Journal of the American Society for Mass Spectrometry,
Год журнала:
2023,
Номер
34(7), С. 1511 - 1518
Опубликована: Июнь 26, 2023
Supercritical
fluid
chromatography
(SFC)
is
a
promising,
sustainable,
and
complementary
alternative
to
liquid
(LC)
has
often
been
coupled
with
high
resolution
mass
spectrometry
(HRMS)
for
nontarget
screening
(NTS).
Recent
developments
in
predicting
the
ionization
efficiency
LC/ESI/HRMS
have
enabled
quantification
of
chemicals
detected
NTS
even
if
analytical
standards
tentatively
identified
are
unavailable.
This
poses
question
whether
standard
free
can
also
be
applied
SFC/ES/HRMS.
We
evaluate
both
possibility
transfer
an
predictions
model,
previously
trained
on
data,
SFC/ESI/HRMS
as
well
training
new
predictive
model
data
127
chemicals.
The
response
factors
these
ranged
over
4
orders
magnitude
spite
postcolumn
makeup
flow,
expectedly
enhancing
analytes.
values
were
predicted
based
random
forest
regression
from
PaDEL
descriptors
showed
statistically
significant
correlation
measured
(p
<
0.05)
Spearman's
rho
0.584
0.669
SFC
LC
respectively.
Moreover,
most
similarities
independent
used
collecting
data.
investigated
quantify
values.
very
prediction
accuracy
median
error
2.20×,
while
pretrained
yielded
5.11×.
expected,
test
collected
same
instrument
chromatography.
Still,
observed
between
hints
that
more
abundant
prove
useful
understanding
behavior
SFC/ESI/HRMS.
Nucleic Acids Research,
Год журнала:
2023,
Номер
52(D1), С. D640 - D646
Опубликована: Ноя. 16, 2023
Abstract
MetaboLights
is
a
global
database
for
metabolomics
studies
including
the
raw
experimental
data
and
associated
metadata.
The
cross-species
cross-technique
covers
metabolite
structures
their
reference
spectra
as
well
biological
roles
locations
where
available.
recommended
repository
number
of
leading
journals
ELIXIR,
European
infrastructure
life
science
information.
In
this
article,
we
describe
continued
growth
diversity
submissions
significant
developments
in
recent
years.
particular,
highlight
Labs,
our
new
Galaxy
Project
instance
with
repository-scale
standardized
workflows,
how
public
on
are
being
reused
by
community.
Metabolomics
resources
available
under
EMBL-EBI’s
Terms
Use
at
https://www.ebi.ac.uk/metabolights
Apache
2.0
https://github.com/EBI-Metabolights.
Analytical Chemistry,
Год журнала:
2023,
Номер
95(8), С. 3909 - 3916
Опубликована: Фев. 15, 2023
Metabolite
identification
represents
a
major
bottleneck
in
contemporary
metabolomics
research
and
step
where
critical
errors
may
occur
pass
unnoticed.
This
is
especially
the
case
for
studies
employing
liquid
chromatography-mass
spectrometry
technology,
there
increased
concern
on
validity
of
proposed
identities.
In
present
perspective
article,
we
describe
issue
categorize
into
two
types:
identities
that
show
poor
biological
plausibility
do
not
comply
with
chromatographic
data
thus
to
physicochemical
properties
(usually
hydrophobicity/hydrophilicity)
molecule.
We
discuss
problem,
characteristic
examples,
propose
measures
improve
situation.
TrAC Trends in Analytical Chemistry,
Год журнала:
2022,
Номер
158, С. 116825 - 116825
Опубликована: Ноя. 17, 2022
Current
metabolomics
and
lipidomics
studies
are
limited
in
the
number
of
examined
matrices,
breadth
scope
methods,
reporting
metabolites,
data
sharing.
Here,
we
discuss
concept
atlases
that
characterize
quantitative
distribution
relationships
metabolites
biological
matrices
serve
as
a
resource
for
future
studies.
