Generating an IPDB for a formula list
An isotopic profile represent all the m/z values and their natural abundances for all atoms in a molecular formula. IDSL.UFA needs the isotope profile information for all formulas in a targeted database. The collection is known as IPDB, the Isotopic Profile DataBase.
Follow these steps to generate an IPDB for a list of molecular formula.
Step 1: Prepare the list of molecular formula. It has to be a .CSV file.
Step 2: Prepare the parameter excel file for isotope profile computation. See the below example.
Step 3: Run the IDSL.UFA command to generate the IPDB.
IPDBs for selected databases are provided at https://zenodo.org/record/5823455
We recommend folllowing known sources of molecular formula for human specimens.
1) The Blood Exposome Database: https://bloodexposome.org/
2) RefMetDB: It also covers all formula from the lipid maps database https://www.metabolomicsworkbench.org/databases/refmet/index.php
3) FDA drugs: https://pubchem.ncbi.nlm.nih.gov/source/FDA%20Drugs
4) MeSH Database: NLM - MeSH ontology and linked compunds in the PubChem database. https://pubchem.ncbi.nlm.nih.gov/source/11939
5) PubChem CID-PMID link: https://ftp.ncbi.nlm.nih.gov/pubchem/Compound/Extras/CID-PMID.gz
It is best to first try out the source of molecular formula known for a biospecimen before venturing out for the unknown-known.