[ICNTS25] (Chemical) Data Handling in a Modern NTS World

Author: Schymanski, Emma

Publisher: Zenodo

DOI: 10.5281/zenodo.17320946

Source: https://zenodo.org/records/17320946/files/ICNTS25_DataHandlingNTS_Oct2025.pdf

P o . D . Emma L. Schymanski
(plus many, many colleagues and collabo a o s!)
En i onmen al Chemin o ma ics G oup,
Luxembou g Cen e o Sys ems Biomedicine, Uni e si y o Luxembou g
[email protected] / h ps://gi lab.com/uniluxembou g/lcsb/eci
h ps://wwwen.uni.lu/lcsb/ esea ch/en i onmen al_chemin o ma ics/
(Chemical) Da a Handling in a
Mode n NTS Wo ld
Slides a ailable a DOI:
10.5281/zenodo.17320946
In e na ional Con e ence on Non-Ta ge Sc eening
(ICNTS25): E ding, Ge many, 13-16 Oc obe 2025
The Exposome mee s he Me abolome
2
Mod. om Ve meulen, Schymanski e al. (2020). Science. DOI: 10.1126/science.aay3164, Mille & Jones (2014) DOI: 10.1093/ oxsci/k 251.
“The cumula i e measu e o
en i onmen al in luences and
associa ed biological esponses
h oughou he li espan, including
exposu es om he en i onmen ,
die , beha iou and endogenous
p ocesses”
(Mille & Jones, 2014)
4
Sou ce: Begoña Tala e a Andúja , PhD Thesis. h ps://hdl.handle.ne /10993/61575.
Measu ing he Exposome – Mul iple Chemical Classes!
5
Sou ce: Begoña Tala e a Andúja , PhD Thesis. h ps://hdl.handle.ne /10993/61575.
Measu ing he Exposome – Mul iple Chemical Classes!

6
Concen a ion
D ug me aboli es
En i onmen al chemicals
MmM µM nM pM M
Endogenous me aboli es
D ugs
Food and Plan chemicals
Human me abolome
and exposome
Limi ed dynamic ange
LC-ESI-HRMS
Sou ce: Begoña Tala e a Andúja , PhD Thesis. h ps://hdl.handle.ne /10993/61575.
Measu ing he Exposome – Wide Range o Concen a ions
G and Challenge: HR-MS “Chemical Space” is oo Big!
290 million 122 million 129 million
Candida es wi h high in o ma ion con en
Candida es wi h low in o ma ion con en
1.2 million
…and p ohibi i e un imes!
7
122 million
The Vas Chemical Space o Exposomics …
Numbe s upda ed 9 Oc . 2025.
Mod. om Esche e al (2020). Science. DOI: 10.1126/science.aay6636
Image: ESO/IDA/Danish 1.5 m h p://www.eso.o g/public/images/po w1015a/
122 million
The Vas Chemical Space o Exposomics …
Numbe s upda ed 9 Oc . 2025.
Mod. om Esche e al (2020). Science. DOI: 10.1126/science.aay6636
Image: ESO/IDA/Danish 1.5 m h p://www.eso.o g/public/images/po w1015a/
h ps://pubchem.ncbi.nlm.nih.go /
Ga he ing Expe Knowledge: NORMAN-SLE
h ps://www.no man-ne wo k.com/nds/SLE/
16
Mohammed Taha e al. (2022) DOI: 10.1186/s12302-022-00680-6

Ga he ing Expe Knowledge: NORMAN-SLE
h ps://www.no man-ne wo k.com/nds/SLE/
17
Mohammed Taha e al. (2022) DOI: 10.1186/s12302-022-00680-6
Mohammed Taha e al. (2022) DOI: 10.1186/s12302-022-00680-6
18
122 million
< 0.01% o PubChem
The Vas Chemical Space o Exposomics …
566,122
133,573
suspec s
Non- a ge
Sc eening
Suspec
Sc eening
Ta ge
Analysis
Numbe s upda ed 9 Oc . 2025.
Mod. om Esche e al (2020). Science. DOI: 10.1126/science.aay6636
Image: ESO/IDA/Danish 1.5 m h p://www.eso.o g/public/images/po w1015a/
C ea ing In o ma i e Subse s o
20
Elapa alo e e al. (2025) DOI: 10.1021/acs.es le .4c01003
Schymanski e al. (2021) DOI: 10.1186/s13321-021-00489-0
C ea ing In o ma i e Subse s o
~500,000 en ies “small”
Elapa alo e e al. (2025) DOI: 10.1021/acs.es le .4c01003
Schymanski e al. (2021) DOI: 10.1186/s13321-021-00489-0
21