Combined
sample
extraction
is
recommended
to
screen
metabolome
lipidome
comprehensively.
A
multiplatform
mass
spectrometry-based
approach
with
methods
each
fraction
should
follow
separate
detect
differing
their
physicochemical
properties.
Since
many
known
detected
through
untargeted
analysis,
routine
use
multiple
internal
standards
quantification
advised.
This
provides
semiquantitative
delivers
molar
concentrations
selected
polar
lipids.
An
interactive
web
tool
query
generate
statistical
models,
visualize
data,
download
results
be
developed
access
generated
easily.
Analytical Chemistry,
Год журнала:
2023,
Номер
95(51), С. 18645 - 18654
Опубликована: Дек. 6, 2023
Untargeted
metabolomics
is
an
analytical
approach
with
numerous
applications
serving
as
effective
metabolic
phenotyping
platform
to
characterize
small
molecules
within
a
biological
system.
Data
quality
can
be
challenging
evaluate
and
demonstrate
in
experiments.
This
has
driven
the
use
of
pooled
control
(QC)
samples
for
monitoring
and,
if
necessary,
correcting
variance
introduced
during
sample
preparation
data
acquisition
stages.
Described
herein
scoping
literature
review
detailing
QC
published
untargeted
liquid
chromatography-mass
spectrometry
(LC-MS)
based
studies.
A
query
was
performed,
list
papers
filtered,
suitable
articles
were
randomly
sampled.
In
total,
109
each
reviewed
by
at
least
five
reviewers,
answering
predefined
questions
surrounding
samples.
The
results
indicate
that
been
relatively
widely
adopted
community
it
used
similar
frequency
across
taxa
types
both
small-
large-scale
However,
while
many
studies
generated
analyzed
samples,
few
reported
improve
quality.
demonstrates
clear
opportunity
field
more
frequently
utilize
reporting,
feature
filtering,
drift
correction,
metabolite
annotation.
Additionally,
our
survey
enabled
us
assess
ambiguity
reporting
methods
describe
generation
analysis
indicates
details
framework
are
missing
or
unclear,
limiting
reader's
ability
determine
which
steps
have
taken.
Collectively,
these
capture
current
state
usage
highlight
existing
strengths
deficiencies
they
applied
LC-MS
metabolomics.
Magnetic Resonance in Chemistry,
Год журнала:
2023,
Номер
61(12), С. 628 - 653
Опубликована: Апрель 3, 2023
Metabolomics
samples
like
human
urine
or
serum
contain
upwards
of
a
few
thousand
metabolites,
but
individual
analytical
techniques
can
only
characterize
hundred
metabolites
at
best.
The
uncertainty
in
metabolite
identification
commonly
encountered
untargeted
metabolomics
adds
to
this
low
coverage
problem.
A
multiplatform
(multiple
techniques)
approach
improve
upon
the
number
reliably
detected
and
correctly
assigned.
This
be
further
improved
by
applying
synergistic
sample
preparation
along
with
use
combinatorial
sequential
non-destructive
destructive
techniques.
Similarly,
peak
detection
strategies
that
employ
multiple
probabilistic
approaches
have
led
better
annotation
decisions.
Applying
these
also
addresses
issues
reproducibility
found
single
platform
methods.
Nevertheless,
analysis
large
data
sets
from
disparate
presents
unique
challenges.
While
general
processing
workflow
is
similar
across
platforms,
many
software
packages
are
fully
capable
types
instrument.
Traditional
statistical
methods
such
as
principal
component
were
not
designed
handle
multiple,
distinct
sets.
Instead,
multivariate
requires
multiblock
other
model
for
understanding
contribution
instruments.
review
summarizes
advantages,
limitations,
recent
achievements
metabolomics.
