metabolomics-practical
Metabolite Databases
| toc | next |
The key metabolite databases are the following list:
- Human Metabolomics Database (HMDB): focuses on human metabolites
- Chemical Entities of Biological Interest (ChEBI): focuses on accurate description of the chemistry
- LIPID MAPS: focuses on lipids in any species
- LOTUS: focuses on natural products
More general databases include the following two, but because also human samples contain non-human metabolites, they are of relevance. They both have a chemistry focus but link out to many useful databases:
- PubChem: 114 million chemical structures, by the American NCBI
- ChemSpider: >100 millsion structures, and like PubChem, but by the British RSC
- Wikidata: 1.3 million structures; a machine-readable sister of Wikipedia (via Scholia interface)
During this practical you will use another biological database, WikiPathways, which describes many of the biological processes metabolites are involved in. These pathways are used in pathways analysis, which you will do at the end of this practical.
Identifier structure
Different databases use different structure of the identifier. PubChem, ChemSpider use integers. This has the disadvantage that with only the identifier (a number), you do not know what database it belongs too, unless you specify that. The latter can be done with compact uniform resource identifiers (CURIEs). The PubChem numeric identifier 5288826 then becomes the CURIE pubchem:5288826.
Other databases have a source indication in the identifier itself. For example, HMDB identifiers always start with the upper-cased “HMDB”, ChEBI prefixes identifiers with “CHEBI:” or “CHEBI_” (depending on the situation), and Wikidata uses the “Q” prefix.
Questions
What are the database identifiers for ChEBI, HMDB, PubChem, and Wikidata for the following compounds:
- glycine, found as residue in human protein? CHEBI:15428, HMDB0000123, 750, Q620730
- paracetamol? CHEBI:46195, HMDB0001859, 1983, Q57055
Stereoisomers
The stereochemistry of a chemical compound determines the spatial orientation of atoms in the molecule.
Questions
- does butane have stereoisomers? Yes, the single bonds can be rotated freely, it has various rotamers.
- does 2-butene have diastereoisomers? Yes, it has rotamers and two cis/trans isomers: the double bond can be cis and trans.
- what are the ChEBI identifiers of the enantiomers of lysine? CHEBI:16855 and CHEBI:18019 (CHEBI:25094 is a non-existing entity used to specify a compound with unknown stereochemistry)
Charge states
ChEBI has different entries in the database for different the protonated and deprotonated compound.
Questions
- what are the ChEBI identifiers for acetic acid and acetate? CHEBI:15366 and CHEBI:30089
Isotopes
Most ChEBI entries represent the chemical structure and the mass is given for the structure where all atoms have the most abundant isotope (e.g. 12C and 1H). However, it can also have entries for compounds with a specific isotope. Of course, with different identifiers.
Questions
- what are the ChEBI identifiers for water and heavy water? CHEBI:15377 and CHEBI:33813
Spectral databases
There are many databases that have spectra for small compounds, two of them are:
- MassBank Europe (for mass spectra)
- NMRShiftDb (for NMR spectra)
- how many peaks does the 1H NMR spectrum of isopropanol have? Two. The hydroxyl proton is not visible in polar solvents, so we only see peaks at 4.04 ppm and 1.22 ppm.
- at what m/z value does glycine the highest peak? That actually depends on the method used. The [M+H]+ peak is around 76, while the [M-H]- peak is around 74. Why do we not measure the [M] peak?
| toc | next |
Copyright 2020-2023 (C) Egon Willighagen - CC-BY Int. 4.0