Post on 16-Apr-2017
Identifying toxicants
and metabolites
well, -Annotating in most cases
Steffen NeumannLeibniz Institute of Plant BiochemistryMass Spectrometry and Bioinformatics groupsneumann@ipb-halle.de
A criminal story
CSI: You want to identify somebody,
based on one or more
of the following evidence:You know the weight
You know the first name
You know the fingerprint
You know the fingerprint, but he's not in the files
And if nobody else has seen him ?
I know his weight
So you can do a search
in KEGG, PubChem,
ChemSpider, ChEBI, CAS,
(Usually) no extra software needed
And obtain zillions of hits
Caveat: you know the
monoisotopic mass,
not the average mass
www.msu.edu/~gallego7/MassSpect/
DB Mass Distribution
KEGG (3/2010)12788 entries
Median mass : 310
PubChem Compound (3/2010)26.167.050 entries
Median mass : 383
Search for a given mass
KEGG hits
with given ppm
3000ppm @300Da
nominal mass
Hardly improvement
below 10ppm:
same elemental
composition
I know his first name
Calculate elemental composition
with an accurate mass
and proper Isotopic pattern
Add N-rule, DBE, CH ratios, MS/MS etc.
to narrow down relevant formulas
(Caveat: don't filter compounds of interest!)
So you can do a better search in KEGG, PubChem, ChemSpider, ChEBI, CAS,
Not zillion hits, but still too many
Chemical Space beyond DBs
http://fiehnlab.ucdavis.edu
Somewhat exaggerated, 97% of KEGG