DIA-NN: neural networks and interference correction enable deep proteome coverage in high throughput
Nature Methods,
Journal Year:
2019,
Volume and Issue:
17(1), P. 41 - 44
Published: Nov. 25, 2019
Language: Английский
mRNAs, proteins and the emerging principles of gene expression control
Nature Reviews Genetics,
Journal Year:
2020,
Volume and Issue:
21(10), P. 630 - 644
Published: July 24, 2020
Language: Английский
Revisiting biomarker discovery by plasma proteomics
Molecular Systems Biology,
Journal Year:
2017,
Volume and Issue:
13(9)
Published: Sept. 1, 2017
Clinical
analysis
of
blood
is
the
most
widespread
diagnostic
procedure
in
medicine,
and
biomarkers
are
used
to
categorize
patients
support
treatment
decisions.
However,
existing
far
from
comprehensive
often
lack
specificity
new
ones
being
developed
at
a
very
slow
rate.
As
described
this
review,
mass
spectrometry
(MS)-based
proteomics
has
become
powerful
technology
biological
research
it
now
poised
allow
characterization
plasma
proteome
great
depth.
Previous
"triangular
strategies"
aimed
discovering
single
biomarker
candidates
small
cohorts,
followed
by
classical
immunoassays
much
larger
validation
cohorts.
We
propose
"rectangular"
profiling
strategy,
which
patterns
large
cohorts
correlated
with
their
phenotypes
health
disease.
Translating
such
concepts
into
clinical
practice
will
require
restructuring
several
aspects
decision-making,
we
discuss
some
first
steps
direction.
Language: Английский
Ultra-High-Throughput Clinical Proteomics Reveals Classifiers of COVID-19 Infection
Cell Systems,
Journal Year:
2020,
Volume and Issue:
11(1), P. 11 - 24.e4
Published: June 2, 2020
The
COVID-19
pandemic
is
an
unprecedented
global
challenge,
and
point-of-care
diagnostic
classifiers
are
urgently
required.
Here,
we
present
a
platform
for
ultra-high-throughput
serum
plasma
proteomics
that
builds
on
ISO13485
standardization
to
facilitate
simple
implementation
in
regulated
clinical
laboratories.
Our
low-cost
workflow
handles
up
180
samples
per
day,
enables
high
precision
quantification,
reduces
batch
effects
large-scale
longitudinal
studies.
We
use
our
collected
from
cohort
of
early
hospitalized
cases
the
SARS-CoV-2
identify
27
potential
biomarkers
differentially
expressed
depending
WHO
severity
grade
COVID-19.
They
include
complement
factors,
coagulation
system,
inflammation
modulators,
pro-inflammatory
factors
upstream
downstream
interleukin
6.
All
protocols
software
implementing
approach
freely
available.
In
total,
this
work
supports
development
routine
proteomic
assays
aid
decision
making
generate
hypotheses
about
therapeutic
targets.
Language: Английский
Extracellular Vesicles Provide a Means for Tissue Crosstalk during Exercise
Cell Metabolism,
Journal Year:
2018,
Volume and Issue:
27(1), P. 237 - 251.e4
Published: Jan. 1, 2018
Language: Английский
Plasma proteomic signature of age in healthy humans
Aging Cell,
Journal Year:
2018,
Volume and Issue:
17(5)
Published: July 11, 2018
Abstract
To
characterize
the
proteomic
signature
of
chronological
age,
1,301
proteins
were
measured
in
plasma
using
SOMAscan
assay
(SomaLogic,
Boulder,
CO,
USA)
a
population
240
healthy
men
and
women,
22–93
years
old,
who
disease‐
treatment‐free
had
no
physical
cognitive
impairment.
Using
p
≤
3.83
×
10
−5
significance
threshold,
197
positively
associated,
20
negatively
associated
with
age.
Growth
differentiation
factor
15
(GDF15)
strongest,
positive
association
age
(GDF15;
0.018
±
0.001,
=
7.49
−56
).
In
our
sample,
GDF15
was
not
other
cardiovascular
risk
factors
such
as
cholesterol
or
inflammatory
markers.
