PubChemLite for Exposomics with Predicted Collision Cross Section Values

PubChemLite for Exposomics is a curated subset of PubChem, compiled from 11 annotation categories including AgroChemInfo, ToxicityInfo, and FoodRelated. It includes predicted collision cross section values for 11 adducts, calculated using the c3sdb code from CCSbase. The dataset is maintained by Emma Schymanski at the University of Luxembourg and is updated monthly, with the latest version available via a Zenodo DOI.

Use Cases

• Compound identification in mass spectrometry based on predicted collision cross section values for 11 adducts.
• Exposomics research based on chemical annotations from 11 categories like ToxicityInfo and FoodRelated.
• Metabolite annotation and filtering based on the removal of entries that cause errors in tools like MetFrag.
• Building local compound databases for mass spectrometry software based on the structured PubChem subset.

Strengths

• Includes predicted collision cross section values for 11 specific adducts, such as [M+H]+ and [M-H]-.
• Compiled from 11 distinct annotation categories within the PubChem Classification Browser.
• Entries causing errors in MetFrag have been removed, suggesting pre-filtering for usability.
• Updated monthly, indicating ongoing maintenance.

Limitations

• Column-level documentation is absent; field semantics must be inferred after download.
• Row count is unknown, which may limit suitability assessment for large-scale projects.
• The description does not specify the exact number of unique chemical structures.

Provenance

Source

PubChem and CCSbase (ccsbase.net).

Collection Method

Curated subset from PubChem categories with CCS predictions added using c3sdb code.

Freshness

Updated monthly.