o Exposomics
22
h p://pubchemli e.lcsb.uni.lu/
ca eine
Da abase: o Exposomics
23
h ps://pubchemli e.lcsb.uni.lu/e/compound/2519
ca eine
Da abase: o Exposomics
24
h ps://pubchemli e.lcsb.uni.lu/e/compound/2519
ca eine
Da abase: o Exposomics
25
h ps://pubchemli e.lcsb.uni.lu/e/compound/2519
ca eine
…and now in 2025: Fluo ina ed ions a e e e ywhe e…
Tisle e al. (2025) DOI: 10.1021/acs.es .5c06876
32

Elapa alo e e al. (2025) DOI: 10.1021/acs.es le .4c01003 & Schymanski e al. (2021) DOI: 10.1186/s13321-021-00489-0
33
: Fewe and mo e ele an candida es – wi h
con ex
is a Dynamic Collec ion …
•… buil e e y week, upda ed online e e y mon h
•… e-e alua ed wi h e e y build o con inuous quali y con ol
•… g owing as knowledge g ows!
DOI: 10.5281/
zenodo.5995885
34
h p://pubchemli e.lcsb.uni.lu/
Va ia ion o Con en O e Time (2022-2024)
•Va ia ion o con en o e ime
Elapa alo e e al. (2025) DOI: 10.1021/acs.es le .4c01003
35
Key Fac s Abou
•All TPs in he NORMAN-SLE a e in
•Mos “suspec classes” a e in
Elapa alo e e al. (2025) DOI: 10.1021/acs.es le .4c01003 & h ps:// ai ps.lcsb.uni.lu/s a s/
36
Key Fac s Abou
•All TPs in he NORMAN-SLE a e in
•Mos “suspec classes” a e in
•Sco ing e ms “Me F ag Sco e, MoNA Exac Simila i y,
PubMed Coun , Pa en Coun & Anno a ion Coun ” yield:
o81 % o co ec candida es in i s place
o98.4 % o co ec candida es in Top 3
Elapa alo e e al. (2025) DOI: 10.1021/acs.es le .4c01003
37
=> High h oughpu iden i ica ion
(quickly!)

