Immunopeptidomics mapping of Listeria monocytogenes T cell epitopes in mice
Molecular & Cellular Proteomics,
Год журнала:
2024,
Номер
23(9), С. 100829 - 100829
Опубликована: Авг. 14, 2024
Listeria
monocytogenes
is
a
foodborne
intracellular
bacterial
model
pathogen.
Protective
immunity
against
depends
on
an
effective
CD8
Язык: Английский
Integrated View of Baseline Protein Expression in Human Tissues Using Public Data Independent Acquisition Data Sets
Journal of Proteome Research,
Год журнала:
2025,
Номер
24(2), С. 685 - 695
Опубликована: Янв. 7, 2025
The
PRIDE
database
is
the
largest
public
data
repository
of
mass
spectrometry-based
proteomics
and
currently
stores
more
than
40,000
sets
covering
a
wide
range
organisms,
experimental
techniques,
biological
conditions.
During
past
few
years,
has
seen
significant
increase
in
amount
submitted
data-independent
acquisition
(DIA)
sets.
This
provides
an
excellent
opportunity
for
large-scale
reanalysis
reuse.
We
have
reanalyzed
15
label-free
DIA
across
various
healthy
human
tissues
to
provide
state-of-the-art
view
proteome
baseline
conditions
(without
any
perturbations).
computed
protein
abundances
compared
them
tissues,
samples,
Our
second
aim
was
compare
obtained
here
from
results
previous
analyses
using
data-dependent
(DDA)
observed
good
correlation
some
especially
liver
colon,
but
weak
correlations
were
found
others,
such
as
lung
pancreas.
including
abundance
values
curated
metadata
are
made
available
download
resource
Expression
Atlas.
Язык: Английский
The plant proteome delivers from discovery to innovation
Trends in Plant Science,
Год журнала:
2025,
Номер
unknown
Опубликована: Апрель 1, 2025
Язык: Английский
Integrated View of Baseline Protein Expression in Human Tissues using public Data Independent Acquisition datasets
bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2024,
Номер
unknown
Опубликована: Сен. 19, 2024
Abstract
The
PRIDE
database
is
the
largest
public
repository
of
mass
spectrometry-based
proteomics
data
and
currently
stores
more
than
40,000
datasets
covering
a
wide
range
organisms,
experimental
techniques
biological
conditions.
During
past
few
years,
has
seen
an
increase
in
amount
submitted
Data-Independent
Acquisition
(DIA)
datasets,
parallel
with
trends
field.
This
provides
excellent
opportunity
for
large
scale
reanalysis
reuse.
We
have
systematically
reanalysed
15
label-free
DIA
across
various
healthy
human
tissues,
to
provide
state-of-the-art
view
proteome
baseline
conditions
(without
any
perturbations),
coming
from
datasets.
computed
protein
abundances
compared
them
samples
Our
second
aim
was
make
comparison
obtained
previous
analyses
Data-Dependent
(DDA)
Results
were
heterogeneous.
On
one
hand,
we
observed
good
correlation
some
especially
liver
colon.
other
weak
correlations
however
found
others
such
as
lung
pancreas.
It
likely
this
reflects
mostly
differences
sample
preparation
processing
derived
these
opposed
fundamental
between
DDA
proteomics.
results
including
curated
metadata
are
made
available
download
resource
Expression
Atlas.
Язык: Английский
Differences in Uniquely Identified Peptides Between ddaPASEF and diaPASEF
Cells,
Год журнала:
2024,
Номер
13(22), С. 1848 - 1848
Опубликована: Ноя. 7, 2024
Recent
advancements
in
mass
spectrometry-based
proteomics
have
made
it
possible
to
conduct
comprehensive
protein
analysis.
In
particular,
the
emergence
of
data-independent
acquisition
(DIA)
method
powered
by
machine
learning
has
significantly
improved
identification
efficiency.
However,
compared
with
conventional
data-dependent
(DDA)
method,
degree
which
peptides
are
uniquely
identified
DIA
and
DDA
not
been
thoroughly
examined.
this
study,
we
over
10,000
proteins
using
methods
analyzed
characteristics
unique
each
method.
Results
showed
that
number
same
column
type
was
19%
32%,
respectively,
shorter
preferentially
detected
addition,
more
DIA-specific
were
identified,
especially
during
first
10%
elution
time,
overall
1/
Язык: Английский