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Informative subset of PubChem relevant for various environmental, metabolomics, exposomics and mass spec. applications

What is PubChemLite?

PubChemLite is a subset of 398406 compounds from PubChem,
with predicted collision cross section (CCS) values for 8 adducts.

PubChemLite exposomics is compiled from 10 categories:

  • AgroChemInfo
  • BioPathway
  • DrugMedicInfo
  • FoodRelated
  • PharmacoInfo
  • SafetyInfo
  • ToxicityInfo
  • KnownUse
  • DisorderDisease
  • Identification

PubChemLite in a nutshell

PubChemLite is a subset of PubChem selected from major categories of the Table of Contents (TOC) page, including predicted collision cross section (CCS) values from CCSbase.

PubChemLite for Exposomics is currently compiled from 10 TOC categories: Agrochemical Information (AgroChemInfo), Associated Disorders and Diseases (DisorderDisease), Drug and Medication Information (DrugMedicInfo), Food Additives and Ingredients (FoodRelated), Identification (Identification), Interactions and Pathways – Pathways subset (BioPathway), Pharmacology and Biochemistry (PharmacoInfo), Safety and Hazards (SafetyInfo), Toxicity (ToxicityInfo), Use and Manufacturing (KnownUse).

CCS adducts provided from CCSbase are: [M+H]+, [M+K]+, [M+NH4]+, [M+Na-2H]-, [M+Na]+, [M-H]-, [M]+, [M]-.

How to cite?

PubChemLite + CCS

Elapavalore et al. (2025) EST Letters DOI: 10.1021/acs.estlett.4c01003

PubChemLite

Schymanski et al. (2021) DOI: 10.1186/s13321-021-00489-0

CCSbase

Ross et al. (2020) DOI: 10.1021/acs.analchem.9b05772

Download PubChemLite

You can grab the latest PubChemLite from Zenodo

Current version: PubChemLite-CCSbase-20250204 (Published February 04, 2025) DOI zenodo