As the de facto global hub for chemical structures, associated bioactivity data and a massive range of informatic connectivity it was of considerable interest to profile probe sets against the 110 million compounds in PubChem . The first part of this necessitated the mapping of all P&D probe structures to PubChem CIDs via InChIKey matches and SMILES strings for cross-corroboration. This was done using the PubChem Identifier Exchange Service 67 . We expected high coverage from the probe sources we knew to have entered PubChem by various routes. From the 940 experimental probes, we recorded 915 CID matches (910 from IKs plus five more from SMILES). Inspection of the unmapped probes confirmed that most from SGC Probes, opnMe Portal and Gray Laboratory had no submission path into PubChem (directly, or via other source). In addition, we found the three unmatched MLP probes had different or flattened stereochemistry in PubChem (i.e. matched different non-isomeric CIDs). The corresponding 3670 calculated probes matched 3557 CIDs. While the mismatches were still only 3%, the reasons behind these are (again) differences in the handling of stereochemistry between PubChem and P&D (the latter uses RDKit as its main cheminformatics framework ). We also discovered that the links to some compounds are missing from ChEMBL because of InChIKey differences (ChEMBL is also using the RDKit framework ).