Nature Communications,
Год журнала:
2024,
Номер
15(1)
Опубликована: Апрель 8, 2024
Abstract
The
human
gut
microbiome
establishes
and
matures
during
infancy,
dysregulation
at
this
stage
may
lead
to
pathologies
later
in
life.
We
conducted
a
multi-omics
study
comprising
three
generations
of
family
members
investigate
the
early
development
microbiota.
Fecal
samples
from
200
individuals,
including
infants
(0-12
months
old;
55%
females,
45%
males)
their
respective
mothers
grandmothers,
were
analyzed
using
two
independent
metabolomics
platforms
metagenomics.
For
metabolomics,
gas
chromatography
capillary
electrophoresis
coupled
mass
spectrometry
applied.
metagenomics,
both
16S
rRNA
gene
shotgun
sequencing
performed.
Here
we
show
that
greatly
vary
elders
fecal
microbiota
populations,
function,
metabolome.
Infants
have
less
diverse
than
adults
present
differences
several
metabolite
classes,
such
as
short-
branched-chain
fatty
acids,
which
are
associated
with
shifts
bacterial
populations.
These
findings
provide
innovative
biochemical
insights
into
shaping
within
same
generational
line
could
be
beneficial
improving
childhood
health
outcomes.
Analytical Chemistry,
Год журнала:
2024,
Номер
96(3), С. 1064 - 1072
Опубликована: Янв. 5, 2024
The
implementation
of
quality
control
strategies
is
crucial
to
ensure
the
reproducibility,
accuracy,
and
meaningfulness
metabolomics
data.
However,
this
pivotal
step
often
overlooked
within
workflow
frequently
relies
on
use
nonstandardized
poorly
reported
protocols.
To
address
current
limitations
in
respect,
we
have
developed
QComics,
a
robust,
easily
implementable
reportable
method
for
monitoring
controlling
data
quality.
protocol
operates
various
sequential
steps
aimed
(i)
correct
background
noise
carryover,
(ii)
detect
signal
drifts
"out-of-control"
observations,
(iii)
deal
with
missing
data,
(iv)
remove
outliers,
(v)
monitor
markers
identify
samples
affected
by
improper
collection,
preprocessing,
or
storage,
(vi)
assess
overall
terms
precision
accuracy.
Notably,
tool
considers
important
issues
neglected
along
control,
such
as
need
separately
handling
values
truly
absent
avoid
losing
relevant
biological
information,
well
large
impact
that
preanalytical
factors
may
elicit
results.
Altogether,
guidelines
compiled
QComics
might
contribute
establishing
gold
standard
recommendations
best
practices
community.
Abstract
Background
Quality
assurance
(QA)
and
quality
control
(QC)
practices
are
key
tenets
that
facilitate
study
data
across
all
applications
of
untargeted
metabolomics.
These
important
will
strengthen
this
field
accelerate
its
success.
The
Best
Practices
Working
Group
(WG)
within
the
Metabolomics
Assurance
Control
Consortium
(mQACC)
focuses
on
community
use
QA/QC
protocols
aims
to
identify,
catalogue,
harmonize,
disseminate
current
best
in
metabolomics
through
community-driven
activities.
Aim
review
A
present
goal
WG
is
develop
a
working
strategy,
or
roadmap,
guides
actions
practitioners
progress
field.
framework
which
mQACC
operates
promotes
harmonization
dissemination
practice
guidance
encourages
widespread
adoption
these
essential
activities
for
liquid
chromatography-mass
spectrometry.
Key
scientific
concepts
Community
engagement
information
gathering
have
been
occurring
conference
workshops,
virtual
in-person
interactive
forum
discussions,
surveys.
Seven
principal
QC
stages
prioritized
by
internal
discussions
received
participant
input,
feedback
discussion.
We
outline
stages,
each
involving
multitude
activities,
as
identifying
practices.
ultimate
planned
product
endeavors
“living
guidance”
document
grow
change
with
evolution
