Analytical Chemistry,
Journal Year:
2023,
Volume and Issue:
95(20), P. 8020 - 8027
Published: May 11, 2023
Recent
developments
in
mass
spectrometry-based
single-cell
proteomics
(SCP)
have
resulted
dramatically
improved
sensitivity,
yet
the
relatively
low
measurement
throughput
remains
a
limitation.
Isobaric
and
isotopic
labeling
methods
been
separately
applied
to
SCP
increase
through
multiplexing.
Here
we
combined
both
forms
of
achieve
multiplicative
scaling
for
higher
throughput.
Two-plex
stable
isotope
amino
acids
cell
culture
(SILAC)
isobaric
tandem
tag
(TMT)
enabled
up
28
single
cells
be
analyzed
liquid
chromatography–mass
spectrometry
(LC–MS)
analysis,
addition
carrier,
reference,
negative
control
channels.
A
custom
nested
nanowell
chip
was
used
nanoliter
sample
processing
minimize
losses.
Using
145-min
total
LC–MS
cycle
time,
∼280
were
per
day.
This
could
increased
∼700
samples
day
with
high-duty-cycle
multicolumn
LC
system
producing
same
active
gradient.
The
efficiency
achievable
proteome
coverage
characterized
multiple
analysis
conditions.
International Journal of Molecular Sciences,
Journal Year:
2023,
Volume and Issue:
24(3), P. 2415 - 2415
Published: Jan. 26, 2023
The
progressive
loss
of
skeletal
muscle
mass
and
concomitant
reduction
in
contractile
strength
plays
a
central
role
frailty
syndrome.
Age-related
neuronal
impairments
are
closely
associated
with
sarcopenia
the
elderly,
which
is
characterized
by
severe
muscular
atrophy
that
can
considerably
lessen
overall
quality
life
at
old
age.
Mass-spectrometry-based
proteomic
surveys
senescent
human
muscles,
as
well
animal
models
sarcopenia,
have
decisively
improved
our
understanding
molecular
cellular
consequences
fiber-type
shifting
during
aging.
This
review
outlines
spectrometric
identification
proteome-wide
changes
atrophying
focus
on
proteins
potential
markers
distribution
patterns.
observed
trend
fast-to-slow
transitions
individual
muscles
aging
process
most
likely
linked
to
preferential
susceptibility
fast-twitching
fibers
atrophy.
Studies
models,
including
mostly
aged
rodent
confirmed
shifting.
analysis
fast
versus
slow
isoforms
key
proteins,
such
myosin
heavy
chains,
light
actins,
troponins
tropomyosins,
suggests
them
suitable
bioanalytical
tools
Analytical and Bioanalytical Chemistry,
Journal Year:
2023,
Volume and Issue:
415(28), P. 6889 - 6899
Published: June 7, 2023
Abstract
Single-cell
methodologies
and
technologies
have
started
a
revolution
in
biology
which
until
recently
has
primarily
been
limited
to
deep
sequencing
imaging
modalities.
With
the
advent
subsequent
torrid
development
of
single-cell
proteomics
over
last
5
years,
despite
fact
that
proteins
cannot
be
amplified
like
transcripts,
it
now
become
abundantly
clear
is
worthy
complement
transcriptomics.
In
this
review,
we
engage
an
assessment
current
state
art
including
workflow,
sample
preparation
techniques,
instrumentation,
biological
applications.
We
investigate
challenges
associated
with
working
very
small
volumes
acute
need
for
robust
statistical
methods
data
interpretation.
delve
into
what
believe
promising
future
research
at
resolution
highlight
some
exciting
discoveries
already
made
using
proteomics,
identification
rare
cell
types,
characterization
cellular
heterogeneity,
investigation
signaling
pathways
disease
mechanisms.
Finally,
acknowledge
there
are
number
outstanding
pressing
problems
scientific
community
vested
advancing
technology
needs
resolve.
Of
prime
importance
set
standards
so
becomes
widely
accessible
allowing
novel
easily
verifiable.
conclude
plea
solve
these
rapidly
can
part
robust,
high-throughput,
scalable
multi-omics
platform
ubiquitously
applied
elucidating
insights
diagnosis
treatment
all
diseases
afflict
us.
Nature Communications,
Journal Year:
2024,
Volume and Issue:
15(1)
Published: Feb. 10, 2024
Abstract
The
shotgun
proteomic
analysis
is
currently
the
most
promising
single-cell
protein
sequencing
technology,
however
its
identification
level
of
~1000
proteins
per
cell
still
insufficient
for
practical
applications.
