Documenting the chemistry of Life, why and how?

Author: Allard, Pierre-Marie

Publisher: Zenodo

DOI: 10.5281/zenodo.17310143

Source: https://zenodo.org/records/17310143/files/20251010_SMS2025.pdf

Documen ing he chemis y o
Li e, why and how?
Pie e-Ma ie Alla d - COMMONS Lab
h ps://doi.o g/10.5281/zenodo.17310143!
Slide con en s licensed unde !CC-BY-SA 4.0
Feel ee o sha e and/o modi y.
To heal ou sel esTo unde s and Na u e
200 yea s o na u al p oduc s esea ch
< 1% o plan me aboli es
ha e been cha ac e ized
Cen u ies equi ed o ully documen
plan me aboli es
-Physical isola ion o a compound
can equi es mon hes o wo k!
-S ong publica ion bias (new o
bioac i es only a e epo ed)
~ 350'000 compounds
~ 30'000 species
200 yea s o na u al p oduc s esea ch
< 1% o plan me aboli es
ha e been cha ac e ized
~ 350'000 compounds
~ 30'000 species
1 sample - 10 min
> 100 samples / day
1 sample
10 min
10'000 spec a
500 anno a ions

Yes ... bu !
1. LCMS da a sucks
m/z signal in ensi y
RT
m/z RT signal in ensi y
RT
RTRT
RT RT signal in ensi y
signal in ensi y
signal in ensi y
signal in ensi y
signal in ensi y
signal in ensi y
signal in ensi y
signal in ensi y
signal in ensi y
signal in ensi y
signal in ensi y
RT RT
h ps://www.wo ldwildli e.o g/publica ions/li ing-plane - epo -2020!

METABOLOME
EARTH
INITIATIVE
P o ile he me abolic con en o all
cu en ly known species on Ea h.
A massi e unde aking ...
METABOLOME
EARTH
INITIATIVE
... wi h h ee objec i es
•Explo e and unde s and he chemical
ounda ions o he biosphe e
•Bene i human socie y
•P o ec biodi e si y
P ojec 1
P ojec III
P ojec 1

P ojec IV
P ojec III
P ojec 1
P ojec n
P ojec IV
P ojec III
P ojec 1
P ojec n
P ojec IV
P ojec III
P ojec 1
P ojec II
P ojec n
P ojec IV
P ojec III
P ojec 1
P ojec II
Use communi y
Resea che s, policy make s,
indus y, na ional pa ks,
cu a o s, public e c.
HO
O
OH
OH
OH
P ojec n
P ojec IV
P ojec III
P ojec 1
METABOLOME
EARTH
KNOWLEDGE
BASE
BUILDING KNOWLEDGE
Accessing
chemodi e si y
Knowledge
acquisi ion
Knowledge
dissemina ion
P ojec II
Knowledge
o ganisa ion

Use communi y
Resea che s, policy make s,
indus y, na ional pa ks,
cu a o s, public e c.
HO
O
OH
OH
OH
P ojec n
P ojec IV
P ojec III
P ojec 1
METABOLOME
EARTH
KNOWLEDGE
BASE
BUILDING KNOWLEDGE
Accessing
chemodi e si y
Knowledge
acquisi ion
Knowledge
dissemina ion
Ad ance
li e sciences
P ojec II
Knowledge
o ganisa ion
Use communi y
Resea che s, policy make s,
indus y, na ional pa ks,
cu a o s, public e c.
HO
O
OH
OH
OH
P ojec n
P ojec IV
P ojec III
P ojec 1
METABOLOME
EARTH
KNOWLEDGE
BASE
BUILDING KNOWLEDGE
Accessing
chemodi e si y
Bene i
human socie y
Knowledge
acquisi ion
Knowledge
dissemina ion
Ad ance
li e sciences
P ojec II
Knowledge
o ganisa ion
Use communi y
Resea che s, policy make s,
indus y, na ional pa ks,
cu a o s, public e c.
HO
O
OH
OH
OH
P ojec n
P ojec IV
P ojec III
P ojec 1
METABOLOME
EARTH
KNOWLEDGE
BASE
BUILDING KNOWLEDGE
Accessing
chemodi e si y
P o ec
biodi e si y
Bene i
human socie y
Knowledge
acquisi ion
Knowledge
dissemina ion
Ad ance
li e sciences
P ojec II
Knowledge
o ganisa ion
Use communi y
Resea che s, policy make s,
indus y, na ional pa ks,
cu a o s, public e c.
HO
O
OH
OH
OH
P ojec n
P ojec IV
P ojec III
P ojec 1
METABOLOME
EARTH
KNOWLEDGE
BASE
BUILDING KNOWLEDGE
MAKING IMPACT
Accessing
chemodi e si y
P o ec
biodi e si y
Bene i
human socie y
Knowledge
acquisi ion
Knowledge
dissemina ion
Ad ance
li e sciences
P ojec II
Knowledge
o ganisa ion
METABOLOME
EARTH
INITIATIVE

