Biomolecules,
Journal Year:
2025,
Volume and Issue:
15(3), P. 325 - 325
Published: Feb. 24, 2025
Breastmilk
is
a
complex
biological
fluid
containing
over
thousand
bioactive
proteins,
lipids,
cells
and
small
molecules
that
provide
nutrition
immunological
protection
for
infants
children.
The
composition
of
breastmilk
unique
to
each
individual
can
also
vary
within
individuals
according
breastfeeding
duration,
maternal
health,
time
day,
other
factors.
As
such,
the
be
considered
“fingerprint”
could
interrogated
identify
biomarkers
breast
health
disease.
However,
accurate
quantification
components
in
remains
significant
challenge.
Approaches
such
as
immunoassays
mass
spectrometry
have
been
largely
applied
study
blood
or
fluids
require
validation
optimisation
before
these
techniques
used
accurately
quantify
compounds
breastmilk.
Development
protocols
specific
should
carried
out
with
high
precision,
confidence,
sensitivity.
This
review
explores
challenges
opportunities
associated
different
components.
Journal of Proteome Research,
Journal Year:
2023,
Volume and Issue:
22(11), P. 3652 - 3659
Published: Oct. 11, 2023
The
growing
complexity
and
volume
of
proteomics
data
necessitate
the
development
efficient
software
tools
for
peptide
identification
quantification
from
mass
spectra.
Given
their
central
role
in
proteomics,
it
is
imperative
that
these
are
auditable
extensible─requirements
best
fulfilled
by
open-source
permissively
licensed
software.
This
work
presents
Sage,
a
high-performance,
open-source,
freely
available
pipeline.
Scalable
cloud-ready,
Sage
matches
performance
state-of-the-art
while
running
an
order
magnitude
faster.
ACS Measurement Science Au,
Journal Year:
2024,
Volume and Issue:
4(4), P. 338 - 417
Published: June 4, 2024
Proteomics
is
the
large
scale
study
of
protein
structure
and
function
from
biological
systems
through
identification
quantification."Shotgun
proteomics"
or
"bottom-up
prevailing
strategy,
in
which
proteins
are
hydrolyzed
into
peptides
that
analyzed
by
mass
spectrometry.Proteomics
studies
can
be
applied
to
diverse
ranging
simple
proteoforms,
protein-protein
interactions,
structural
alterations,
absolute
relative
quantification,
post-translational
modifications,
stability.To
enable
this
range
different
experiments,
there
strategies
for
proteome
analysis.The
nuances
how
proteomic
workflows
differ
may
challenging
understand
new
practitioners.Here,
we
provide
a
comprehensive
overview
proteomics
methods.We
cover
biochemistry
basics
extraction
interpretation
orthogonal
validation.We
expect
Review
will
serve
as
handbook
researchers
who
field
bottom-up
proteomics.
Industrial & Engineering Chemistry Research,
Journal Year:
2024,
Volume and Issue:
63(15), P. 6685 - 6700
Published: April 8, 2024
Metabolic
cybergenetics
is
a
promising
concept
that
interfaces
gene
expression
and
cellular
metabolism
with
computers
for
real-time
dynamic
metabolic
control.
The
focus
on
control
at
the
transcriptional
level,
serving
as
means
to
modulate
intracellular
fluxes.
Recent
strategies
in
this
field
have
employed
constraint-based
models
process
optimization,
control,
estimation.
However,
results
bilevel
optimization
problems,
which
pose
considerable
numerical
conceptual
challenges.
In
study,
we
present
an
alternative
hybrid
physics-informed
modeling
framework
cybergenetics,
aimed
simplifying
estimation
tasks.
By
utilizing
machine-learning
surrogates,
our
approach
effectively
embeds
physics
of
networks
into
rates
structurally
simpler
macrokinetic
coupled
expression.
These
informed
by
flux
balance
analysis,
link
domains
manipulatable
enzymes
exchange
This
ensures
critical
knowledge
captured
system's
network
preserved.
resulting
can
be
integrated
cybergenetic
schemes
involving
single-level
optimizations.
Additionally,
maintains
number
system
states
necessary
minimum,
easing
burden
monitoring
Our
demonstrated
using
computational
case
study
optogenetically
assisted
production
itaconate
Escherichia
coli.
Toxics,
Journal Year:
2025,
Volume and Issue:
13(3), P. 163 - 163
Published: Feb. 25, 2025
This
study
categorizes
pollutant-induced
inflammation–cancer
transition
into
three
stages:
non-alcoholic
fatty
liver
disease
(NAFLD),
fibrosis,
and
hepatocellular
carcinoma
(HCC).
It
systematically
reveals
the
temporal
heterogeneity
of
damage.
The
findings
indicate
that
pollutants
not
only
directly
damage
hepatocytes
but
also
modulate
key
cells
in
immune
microenvironment,
such
as
hepatic
stellate
(HSCs)
Kupffer
cells,
thereby
amplifying
inflammatory
fibrotic
responses,
ultimately
accelerating
progression
HCC.
Mechanistically,
early
stage
primarily
cause
hepatocyte
injury
through
oxidative
stress
lipid
metabolism
dysregulation.
During
fibrosis
stage,
promote
by
inducing
extracellular
matrix
accumulation,
while
HCC
they
drive
tumorigenesis
via
activation
Wnt/β-catenin
pathway
p53
inactivation.
Through
multi-omics
analyses,
this
identifies
critical
pathogenic
molecules
signaling
pathways
regulated
pollutants,
providing
new
insights
their
mechanisms,
potential
biomarkers,
therapeutic
targets.
These
offer
valuable
guidance
for
development
diagnostic
strategies
diseases
formulation
environmental
health
risk
prevention
measures.
Expert Review of Proteomics,
Journal Year:
2025,
Volume and Issue:
unknown
Published: March 19, 2025
Liquid
chromatography-tandem
mass
spectrometry
(LC-MS/MS)
has
been
a
leading
method
for
proteomics
thirty
years.
Advantages
provided
by
LC-MS/MS
are
offset
significant
disadvantages,
including
cost.
Recently,
several
non-mass
spectrometric
methods
have
emerged,
but
little
information
is
available
about
their
capacity
to
analyze
the
complex
mixtures
routine
spectrometry.
We
review
recent
non-mass-spectrometric
sequencing
proteins
and
peptides,
using
nanopores,
degradation,
reverse
translation,
short-epitope
mapping,
with
comments
on
bioinformatics
challenges,
fundamental
limitations,
areas
where
new
technologies
will
be
more
or
less
competitive
LC-MS/MS.
In
addition
conventional
literature
searches,
instrument
vendor
websites,
patents,
webinars,
preprints
were
also
consulted
give
up-to-date
picture.
Many
promising.
However,
demonstrations
that
they
outperform
in
terms
of
peptides
identified
not
yet
published,
astute
observers
note
important
especially
relating
dynamic
range
single-molecule
measurements
mixtures.
Still,
even
if
performance
emerging
proves
inferior
LC-MS/MS,
low
cost
could
create
different
kind
revolution:
dramatic
increase
number
biology
laboratories
engaging
forms
research.
