compounds. Within this field, Schymanski is working to automate the identification of a group of fluorinated compounds called ‘per- and poly-fluoroalkyl substances’ (PFASs) in order to increase the ability of researchers to find unknown PFAS in the environment.
Schymanski is an advocate for open science and data sharing. Within the NORMAN network, a collaborative activity across Europe, North America, and Asia, Schymanski worked in 2011 with the team that established NORMAN MassBank, which was a community-driven project to gather information about small molecules. In 2015, Schymanski expanded this type of data with the NORMAN Suspect List Exchange. Schymanski has also worked to develop computational tools that allow the processing of complex high resolution mass spectrometry data and sought to establish standards to consider the quality of the mass spectrometry data. Schymanskis 2014 publication in Environmental Science & Technology' establishes a means to estimate confidence in the quality of unknown organic compound identifications and, as of 2021, has over 1000 citations. In 2018, Schymanski considered this paper her greatest achievement because it established the standard for compound identification in metabolomics and encouraged community conversation about future of these tools.