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