The
functional
pathways
enriched
217
age‐associated
included
blood
coagulation,
chemokine
pathways,
axon
guidance,
peptidase
activity,
apoptosis.
elastic
net
regression
models,
we
created
based
on
relative
concentrations
76
that
highly
correlated
(
r
0.94).
generalizability
findings
needs
replication
an
independent
cohort.
Language: Английский
A Novel LC System Embeds Analytes in Pre-formed Gradients for Rapid, Ultra-robust Proteomics
Molecular & Cellular Proteomics,
Journal Year:
2018,
Volume and Issue:
17(11), P. 2284 - 2296
Published: Aug. 13, 2018
To
further
integrate
mass
spectrometry
(MS)-based
proteomics
into
biomedical
research
and
especially
clinical
settings,
high
throughput
robustness
are
essential
requirements.
They
largely
met
in
high-flow
rate
chromatographic
systems
for
small
molecules
but
these
not
sufficiently
sensitive
applications.
Here
we
describe
a
new
concept
that
delivers
on
requirements
while
maintaining
the
sensitivity
of
current
nano-flow
LC
systems.
Low-pressure
pumps
elute
sample
from
disposable
trap
column,
simultaneously
forming
gradient
is
stored
long
storage
loop.
An
auxiliary
creates
an
offset,
ensuring
re-focusing
peptides
before
separation
analytical
column
by
single
high-pressure
pump.
This
simplified
design
enables
robust
operation
over
thousands
injections.
Furthermore,
steps
between
injections
performed
parallel,
reducing
overhead
time
to
few
minutes
allowing
analysis
more
than
200
samples
per
day.
From
fractionated
HeLa
cell
lysates,
deep
proteomes
covering
130,000
sequence
unique
close
10,000
proteins
were
rapidly
acquired.
Using
this
data
as
library,
demonstrate
quantitation
5200
only
21
min.
Thus,
system
-
termed
Evosep
One
analyzes
extremely
manner,
without
sacrificing
depth
coverage.
Bottom-up
highly
successful
generic
technology,
which
now
allows
complex
ranging
bacteria
through
line
even
human
tissue
(1Aebersold
R.
Mann
M.
Mass-spectrometric
exploration
proteome
structure
function.Nature.
2016;
537:
347-355Crossref
PubMed
Scopus
(1105)
Google
Scholar).
State-of-the-art
workflows
begin
with
preparation
digest
harvest
purified
(2Kulak
N.A.
Pichler
G.
Paron
I.
Nagaraj
N.
Minimal,
encapsulated
proteomic-sample
processing
applied
copy-number
estimation
eukaryotic
cells.Nat.
Methods.
2014;
11:
319-324Crossref
(991)
Scholar),
separated
liquid
chromatography
(LC)
1The
abbreviation
used
is:LCliquid
chromatography.
they
analyzed
spectrometer
(MS).
Established
software
solutions
automatically
interpret
acquired
spectra,
generating
lists
quantified
(3Cox
J.
MaxQuant
peptide
identification
rates,
individualized
p.p.b.-range
accuracies
proteome-wide
protein
quantification.Nat.
Biotechnol.
2008;
26:
1367-1372Crossref
(9154)
Scholar,
4Bekker-Jensen
D.B.
Kelstrup
C.D.
Batth
T.S.
Larsen
S.C.
Haldrup
C.
Bramsen
J.B.
Sørensen
K.D.
Høyer
S.
Ørntoft
T.F.
Andersen
C.L.
Nielsen
M.L.
Olsen
J.V.
optimized
shotgun
strategy
rapid
generation
comprehensive
proteomes.Cell
Systems.
2017;
4:
587-599Abstract
Full
Text
PDF
(255)
5Kelstrup
Bekker-Jensen
Arrey
T.N.
Hogrebe
A.
Harder
Performance
evaluation
Q
Exactive
HF-X
proteomics.J
Proteome
Res,.
2018;
17:
727-738Crossref
(159)
6Kulak
Geyer
P.E.
Loss-less
nano-fractionator
sensitivity,
coverage
proteomics.Mol.
Cell.
Proteomics.
(Manuscript
Press,
2017)Abstract
(104)
7Bruderer
Bernhardt
OM
Gandhi
T
Xuan
Y
Sondermann
J
Schmidt
M
Gomez-Varela
D
Reiter
L
Optimization
experimental
parameters
data-independent
significantly
increases
reproducibility
results.Mol.
