Journal of Proteome Research,
Journal Year:
2024,
Volume and Issue:
unknown
Published: Oct. 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
bioRxiv (Cold Spring Harbor Laboratory),
Journal Year:
2024,
Volume and Issue:
unknown
Published: April 6, 2024
ABSTRACT
Tremendous
advances
in
mass
spectrometric
and
bioinformatic
approaches
have
expanded
proteomics
into
the
field
of
microbial
ecology.
The
commonly
used
spectral
annotation
method
for
metaproteomics
data
relies
on
database
searching,
which
requires
sample-specific
databases
obtained
from
whole
metagenome
sequencing
experiments.
However,
creating
these
is
complex,
time-consuming,
prone
to
errors,
potentially
biasing
experimental
outcomes
conclusions.
This
asks
alternative
that
can
provide
rapid
orthogonal
insights
data.
Here
we
present
NovoLign,
a
de
novo
pipeline
performs
sequence
alignment
sequences
complete
enables
taxonomic
profiling
complex
communities
evaluates
coverage
searches.
Furthermore,
NovoLign
supports
creation
reference
searching
ensure
comprehensive
coverage.
publicly
available
via:
https://github.com/hbckleikamp/NovoLign
.
International Dairy Journal,
Journal Year:
2024,
Volume and Issue:
159, P. 106070 - 106070
Published: Aug. 24, 2024
Using
a
metaproteomics
approach,
we
showed
that
the
initial
milk
quality
impacts
proteome
allocation
of
starter
cultures
used
in
cheese
production
and
can
be
considered
fundamental
source
batch-to-batch
variation.
Raw
was
spiked
with
highly
proteolytic
strain
Pseudomonas
trivialis,
previously
isolated
from
raw
milk,
incubated
for
1,
3,
6
days
at
refrigerated
temperature.
After
incubation,
heat-treated
then
fermented
mesophilic
culture
commonly
to
produce
Gouda-type
cheeses.
The
development
metabolites
analyzed
taxonomical
functional
characterization
performed.
Milk
storage
time
impacted
both
metaproteome
culture,
consequently
affecting
metabolite
levels
after
fermentation
level
protein
expressed
by
different
taxa;
Lactococcus
more
abundant
samples
made
stored
longer
while
proteins
Leuconostoc
spp.
decreased
abundance.
bioRxiv (Cold Spring Harbor Laboratory),
Journal Year:
2024,
Volume and Issue:
unknown
Published: April 15, 2024
ABSTRACT
BACKGROUND
Microbial
communities
play
a
crucial
role
in
human
health
and
environmental
regulation,
but
present
an
especial
challenge
for
the
analytical
science
due
to
their
diversity
dynamic
range.
Tandem
mass
spectrometry
provides
functional
insights
on
microorganisms
life
cycle,
still
lacks
throughput
sensitivity.
MALDI
TOF
is
widely
used
ultrafast
identification
of
species,
does
not
assess
activity.
Development
methods
bioinformatic
approaches
applicable
both
accurate
assessment
microbial
based
protein
content
high
interest.
RESULTS
We
show
first
time
that
identity
activity
can
be
accurately
determined
experiments
as
short
7
minutes
per
sample,
using
basic
Orbitrap
MS
configuration
without
peptide
fragmentation.
The
approach
was
validated
strain
isolates,
mock
microbiomes
composed
bacteria
spiked
at
known
concentrations
fecal
microbiomes.
Our
new
algorithm
identifies
bacterial
species
with
accuracy
95
%,
when
no
prior
information
sample
available.
Microbiome
composition
resolved
genus
level
mean
difference
between
actual
identified
components
12
%.
For
microbiomes,
Pearson
coefficient
up
0.97
achieved
estimates
biomass
change.
By
example
Rhodococcus
biodegradation
n
-alkanes,
phenols
its
derivatives,
we
showed
compared
standard
label-free
label-based
approaches.
SIGNIFICANCE
makes
proteomics
fast,
insightful
instruments
even
employing
fragmentation
technology.
applied
any
take
niche
routine
pathogens
consortiums
clinical
diagnostics
together
16S
rRNA
gene
sequencing.
PROTEOMICS,
Journal Year:
2024,
Volume and Issue:
24(21-22)
Published: June 2, 2024
Abstract
The
human
gut
microbiome
plays
a
vital
role
in
preserving
individual
health
and
is
intricately
involved
essential
functions.
Imbalances
or
dysbiosis
within
the
can
significantly
impact
are
associated
with
many
diseases.
Several
metaproteomics
platforms
currently
available
to
study
microbial
proteins
complex
communities.
In
this
study,
we
attempted
develop
an
integrated
pipeline
provide
deeper
insights
into
both
taxonomic
functional
aspects
of
cultivated
microbiomes
derived
from
clinical
colon
biopsies.
We
combined
rapid
peptide
search
by
MSFragger
against
Unified
Human
Gastrointestinal
Protein
database
analyses
Unipept
Desktop
MetaLab‐MAG.
Across
seven
samples,
identified
matched
nearly
36,000
unique
peptides
approximately
300
species
11
phyla.
provided
gene
ontology,
InterPro
entries,
enzyme
commission
number
annotations,
facilitating
identification
relevant
metabolic
pathways.
MetaLab‐MAG
contributed
annotations
through
Clusters
Orthologous
Genes
Non‐supervised
Groups
categories.
These
results
unveiled
similarities
differences
among
samples.
This
holds
potential
taxonomy
functions
for
interrogating
intricate
connections
between
balance
The
fields
of
biology,
computer
science,
statistics,
and
mathematics
are
all
brought
together
in
the
field
bioinformatics.
Utilizing
tools
to
decode,
analyze,
manage
huge
amounts
biological
data,
particularly
genomic
sequences,
which
beyond
capabilities
normal
scientific
methodologies,
is
core
objective
future
chapter
provides
an
introduction
bioinformatics
discusses
importance
comprehending
complex
systems.
precision
medicine,
drug
development,
evolutionary
biology
driven
by
In
addition
that,
it
sequence
alignment,
analysis
gene
protein
expression,
databases,
tools,
machine
learning
related
Concerns
include
quality
integration
concerns
pertaining
data
privacy
security,
requirement
for
efficient
algorithms
complexity
variety
data.
presents
overview
bioinformatics,
including
its
applications
potential
impact
will
have
on
research
sciences.
this
era
big
has
had
a
profound
research,
paving
way
new
avenues
exploration
medical
advancement.
This
also
emphasizes
continuously
improving
quality,
integration,
privacy,
as
well
development
algorithmic
solutions,
order
effectively
apply
management
vast
diverse
information.
