plantMASST: A New Tool for Plant Metabolite Research

Our planet has around 450 plant families, 16,000 genera, and 350,000 species of vascular plants. Plants play a vital role in keeping our planet healthy by changing carbon dioxide into oxygen. They also support animal life, including humans, and have been used for treating diseases. Despite their importance, figuring out where Plant Metabolites are found in different species is challenging. This difficulty arises because there is no common open-access database for plant metabolites and their known compounds. Additionally, not every plant species has been studied, and not every possible metabolite has been found.

#The Need for a Database

Most studies focusing on plant chemicals are limited to certain groups of plants and rely on data that is already available. This limits the ability to find molecules that have not yet been described. However, we can create a comprehensive inventory of plant metabolites worldwide because new technologies and methods in Mass Spectrometry (MS) are improving. To support this effort, a new tool called plantMASST has been created. It helps search for plant metabolites within a large network called GNPS.

#What is plantMASST?

plantMASST is designed to make searching for plant metabolites easier. It builds on the methods used for studying microbes. This tool creates a digital collection of plant metabolomic data that has not been targeted. Users can search for both known and unknown molecules using a curated database of liquid chromatography-tandem mass spectrometry (LC-MS/MS) data from plant samples. The results can be connected to the broader Taxonomic Tree of plants.

As of May 2024, the plantMASST database has over 19,000 plant extracts and more than 100 million MS/MS spectra linked to their taxonomic details. This project has been supported by contributions from 90 scientists all over the world. Currently, it includes 246 plant families, 1,469 genera, and 2,793 species. The community is encouraged to add new plant datasets to a specific database to expand plantMASST.

#How plantMASST Works

Using plantMASST is straightforward. A user can search for a specific MS/MS spectrum through its web interface. The output of the search lists all files where the chosen spectrum is found, based on user-defined criteria. The tool also generates an interactive taxonomic tree to visualize the results.

To perform a search, users can provide a Universal Spectrum Identifier or the mass-to-charge ratio and a list of fragment ions. The default settings for the search include specific tolerances for mass variations and similarity scores, ensuring accurate matches. Users can also look for related analogs of known molecules and check against public spectral libraries for direct identification.

#Applications of plantMASST

#Discovering Natural Products

One key application of plantMASST is in the discovery of natural products. Researchers are interested in knowing where specific plant-derived molecules occur. For instance, they recently searched for moroidin, a compound that has shown promise in treating lung cancer. Using plantMASST, they identified several plant species producing moroidin, including one not previously known to produce it. This expands our knowledge of where valuable compounds can be found.

Similarly, the search for piperlongumine, which has cancer-fighting properties, revealed its presence in new plant species not previously associated with this molecule. This highlights how plantMASST can uncover the production of important compounds across different plants.

#Exploring Neuroactive Compounds

Another significant use of plantMASST is in identifying neuroactive compounds in plants. These compounds affect brain function and are also known to be produced by humans. For example, the search for serotonin, a common neuroactive, showed its presence in many plant families. Notably, certain plants like those in the Banisteriopsis genus, which are used traditionally for mental health treatment, were found to have high levels of serotonin. This suggests further investigation on how these plants might affect human health.

Furthermore, other known neuroactive compounds such as dopamine, GABA, and THC were also explored through plantMASST. Results indicated that specific plants are rich sources of these compounds, providing leads for potential medicinal uses.

#Dietary Studies

Lastly, plantMASST can help in analyzing how plants are consumed in human diets. Recent studies investigated diet patterns, comparing vegan and omnivorous diets, as well as American and Mediterranean diets. The results indicated that individuals following a vegan or Mediterranean diet had a higher percentage of plant-derived metabolites in their samples compared to the other groups. This suggests that plantMASST may be useful in examining how dietary choices impact health.

#Limitations of plantMASST

While plantMASST is powerful, users should be aware of its limitations. The current database includes a mix of samples with different experimental conditions. Factors like the type of plant part used, growth conditions, and extraction methods can affect the results. This means that even if a plant is known to produce a certain compound, it may not always show up in the database due to various reasons, including low concentration of the compound.

Moreover, some molecules can have similar mass-to-charge ratios, making it hard to distinguish between them based solely on their spectra. Although plantMASST includes a wealth of information, it currently only represents a small fraction of the entire plant kingdom.

#Collecting Data for PlantMASST

To make the extensive taxonomic search possible, researchers compiled over 200 publicly available MS/MS datasets and carefully reviewed each one. This included a variety of plant tissues and types. The scientific community has played a vital role in contributing to this growing database, and it will continue to expand as more datasets are shared.

#Building the Taxonomic Tree

The taxonomic tree for plantMASST was created using specific software to ensure accurate classification of plants. It includes only unique taxonomic IDs and maintains comprehensive lineage for each plant species. This tree helps users easily visualize the relationships between different plant families, genera, and species.

#Conclusion

In summary, plantMASST is a significant advancement in the ability to study plant metabolites across the globe. With its user-friendly interface and vast database, researchers can uncover important information about plant chemistry. This tool opens up new possibilities in drug discovery, nutrition research, and understanding plant interactions in ecosystems. Although it has some limitations, the potential implications for multiple fields are substantial as researchers continue to gather and analyze data.