16:
2296-2309Abstract
(189)
8Meier
F.
Virreira
Winter
Cox
BoxCar
acquisition
method
single-shot
at
100
minutes.Nat.
10.1038/s41592-018-0003-5Crossref
(218)
The
performance
level
result
improvements
spectrometric
components
also
part
LC-MS
workflow.
In
quest
ever
increasing
power,
columns
have
become
longer
particle
sizes
smaller
reaching
sub
2
μm
range.
may
require
pump
pressures
1000
bar,
presenting
great
engineering
challenges
both
entire
system,
often
limiting
routine
operation.
remains
weak
link
MS-based
workflows,
leading
calls
approaches
(9Riley
N.M.
Hebert
A.S.
Coon
J.J.
Proteomics
Moves
Fast
Lane.Cell
Syst,.
2:
142-143Abstract
(33)
irreproducibility
retention
times
within
laboratories
severely
limits
strategies
rely
transfer
accurate
times,
targeted
(10Picotti
P.
Aebersold
Selected
reaction
monitoring-based
proteomics:
potential,
pitfalls
future
directions.Nat.
2012;
9:
555-566Crossref
independent
(11Gillet
L.C.
Leitner
Mass
bottom-up
entering
high-throughput
era
hypothesis
testing.Annu.
Rev.
Anal.
Chem.
449-472Crossref
(207)
Scholar)
"match
runs"
MS
(12Cox
Hein
M.Y.
Luber
C.A.
Accurate
label-free
quantification
delayed
normalization
maximal
ratio
extraction,
MaxLFQ.Mol.
13:
2513-2526Abstract
(2688)
13Geiger
T.
Wehner
A
Schaab
C
Comparative
proteomic
eleven
common
lines
reveals
ubiquitous
varying
expression
most
proteins.Mol.
11M111.014050Abstract
(577)
There
interest
applying
power
diagnostic
questions
(14Geyer
Holdt
L.M.
Teupser
D.
Revisiting
biomarker
discovery
plasma
proteomics.Mol
Syst
Biol,.
942Crossref
(390)
"Clinical
proteomics",
however,
requires
far
stability
available
advanced
laboratories.
Note
issues
features
se,
measurement
firmly
established
around
world,
routinely
measure
hundreds
two
key
differences
one
their
much
larger
diameters
(20-fold)
flow
rates
(1000-fold),
making
them
easier
control
less
error-prone.
Increasing
achieve
greater
has
already
been
advocated
context
cancer
(15Liu
Y.
Hüttenhain
Collins
B.
maps
research.Expert
Mol.
Diagn.
2013;
811-825Crossref
(99)
However,
signal
intensity
electrospray
ionization
concentration
dependent
higher
μl/min.
Apart
robustness,
other
central
requirement
proteomics,
if
it
enter
use.
Instead,
generally
employ
fractionation—multiplying
time—or
use
relatively
times.
recent
large-scale
study
measured
our
laboratory,
involving
thousand
samples,
80%
overall
down
was
attributable
HPLC
rather
MS.
At
same
time,
equilibration,
loading
washing
runs
limited
attractiveness
very
short
gradients
(16Geyer
Kulak
Plasma
profiling
assess
health
disease.Cell
Syst.
185-195Abstract
(380)
17Geyer
Wewer
Albrechtsen
N.J.
Tyanova
Grassl
Iepsen
E.W.
Lundgren
Madsbad
Holst
Torekov
S.S.
effects
sustained
weight
loss
proteome.Mol.
Biol.
12:
901Crossref
(135)
Several
years
ago,
some
authors
devised
different
injection
approach.
Termed
speLC,
solid-phase-extraction
(nano)
chromatography,
intended
needed
application
(18Falkenby
L.G.
Such-Sanmartín
M.R.
Vorm
O.
Bache
Jensen
O.N.
Integrated
solid-phase
extraction-capillary
(speLC)
interfaced
ESI-MS/MS
fast
characterization
proteomes.J.
Res.
6169-6175Crossref
(18)
speLC
made
StageTips
commonly
employed
micro-scale
purification
crude
manual
fractionation
(19Ishihama
Rappsilber
Modular
stop
go
extraction
tips
stacked
disks
parallel
multidimensional
Peptide
proteomics.J.
