Maximizing Immunopeptidomics-Based Bacterial Epitope Discovery by Multiple Search Engines and Rescoring
Journal of Proteome Research,
Год журнала:
2025,
Номер
unknown
Опубликована: Март 13, 2025
Mass
spectrometry-based
discovery
of
bacterial
immunopeptides
presented
by
infected
cells
allows
untargeted
antigens
that
can
serve
as
vaccine
candidates.
However,
reliable
identification
epitopes
is
challenged
their
extremely
low
abundance.
Here,
we
describe
an
optimized
bioinformatic
framework
to
enhance
the
confident
immunopeptides.
Immunopeptidomics
data
cell
cultures
with
Listeria
monocytogenes
were
searched
four
different
search
engines,
PEAKS,
Comet,
Sage
and
MSFragger,
followed
data-driven
rescoring
MS2Rescore.
Compared
individual
engine
results,
this
integrated
workflow
boosted
immunopeptide
average
27%
led
high-confidence
detection
18
additional
peptides
(+27%)
matching
15
proteins
(+36%).
Despite
strong
agreement
between
a
small
number
spectra
(<1%)
had
ambiguous
matches
multiple
excluded
ensure
identifications.
Finally,
demonstrate
our
sensitive
timsTOF
SCP
acquisition
find
rescoring,
now
inclusion
ion
mobility
features,
identifies
76%
more
compared
Q
Exactive
HF
acquisition.
Together,
results
how
integration
along
maximizes
identification,
boosting
for
development.
Язык: Английский
Rustims: An Open-Source Framework for Rapid Development and Processing of timsTOF Data-Dependent Acquisition Data
Journal of Proteome Research,
Год журнала:
2025,
Номер
unknown
Опубликована: Апрель 22, 2025
Mass
spectrometry
is
essential
for
analyzing
and
quantifying
biological
samples.
The
timsTOF
platform
a
prominent
commercial
tool
this
purpose,
particularly
in
bottom-up
acquisition
scenarios.
additional
ion
mobility
dimension
requires
more
complex
data
processing,
yet
most
current
software
solutions
raw
are
proprietary
or
closed-source,
limiting
integration
into
custom
workflows.
We
introduce
rustims,
framework
implementing
flexible
toolbox
designed
processing
data,
currently
focusing
on
data-dependent
(DDA-PASEF).
employs
dual-language
approach,
combining
efficient,
multithreaded
Rust
code
with
an
easy-to-use
Python
interface.
This
allows
implementations
that
fast,
intuitive,
easy
to
integrate.
With
imspy
as
its
main
scripting
interface
sagepy
Sage
search
engine
bindings,
rustims
enables
integrable,
intuitive
processing.
demonstrate
capabilities
pipeline
DDA-PASEF
including
rescoring
of
third-party
tools
like
the
Prosit
intensity
predictor
extended
model.
supports
tryptic
proteomics
nontryptic
immunopeptidomics
benchmark
comparisons
FragPipe
PEAKS.
Rustims
available
GitHub
under
MIT
license,
installation
packages
multiple
platforms
PyPi
all
analysis
scripts
accessible
via
Zenodo.
Язык: Английский