Introduction

In analytical chemistry, the objective of non-targeted analysis (NTA) is to detect and identify unknown (generally organic) compounds using a combination of advanced analytical instrumentation (e.g. high-resolution mass spectrometry) and computational tools. For NTA using mass spectrometry, the use of reference libraries containing fragmentation mass spectra of known compounds is essential to successfully identifying unknown compounds in complex mixtures. However, due to the diversity of vendors of mass spectrometers and mass spectrometry software, it is difficult to easily share mass spectral data sets between laboratories using different instrument vendor software packages while maintaining the quality and detail of complex data and metadata that makes the mass spectra commutable and useful. Additionally, this diversity can also alter fragmentation patterns as instrument engineering and method settings can differ between analyses.

This report describes a set of tools developed in the NIST Chemical Sciences Division to provide a database infrastructure for the management and use of NTA data and associated metadata. In addition, as part of a NIST-wide effort to make data more Findable, Accessible, Interoperable, and Reusable (FAIR), the database and affiliated tools were designed using only open-source resources that can be easily shared and reused by researchers within and outside of NIST. The information provided in this report includes guidance for the setup, population, and use of the database and its affiliated analysis tools. This effort has been primarily supported by the Department of Defense Strategic Environmental Research and Development Program (DOD-SERDP), project number ER20-1056. As that project focuses on per- and polyfluoroalkyl substances (PFAS), DIMSpec is distributed with mass spectra including compounds on the NIST Suspect List of Possible PFAS (Place, Benjamin J. 2021b) as collected using the Non-Targeted Analysis Method Reporting Tool.

This toolkit1 was developed as part of the NIST PFAS program in the Material Measurement Laboratory’s Chemical Sciences Division. It is primarily developed in R and SQLite. The remainder of this book describes the toolkit, its technical details, and how to use it.

Contributors

The main two contributors to code and data in this project are

Additional members of NIST PFAS project team providing guidance, input, and testing for this project include

Contributing

Contributions to this project are encouraged! NIST engaged in this project to meet the goals of a single research project. We have made this project available in the name of the public interest and with hopes it will prove useful outside the immediate context. Issues with the code are most effectively reported through GitHub. Pull requests are also encouraged.

About this Book

Chapters and sections in this book were originally drafted and approved as NIST Reports of Analysis within the Chemical Sciences Division. This book serves as the official User Guide for the DIMSpec project and will be expanded and updated appropriately. Internal NIST Reports of Analysis describing each aspect of the project were converted to R Markdown documents and stitched together using the bookdown package (v0.29). As a “living” document, this book will be maintained as long as the underlying project is active and as author time obligations allow. If a section is insufficiently documented, let us know.

References

———. 2021b. “Suspect List of Possible Per- and Polyfluoroalkyl Substances (PFAS).” National Institute of Standards; Technology. https://doi.org/10.18434/MDS2-2387.

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