2006;
5:
988-994Crossref
(224)
20Rappsilber
Ishihama
Stop
matrix-assisted
laser
desorption/ionization,
nanoelectrospray,
LC/MS
pretreatment
proteomics.Anal.
2003;
75:
663-670Crossref
(1796)
21Wisniewski
J.R.
Dus
K.
Proteomic
workflow
archival
formalin-fixed
paraffin-embedded
10
000
proteins.Proteomics
Clin.
Appl.
7:
225-233Crossref
(119)
Instead
eluting
autosampler
vial
low-pressure
passed
5–10
min
StageTip
itself
directly
toward
can
analyze
192
E.
coli
30
h,
well
identifying
500
lysate
subsequent
work,
combined
pre-fractionation
such
1D
gel
electrophoresis
or
strong
cation
exchange
(SCX),
capitalizing
its
ability
each
fractions
(22Binai
Marino
Soendergaard
Mohammed
Heck
A.J.
Rapid
analyses
interactomes
using
integrated
extraction-liquid
chromatography-MS/MS
system.J.
2015;
14:
977-985Crossref
(5)
Although
useful
simple
mixtures,
elution
inherently
system.
work
reported
here,
aimed
preserve
benefits
original
device
achieving
desirable
modern
instruments.
We
realized
goal
coupling
novel
downstream
design,
eluted
low
pressure
tens
μl/min
special
EvotipTM.
Notably,
along
analytes
captured
capillary
then
applies
nano-scale
column.
results
undiminished
eliminating
need
form
pressure.
layout
marries
convenience
large
columns,
narrow
low-flow
nano-LC
detail
principle
development
instrument
investigate
throughput,
typical
applications
encountered
proteomics.
incorporates
four
stroke
piston
(A,
B,
C,
D)
(HP)
(Fig.
1A;
supplemental
Fig.
S1A,
S1B).
Together
create
separate
low-
sub-system.
Each
equipped
sensor
monitor
precisely
individual
solvent.
custom
12-port
valve
(operating
low-pressure)
diverts
either
solvent
bottles
(sol
A,
sol
B)
refilling
analysis.
6-port
high-pressure)
refilling.
path
loop,
connected
sub-system
controlled
rotary
1A).
way,
always
in-line
bypasses
contrast,
waste
bypassing
loop
becomes
bridge
sub-systems.
illustrated
timetable
diagrams,
highlighting
stages
run
1B,
S2–S9).
beginning
run,
XYZ-axis
manipulator
picks
up
(Evotip)
ceramic
needle
positions
A/B/C/D
mixing
cross
1A,
second
step,
B
primary
A/B
tee
flows
S2).
organic
content
initial
35%
ensure
off
unwanted
compounds
polymers,
lipids,
hydrophobic
remain
bound
single-use,
any
particulate
matter
loaded
samples.
final
volume
μl
precise
minimize
bleeding
molecules.
"partial
elution"
will
be
described
RESULTS
AND
DISCUSSION.
additional
pumps,
modify
eluent
"offset"
(supplemental
purpose
lowering
contents,
initially
retained
offset
embedded
moved
being
switched
first
steps,
filled
S3)
equilibrated
S4).
Subsequently,
switches
preformed
pushed
S5).
prepared
next
ejecting
needle,
aligning
solvents
S6–S9).
contains
procedures
state
during
detect
parts
warns
potential
leaks
lack
Evotips
designated
position.
It
built
trouble
shooting
Chronos
user
interface.
Moreover,
carries
out
preparatory
actions
run.
cells
cultured
glucose
DMEM
10%
fetal
bovine
serum
1%
penicillin-streptomycin
(Life
Technologies,
Inc.).
Cells
counted
Invitrogen
countess
counter
after
snap
freezing
−80
°C.
Protein
concentrations
determined
8
m
urea
tryptophan
fluorescence
emission
350
nm,
excitation
wavelength
295
nm.
Tryptophan
0.1
μg/μl
establish
standard
calibration
curve
(0–4
μl).
estimated
equivalent
7
extract,
average
accounts
1.3%
amino
acid
composition.
For
iST
kit
starting
106
according
manufacturer's
instructions
(P.O.