Wild ecosys ems
Bo anical ga dens
Labo a o y plan s
Di e si y
(species)
Sampling
(easiness o )
Func ions
(unde s anding o )
Di e si y
(species)
Sampling
(easiness o )
Func ions
(unde s anding o )
Di e si y
(species)
Sampling
(easiness o )
Func ions
(unde s anding o )
Condi ions
(con ol o en i onmen al)
Condi ions
(con ol o en i onmen al)
Condi ions
(con ol o en i onmen al)
Wild ecosys ems
Bo anical ga dens
Labo a o y plan s
Di e si y
(species)
Sampling
(easiness o )
Func ions
(unde s anding o )
Di e si y
(species)
Sampling
(easiness o )
Func ions
(unde s anding o )
Di e si y
(species)
Sampling
(easiness o )
Func ions
(unde s anding o )
Condi ions
(con ol o en i onmen al)
Condi ions
(con ol o en i onmen al)
Condi ions
(con ol o en i onmen al)
Wild ecosys ems
Bo anical ga dens
Labo a o y plan s
Di e si y
(species)
Sampling
(easiness o )
Func ions
(unde s anding o )
Di e si y
(species)
Sampling
(easiness o )
Func ions
(unde s anding o )
Di e si y
(species)
Sampling
(easiness o )
Func ions
(unde s anding o )
Condi ions
(con ol o en i onmen al)
Condi ions
(con ol o en i onmen al)
Condi ions
(con ol o en i onmen al)
"This numbe would be equi alen o gene a ing 1!billion UUIDs pe second o abou 86!yea s."

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C ea edbyOleksand Panaso skyi
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C ea edbyOleksand Panaso skyi
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Li ing
Things
Animals
Dogs Cows He bs
Plan s
is is
is is
ea
is
Li ing
Things
Molecule
Molecule
A
Molecule
B
Plan
Z
Plan s
is
is
is
ound in
is

Li ing
Things
Molecule
Molecule
A
Molecule
B
Plan
Z
Plan s
is
is
is
ound in
is
An ibio ic
has ac i i y
Li ing
Things
Molecule
Molecule
A
Molecule
B
Plan
Z
Plan s
is
is
is
ound in
is
An ibio ic
has ac i i y
Ecuado
endemic o
Li ing
Things
Molecule
Molecule
A
Molecule
B
Plan
Z
Plan s
is
is
is
ound in
is
An ibio ic
has ac i i y
Ecuado
endemic o
Endange ed
s a us
Li ing
Things
Molecule
Molecule
A
Molecule
B
Plan
Z
Plan s
is
is
is
ound in
is
An ibio ic
has ac i i y
MDR
bac e ia Ecuado
endemic o
a ge
Endange ed
s a us
Li ing
Things
Molecule
Molecule
A
Molecule
B
Plan
Z
Plan s
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is
ound in
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An ibio ic
has ac i i y
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bac e ia Ecuado
endemic o
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Endange ed
s a us
SSPHP
(supe se ious
public heal h
p oblems)
cause o

h ps://enpkg.commons-lab.o g/g aphdb/
h ps://doi.o g/10.1021/acscen sci.3c00800!

www.ea hme abolome.o g
I N I T I AT I V E
EARTH
METABOLOME
www.dbgi.o g www.ea hme abolome.o g
www.ea hme abolome.o g
www.dbgi.o g
www.ea hme abolome.o g
I N I T I AT I V E
EARTH
METABOLOME

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