Here,
we
develop
a
pick-up
(PiSPA)
workflow
to
achieve
deep
capable
quantifying
up
3000
groups
in
mammalian
using
label-free
quantitative
method.
PiSPA
specially
established
samples
mainly
based
on
nanoliter-scale
microfluidic
liquid
handling
robot,
achieving
capture,
pretreatment
and
injection
under
operation
strategy.
Using
this
customized
with
remarkable
improvement
identification,
2449–3500,
2278–3257
1621–2904
are
quantified
single
A549
cells
(
n
=
37),
HeLa
44)
U2OS
27)
DIA
(MBR)
mode,
respectively.
Benefiting
from
flexible
picking-up
ability,
study
migration
at
proteome
level,
demonstrating
potential
biological
research
insight.
Cell,
Journal Year:
2025,
Volume and Issue:
unknown
Published: Jan. 1, 2025
Despite
recent
advances
in
imaging-
and
antibody-based
methods,
achieving
in-depth,
high-resolution
protein
mapping
across
entire
tissues
remains
a
significant
challenge
spatial
proteomics.
Here,
we
present
parallel-flow
projection
transfer
learning
omics
data
(PLATO),
an
integrated
framework
combining
microfluidics
with
deep
to
enable
of
thousands
proteins
whole
tissue
sections.
We
validated
the
PLATO
by
profiling
proteome
mouse
cerebellum,
identifying
2,564
groups
single
run.
then
applied
rat
villus
human
breast
cancer
samples,
resolution
25
μm
uncovering
proteomic
dynamics
associated
disease
states.
This
approach
revealed
spatially
distinct
tumor
subtypes,
identified
key
dysregulated
proteins,
provided
novel
insights
into
complexity
microenvironment.
believe
that
represents
transformative
platform
for
exploring
regulation
its
interplay
genetic
environmental
factors.
Molecular & Cellular Proteomics,
Journal Year:
2021,
Volume and Issue:
21(1), P. 100179 - 100179
Published: Nov. 20, 2021
Single-cell
tandem
MS
has
enabled
analyzing
hundreds
of
single
cells
per
day
and
quantifying
thousands
proteins
across
the
cells.
The
broad
dissemination
these
capabilities
can
empower
dissection
pathophysiological
mechanisms
in
heterogeneous
tissues.
Key
requirements
for
achieving
this
goal
include
robust
protocols
performed
on
widely
accessible
hardware,
quality
controls,
community
standards,
automated
data
analysis
pipelines
that
pinpoint
analytical
problems
facilitate
their
timely
resolution.
Toward
meeting
requirements,
perspective
outlines
both
existing
resources
outstanding
opportunities,
such
as
parallelization,
catalyzing
wide
quantitative
single-cell
proteomics
be
scaled
up
to
tens
Indeed,
simultaneous
parallelization
peptides
is
a
promising
approach
multiplicative
increase
speed
performing
deep
proteomics.
ready
begin
virtuous
cycle
increased
adoption
fueling
development
more
technology
turn
drive
broader
adoption,
scientific
discoveries,
clinical
applications.
PROTEOMICS,
Journal Year:
2022,
Volume and Issue:
22(19-20)
Published: June 10, 2022
Mass
spectrometry
(MS)
has
emerged
at
the
forefront
of
quantitative
proteomic
techniques.
Liquid
chromatography-mass
(LC-MS)
can
be
used
to
determine
abundances
proteins
and
peptides
in
complex
biological
samples.
Several
methods
have
been
developed
adapted
for
accurate
quantification
based
on
chemical
isotopic
labeling.
Among
various
labeling
techniques,
isobaric
tagging
approaches
rely
analysis
from
MS2-based
rather
than
MS1-based
quantification.
In
this
review,
we
will
provide
an
overview
several
tags
along
with
some
recent
developments
including
complementary
ion
tags,
improvements
sensitive
quantitation
analytes
lower
abundance,
strategies
increase
multiplexing
capabilities,
targeted
strategies.
We
also
discuss
limitations
alleviate
these
restrictions
through
bioinformatic
tools
data
acquisition
methods.
This
review
highlight
applications
biomarker
discovery
validation,
thermal
proteome
profiling,
cross-linking
structural
investigations,
single-cell
analysis,
top-down
proteomics,
different
molecules
neuropeptides,
glycans,
metabolites,
lipids,
while
providing
considerations
evaluations
each
application.