00001,
PreOmics
GmbH).
test
optimize
injected
2000
tryptic
cells,
exploratory
batches.
experiment,
breadboard
model
coupled
LTQ
Orbitrap
instrument.
All
protocolled,
phase,
stopped
optimization
hardware
components.
last
1500
variation
wear
Blood
taken
venipuncture
commercially
winged
infusion
set
collection
tubes
containing
EDTA
centrifuged
15
×
g
plasma.
sampled
healthy
donor,
who
provided
written
informed
consent,
prior
approval
ethics
committee
Max
Planck
Society.
distributed
96-well
plate
subsequently
processed
automated
Profiling
previously
"UPS1
Standard"
(Sigma-Aldrich)
digested
indicated
above
samples/day
(5.6
gradient)
5
cm
C18
(3
size).
Peptides
reversed-phase
Acquity
CSH
1.7
1
150
mm
(Waters,
Milford,
MA)
Ultimate
3000
(HPLC)
(Dionex,
Sunnyvale,
CA)
operating
Buffer
(5
ammonium
bicarbonate)
buffer
(100%
ACN)
used.
linear
5%
55
min,
followed
increase
70%
total,
46
collected
concatenation.
LC-MS/MS,
amount
kept
constant
ng
Easy-nLC
1200,
fraction
Evotip.
effect
diffusion
function
rig
mimic
figure
2.
Zirconium
nano
(Prolab
Instruments,
GmbH,
Switzerland,
A:
0.1%
formic
(FA)
H2O,
Pump
B:
FA,
acetone
acetonitrile)
programed
following
composition
profile:
0–5
5–95%
10–13
95%
13–15
95–5%,
15–18
5%,
18–23
23–25
25–27
95–5%
27–30
delivered
coiled
(diameter
cm)
fused
silica
(length
m,
i.d.
μm,
OD375,
Polymicro
Technologies).
After
specified
had
passed,
third
UV
detector
(SpectraFlow
501,
SunChrom)
nl)
record
absorption
265
three
all
Vici
(Valco
Instruments
Co.
Inc.)
script.
250
commercial
(Pierce,
no.
1862824)
spiked
fmol
PicoSure
Test
Standard
(eight
synthetic
mix,
New
Objective
PS-STDN)
mix
Evotips.
five
methods,
replicates
Thermo
acquire
full
scans
(resolution
35k)
MS2
17.5k)
eight
scheduled
table
6B).
Skyline
extract
4
6
ions
(parallel
monitoring)
(23MacLean
Tomazela
D.M.
Shulman
Chambers
Finney
G.L.
Frewen
Kern
Tabb
D.L.
Liebler
D.C.
MacCoss
M.J.
Skyline:
open
source
document
editor
creating
analyzing
experiments.Bioinformatics,.
2010;
966-968Crossref
(2964)
Chromatographic
profiles
exported
peak
characteristics
extracted
Tips
activated
consecutive
wash
100%
ACN,
50%
ACN
0.5%
H2O
H2O.
BSA
tip
activation
protocol
later
1-propanol
wetting
material
equilibration.
instrumentation
consisted
production
version
(Thermo
Fisher
Scientific)
experiments.
Purified
3
Reprosil-Pur
beads
(Dr.
Maisch,
Ammerbuch,
Germany)
dimensions
below
6B.
On
MS,
Top6
Top12
Orbitrap,
target
value
scan
spectra
charges
300–1650
m/z
range
maximum
50
ms
resolution
60,000
200.
Fragmentation
precursor
higher-energy
C-trap
dissociation
(HCD)
normalized
collision
energy
27
eV
(24Olsen
et
al.Higher-energy
modification
analysis.Nat.
2007;
709-712Crossref
(719)
MS/MS
15,000
ion
104
25
ms.
Dynamic
exclusion
s
avoid
repeated
sequencing
identical
peptides.
harvested
∼80%
confluence
twice
PBS
adding
boiling
lysis
(6
guanidinium
hydrochloride
(GndCl),
tris(2-carboxyethyl)phosphine,
chloroacetamide,
Tris
pH
8.5)
plate.
scraping
boiled
micro
probe
sonication
(Vibra-Cell
VCX130,
Sonics,
Newton,
CT)
pulses
amplitude.