Small molecule omics: Rapidly g owing ields
38
Tala e a Andúja & Schymanski, unde e iew, Exposome. Mod. om Begoña Tala e a Andúja , h ps://hdl.handle.ne /10993/61575.
Time (yea s)
1998
-Deﬁni ion o me abolome (S.G. Oli e e al.)
2005
-Fi s deﬁni ion o exposome (C. Wild)
-Fo ma ion o MSI
-Comme cial O bi ap
-NORMAN ne wo k s a ed
-METLIN
2007
-HMDB
-MSI publish minimum
epo ing s anda ds
2010
-Me F ag
-MassBank
2012
-Me aboAnalys
-CASMI s a s
2004
-Me abolomics
Socie y
cons i u ed
-PubChem
2013
-HELIX
-HERCULES
2014
-Exposome edeﬁned (Mille and Jones)
-Schymanski e al. conﬁdence le els
2015
-MS-DIAL
-NORMAN-SLE
2017
-CompTox
Dashboa d
-ChemRICH
-mQACC ounded
2022
-PARC s a
-MMDB
-EIRENE
2019
-Blood
Exposome
Da abase
2020
-ReDU
2021
-pa Roon
-PubChemLi e o Exposomics
-Exposome jou nal
E a o AI…
2024
-PARC QA/QC guidelines
-mQACC guidelines
2016
-HBMEU4
-GNPS
2023
-NORMAN guidance on
non- a ge sc eening
-ms2que y
?
-Ha monized QC c i e ia o
me abolomics and exposomics
-Exposomics Socie y
Communi y
eﬀo s!
2025
-NEXUS
ne wo k
2018
-Me abolomics QC
samples guidelines
(B oadhu s e al.)
YOUR Con ibu ions a e Adding S a s in o Space
39
Sou ce: Tala e a Andúja & Schymanski, unde e iew, Exposome. h ps://gi lab.com/uniluxembou g/lcsb/eci/exposomics-plo s .
T iglyce ides
Nucleo ides
EU
Pes icides
PFOS and ela ed
subs ances
Tala e a Andúja e al. (2024). En i onmen In e na ional DOI: 10.1016/j.en in .2024.109151
40
Exposomics Wo k lows – Bes o Many Wo lds!
“T ansla ing” So wa e Ou pu s Isn’ Always Easy …
B)
Le el 2
Le el 1
Le el 5
Le el 4
Le el 3
Unknown
Unequi ocal Molecula
Fo mula
Ten a i e s uc u e
candida es
P obable s uc u e
a) By lib a y spec al ma ch
b) By diagnos ic e idence
Conﬁ med s uc u e
by e e ence s anda d
Inc easing conﬁdence
Iden iﬁca ion Conﬁdence
MS-DIAL pa Roon
>= 3 ion agmen s ma ching
Do p oduc 70-100
F agmen p esence 50-100
Minimum da a equi emen s-So wa e based
>= 3 ion agmen s ma ching
Do p oduc 50-70
F agmen p esence 50-100
MoNASco e > 0.9
One candida e only
MoNASco e 0.7-0.9
2a
3a
Tala e a Andúja & Schymanski, unde e iew, Exposome. Mod. om Begoña Tala e a Andúja , h ps://hdl.handle.ne /10993/61575.
41
B owsing Dead-End (and o he ) P edic ed TPs
48
h ps://gci ps.lcsb.uni.lu/ & Palm e al. (2025) P esen a ion a SETAC Eu ope, 13 May 2025. DOI: 10.5281/zenodo.15574837

P edic ing Dead-end T ans o ma ion P oduc s
49
Sou ce: Emma Palm. Palm e al. (2025) P esen a ion a SETAC Eu ope, 13 May 2025. DOI: 10.5281/zenodo.15574837.
Numbe o p ecu so s: 170
B owsing Dead-End (and o he ) P edic ed TPs
50
Sou ce: Emma Palm. Palm e al. (2025) P esen a ion a SETAC Eu ope, 13 May 2025 . DOI: 10.5281/zenodo.15574837
P edic ing Dead-end T ans o ma ion P oduc s
51
Sou ce: Emma Palm. Palm e al. (2025) P esen a ion a SETAC Eu ope, 13 May 2025. DOI: 10.5281/zenodo.15574837
Numbe o p ecu so s: 13
P edic ing Dead-end T ans o ma ion P oduc s
52
Sou ce: Emma Palm. Palm e al. (2025) P esen a ion a SETAC Eu ope, 13 May 2025. DOI: 10.5281/zenodo.15574837
Numbe o p ecu so s: 13
FAIR-TPs
53
Mayahi, Palm & Schymanski (in p ep.). h ps:// ai ps.lcsb.uni.lu/s a s/ & h ps:// ai ps.lcsb.uni.lu/abou /

NTS @ ECI, LCSB, Uni.lu
PubChemLi e
o explo e
chemical space
Chemin o ma ics
de elopmen s
Chemical
space
challenge
Analy ical
me hod
design
Explo ing
ans o ma ions Disease
impac s
Slide inspi ed
by B. Tala e a
54
Email: emma.schymans[email p o ec ed]
in:emma-schymanski / @schymane@ms dn.social
h ps://wwwen.uni.lu/lcsb/ esea ch/en i onmen al_
chemin o ma ics/
h ps://gi lab.com/uniluxembou g/lcsb/eci/
h ps://pubchemli e.lcsb.uni.lu/
Me ci/Danke schön/Thank you!
H2020:
101036756
55
Analy ical F on ie s
Compu a ional Tools
TPs & PMTs
NTS & Haza d Assessmen
NTS & Managing Chemicals
Please join us in Ascona o Non a ge 2026!
When: Ap il 12-17, 2026
Abs ac submission: No . 30 h, 2025
Mo e de ails: h ps://www.eawag.ch/non a ge 2026

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