Organic Chemistry Frontiers,
Год журнала:
2023,
Номер
10(19), С. 4740 - 4749
Опубликована: Янв. 1, 2023
Unprecedented
sesquiterpenoid
scaffolds,
furnished
by
unexpected
carbon–carbon
linkage
formation
or
cleavage,
were
targeted
and
isolated
from
Daphne
aurantiaca
following
an
integrated
strategy.
Journal of Natural Products,
Год журнала:
2021,
Номер
84(11), С. 2795 - 2807
Опубликована: Окт. 18, 2021
Computational
approaches
such
as
genome
and
metabolome
mining
are
becoming
essential
to
natural
products
(NPs)
research.
Consequently,
a
need
exists
for
an
automated
structure-type
classification
system
handle
the
massive
amounts
of
data
appearing
NP
structures.
An
ideal
semantic
ontology
NPs
should
go
beyond
simple
presence/absence
chemical
substructures,
but
also
include
taxonomy
producing
organism,
nature
biosynthetic
pathway,
and/or
their
biological
properties.
Thus,
holistic
automatic
framework
could
have
considerable
value
comprehensively
navigate
relatedness
NPs,
especially
so
when
analyzing
large
numbers
NPs.
Here,
we
introduce
NPClassifier,
deep-learning
tool
structural
from
counted
Morgan
fingerprints.
NPClassifier
is
expected
accelerate
enhance
discovery
by
linking
structures
underlying
Molecular Horticulture,
Год журнала:
2022,
Номер
2(1)
Опубликована: Июль 23, 2022
Over
the
past
decade,
systems
biology
and
plant-omics
have
increasingly
become
main
stream
in
plant
research.
New
developments
mass
spectrometry
bioinformatics
tools,
methodological
schema
to
integrate
multi-omics
data
leveraged
recent
advances
proteomics
metabolomics.
These
progresses
are
driving
a
rapid
evolution
field
of
research,
greatly
facilitating
our
understanding
mechanistic
aspects
metabolisms
interactions
plants
with
their
external
environment.
Here,
we
review
MS-based
metabolomics
tools
workflows
special
focus
on
applications
research
using
several
case
studies
related
stress
response,
gene/protein
function
characterization,
metabolic
signaling
pathways
exploration,
natural
product
discovery.
We
also
present
projection
concerning
future
perspectives
development
including
challenges
for
system
biology.
This
is
intended
provide
readers
an
overview
how
advanced
MS
technology,
integrated
application
can
be
used
advance
Nature Communications,
Год журнала:
2023,
Номер
14(1)
Опубликована: Март 29, 2023
Abstract
Metabolomics-driven
discoveries
of
biological
samples
remain
hampered
by
the
grand
challenge
metabolite
annotation
and
identification.
Only
few
metabolites
have
an
annotated
spectrum
in
spectral
libraries;
hence,
searching
only
for
exact
library
matches
generally
returns
a
hits.
An
attractive
alternative
is
so-called
analogues
as
starting
point
structural
annotations;
are
molecules
which
not
but
display
high
chemical
similarity.
However,
current
analogue
search
implementations
yet
very
reliable
relatively
slow.
Here,
we
present
MS2Query,
machine
learning-based
tool
that
integrates
mass
embedding-based
similarity
predictors
(Spec2Vec
MS2Deepscore)
well
detected
precursor
masses
to
rank
potential
matches.
Benchmarking
MS2Query
on
reference
spectra
experimental
case
studies
demonstrate
improved
reliability
scalability.
Thereby,
offers
exciting
opportunities
further
increase
rate
metabolomics
profiles
complex
mixtures
discover
new
biology.
Untargeted
metabolomics
approaches
based
on
mass
spectrometry
obtain
comprehensive
profiles
of
complex
biological
samples.
However,
average
only
10%
the
molecules
can
be
annotated.
This
low
annotation
rate
hampers
biochemical
interpretation
and
effective
comparison
studies.
Furthermore,
de
novo
structural
characterization
spectral
data
remains
a
complicated
time-intensive
process.
Recently,
field
computational
has
gained
traction
novel
methods
have
started
to
enable
large-scale
reliable
metabolite
annotation.
Molecular
networking
machine
learning-based
in-silico
tools
been
shown
greatly
assist
in
diverse
fields
such
as
clinical
natural
product
discovery.
Natural Product Reports,
Год журнала:
2021,
Номер
38(11), С. 2066 - 2082
Опубликована: Янв. 1, 2021
This
review
covers
the
current
and
potential
use
of
mass
spectrometry-based
metabolomics
data
mining
in
natural
products.
Public
data,
metadata,
databases
analysis
tools
are
critical.
The
value
success
rely
on
community
participation.
Computational and Structural Biotechnology Journal,
Год журнала:
2022,
Номер
20, С. 2402 - 2414
Опубликована: Янв. 1, 2022
Inflammatory
bowel
disease
(IBD),
comprising
Crohn’s
(CD)
and
ulcerative
colitis
(UC),
is
a
set
of
clinically
chronic,
relapsing
gastrointestinal
inflammatory
lacks
an
absolute
cure.
Although
the
precise
etiology
unknown,
developments
in
high-throughput
microbial
genomic
sequencing
significantly
illuminate
changes
intestinal
structure
functions
patients
with
IBD.
The
application
metabolomics
suggests
that
microbiota
can
influence
IBD
pathogenesis
by
producing
metabolites,
which
are
implicated
as
crucial
mediators
host-microbial
crosstalk.
This
review
aims
to
elaborate
current
knowledge
perturbations
microbiome–metabolome
interface
description
altered
composition
metabolite
profiles
gut
microbiota.
We
emphasized
elaborated
recent
findings
several
potentially
protective
classes
IBD,
including
fatty
acids,
amino
acids
derivatives
bile
acids.
article
will
facilitate
deeper
understanding
new
therapeutic
approach
for
applying
metabolome-based
adjunctive
treatment.
Journal of the American Society for Mass Spectrometry,
Год журнала:
2022,
Номер
33(9), С. 1733 - 1744
Опубликована: Авг. 12, 2022
Spectrum
alignment
of
tandem
mass
spectrometry
(MS/MS)
data
using
the
modified
cosine
similarity
and
subsequent
visualization
as
molecular
networks
have
been
demonstrated
to
be
a
useful
strategy
discover
analogs
molecules
from
untargeted
MS/MS-based
metabolomics
experiments.
Recently,
neutral
loss
matching
approach
has
introduced
an
alternative
networking
with
implied
performance
advantage
in
finding
that
cannot
discovered
existing
MS/MS
spectrum
strategies.
To
comprehensively
evaluate
scoring
properties
matching,
similarity,
measures
955
228
peptide
pairs
10
million
small
molecule
were
compared.
This
comparative
analysis
revealed
outperformed
all
cases.
The
further
indicated
depends
on
location
type
modification,
well
chemical
compound
class
fragmented
molecules.
Natural Product Reports,
Год журнала:
2022,
Номер
39(9), С. 1876 - 1896
Опубликована: Янв. 1, 2022
This
review
discusses
genomics-,
transcriptomics-
and
metabolomics-based
plant
biosynthetic
pathway
discovery,
highlights
the
potential
for
integrative
omics
approaches.