Bradford
assay,
LysC
(Wako)
enzyme/protein
1:100
(w/w)
dilution
Tris,
8.5,
GndCl
overnight
trypsin
(1:100
w/w).
Protease
activity
quenched
acidification
trifluoroacetic
(TFA)
∼1%,
resulting
mixture
concentrated
Sep-Pak
(C18
Classic
Cartridge,
Waters,
MA).
Elution
done
ml
40%
acetonitrile
(ACN),
60%
ACN.
eluates
reduced
SpeedVac
(Eppendorf,
Germany),
measuring
absorbance
280
nm
NanoDrop
spectrophotometer
(NanoDrop
2000C,
Scientific,
Germany).
DIA
iRT
(Biognosys
AB,
Schlieren,
Switzerland)
added
protocol.
One,
in-house
packed
12
cm,
1.9
used,
1200
75
specifications
above.
temperature
maintained
40
°C
oven
(PRSO-V1,
Sonation,
Biberach,
online
spectrometer.
raw
files
(version
1.5.6.8)
fragments
searched
against
Uniprot
Reference
isoforms
(April
2017
release
21,042
sequences)
Andromeda
search
engine
(25Cox
Neuhauser
Michalski
Scheltema
R.A.
Andromeda:
environment.J
2011;
10:
1794-1805Crossref
(3450)
cysteine
carbamidomethylation
fixed
N-terminal
acetylation
methionine
oxidations
variable
modifications.
experiment
UPS1
FASTA
file,
downloaded
homepage
Sigma-Aldrich
2018).
false
(FDR)
0.01
levels
minimum
length
acids
Enzyme
specificity
C-terminal
arginine
lysine
expected
proteases,
missed
cleavages.
deviation
ppm
fragment
20
specified.
Data
(DIA)
Spectronaut
11.0.15038.19.19667,
default
settings
(Biognosys,
Zurich,
Switzerland).
project
specific
spectral
library
imported
pre-fractionated
fractions,
settings.
Information
about
precursors,
identified
Supplemental
Table
S1
S2.
bioinformatics
Perseus
(26Tyanova
Temu
Sinitcyn
Carlson
Geiger
computational
platform
(prote)omics
data.Nat.
Method.
731-740Crossref
(3530)
platform.
Our
idea
decouple
formation
resolution,
As
strategies,
(a
solid
phase
like
(20Rappsilber
Scholar)).
instead
tips,
drying
remove
re-suspending
buffer,
Evotip
accomplished
Language: Английский
BoxCar acquisition method enables single-shot proteomics at a depth of 10,000 proteins in 100 minutes
Nature Methods,
Journal Year:
2018,
Volume and Issue:
15(6), P. 440 - 448
Published: May 4, 2018
Language: Английский
Genetics meets proteomics: perspectives for large population-based studies
Nature Reviews Genetics,
Journal Year:
2020,
Volume and Issue:
22(1), P. 19 - 37
Published: Aug. 28, 2020
Language: Английский
Blood plasma phosphorylated-tau isoforms track CNS change in Alzheimer’s disease
The Journal of Experimental Medicine,
Journal Year:
2020,
Volume and Issue:
217(11)
Published: July 28, 2020
Highly
sensitive
and
specific
plasma
biomarkers
for
Alzheimer’s
disease
(AD)
have
the
potential
to
improve
diagnostic
accuracy
in
clinic
facilitate
research
studies
including
enrollment
prevention
treatment
trials.
We
recently
reported
CSF
tau
hyperphosphorylation,
especially
on
T217,
is
an
accurate
predictor
of
β-amyloidosis
at
asymptomatic
symptomatic
stages.
In
current
study,
we
determine
by
mass
spectrometry
utility
p-tau
isoforms
detect
AD
pathology
investigate
isoforms’
profile
relationships.
Plasma
was
truncated
as
previously
described
CSF.
measures
p-tau-217
p-tau-181
were
correlated.
No
correlation
found
between
total-tau
levels
pS202
measures.
highly
amyloid
plaque
discovery
cohort
(n
=
36,
AUROC
0.99
0.98
respectively).
validation
92),
still
status
(AUROC
0.92),
less
0.75).
Language: Английский