Journal of Proteome Research,
Год журнала:
2024,
Номер
unknown
Опубликована: Окт. 25, 2024
In
metaproteomics
studies,
constructing
a
reference
protein
sequence
database
that
is
both
comprehensive
and
not
overly
large
critical
for
the
peptide
identification
step.
Therefore,
availability
of
well-curated
databases
tools
custom
construction
essential
to
enhance
performance
analyses.
this
review,
we
first
provide
an
overview
by
presenting
concise
historical
background,
outlining
typical
experimental
bioinformatics
workflow,
emphasizing
crucial
step
metaproteomics.
We
then
delve
into
current
available
building
such
databases,
highlighting
their
individual
approaches,
utility,
advantages
limitations.
Next,
examine
existing
detailing
scope
relevance
in
research.
Then,
practical
recommendations
metaproteomics,
along
with
challenges
area.
conclude
discussion
anticipated
advancements,
emerging
trends,
future
directions
medRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2024,
Номер
unknown
Опубликована: Июль 3, 2024
Abstract
Background
The
gut
microbiome
is
an
important
contributor
to
the
development
and
course
of
inflammatory
bowel
disease
(IBD).
While
changes
in
composition
were
observed
response
IBD
therapy
using
biologics,
studies
elucidating
human
microbial
proteins
pathways
dependence
on
success
are
sparse.
Methods
Fecal
samples
a
cohort
patients
collected
before
after
14
weeks
treatment
with
three
different
biologics.
Clinical
activity
scores
used
determine
clinical
remission.
metaproteomes
remitting
(n=12)
non-remitting
compared
within
both
groups
assessed
over
sampling
time
identify
functional
potential
biomarkers.
Results
abundance
associated
intestinal
barrier,
neutrophilic
granulocytes,
immunoglobulins
significantly
decreased
patients.
In
contrast,
increase
those
was
There
significant
metabolism
from
remission
therapy.
This
included,
for
example,
increased
butyrate
fermentation.
Finally,
new
biomarkers
prediction
monitoring
could
be
identified,
e.g.
lysosome-associated
membrane
glycoprotein
1,
cytotoxicity
marker,
or
anthranilate
synthase
component
2,
part
tryptophan
metabolism.
Conclusions
Distinct
related
inflammation
showed
whether
achieved
not.
suggests
that
metaproteomics
useful
tool
therapies.
The
diversity
and
complexity
of
the
microbiome's
genomic
landscape
are
not
always
mirrored
in
its
proteomic
profile.
Despite
anticipated
diversity,
observed
complexities
microbiome
samples
often
lower
than
expected.
Two
main
factors
contribute
to
this
discrepancy:
limitations
mass
spectrometry's
detection
sensitivity
bioinformatics
challenges
metaproteomics
identification.
This
study
introduces
a
novel
approach
evaluating
sample
directly
at
full
spectrum
(MS1)
level
rather
relying
on
peptide
identifications.
When
analyzing
under
identical
spectrometry
conditions,
displayed
significantly
higher
complexity,
as
evidenced
by
spectral
entropy
candidate
entropy,
compared
single-species
samples.
research
provides
solid
evidence
for
proteomics
indicating
optimization
potential
workflow.
Journal of Proteome Research,
Год журнала:
2024,
Номер
unknown
Опубликована: Окт. 25, 2024
In
metaproteomics
studies,
constructing
a
reference
protein
sequence
database
that
is
both
comprehensive
and
not
overly
large
critical
for
the
peptide
identification
step.
Therefore,
availability
of
well-curated
databases
tools
custom
construction
essential
to
enhance
performance
analyses.
this
review,
we
first
provide
an
overview
by
presenting
concise
historical
background,
outlining
typical
experimental
bioinformatics
workflow,
emphasizing
crucial
step
metaproteomics.
We
then
delve
into
current
available
building
such
databases,
highlighting
their
individual
approaches,
utility,
advantages
limitations.
Next,
examine
existing
detailing
scope
relevance
in
research.
Then,
practical
recommendations
metaproteomics,
along
with
challenges
area.
conclude
discussion
anticipated
advancements,
emerging
trends,
future
directions
