Michrom
Magic
C18
AQ
column
(200
µm
x
150
mm
nano-LC)
Michrom
Advance
Plug
and
Play
nanospray
source
CTC
Pal
autosampler
Thermo-Finnigan
LTQ
ion
trap
mass
spectrometer
X!
Tandem,
version
TORNADO
(thegpm.org)
Reagents
and
solutions
SDS
NaHPO4
dithioerythritol
iodoacetamide
ethanol
ammonium
bicarbonate
methylated
bovine
trypsin
acetonitrile
formic
acid
trifluoroacetic
acid
Procedure:
Hair
collection
and
digestion
Samples
(5
mg)
are
rinsed
twice
in
2%
SDS.
Samples
are
incubated
overnight
at
37°C
in
0.4
mL
of
2%
SDS,
0.1M
NaHPO4,
25
mM
dithioerythritol.
Samples
are
alkylated
for
1h
with
iodoacetamide
at
room
temperature
with
magnetic
stirring.
Proteins
are
precipitated
with
1
mL
of
ethanol.
Each
fraction
is
rinsed
twice
with
67%
ethanol,
once
with
0.1
M
ammonium
bicarbonate.
Samples
are
digested
at
room
temperature
with
reductively
methylated
bovine
trypsin
(1%
by
weight)
in
fresh
0.1
M
ammonium
bicarbonate-10%
acetonitrile;
trypsin
is
added
daily
for
3
days.
Samples
are
clarified
and
submitted
for
mass
spectrometry
(see
below).
Procedure:
Mass
spectrometry
Salts
and
polypeptides
resistant
to
elution
from
C18
reversed
phase
material
are
depleted
from
samples
by
solid
phase
extraction
with
Aspire
RP30
C18
desalting
tips;
tips
are
rinsed
exhaustively
with
60%
acetonitrile
and
then
0.1%
trifluoroacetic
acid.
Samples
are
adjusted
to
approximately
equal
peptide
amounts
by
A280.
Samples
are
directly
loaded
onto
an
Agilent
ZORBAX
300
SB
C18
reverse-phase
trap
cartridge,
which
is
switched
in-line
with
a
Michrom
Magic
C18
AQ
nano-LC
column
connected
to
a
Thermo-Finnigan
LTQ
ion
trap
mass
spectrometer
through
a
Michrom
Advance
Plug
and
Play
nanospray
source
and
CTC
Pal
autosampler.
The
nano-LC
column
is
used
with
a
binary
solvent
gradient
(buffer
A:
0.1%
formic
acid;
buffer
B:
100%
acetonitrile);
the
120-min
gradient
consisted
of
the
following
steps:
2-35%
buffer
B
in
85
min,
35-80%
buffer
B
in
23
min,
hold
for
1
min,
80-100%
buffer
B
in
1
min,
then
hold
for
10
min;
flow
rate
of
2
µL/min.
An
MS
survey
scan
is
obtained
for
the
m/z
range
375-1400,
and
the
MS/MS
spectra
are
acquired
from
the
10
most
intense
ions
in
the
MS
scan
by
subjecting
them
to
automated
low
energy
CID.
An
isolation
mass
window
of
2
Da
is
used
for
the
precursor
ion
selection,
and
normalized
collision
energy
of
35%
is
used
for
the
fragmentation;
a
two
min
duration
is
used
for
the
dynamic
exclusion.
Procedure:
Protein
identification
Tandem
mass
spectra
are
extracted
with
Xcalibur
version
2.0.7.
All
MS/MS
samples
are
analyzed
using
X!
Tandem,
version
TORNADO
(thegpm.org).
See
Rice
et
al.,
for
details.
Numbers
of
assigned
spectra
are
tabulated;
assigned
spectra
are
adjusted
for
shared
peptides
using
a
locally
developed
script.
Data
collected
by
investigator
Spectral
counts
Investigator
Notes:
Data
provided
to
MPD
are
corrected
for
shared
peptides,
permitting
MPD
users
to
do
their
own
analyses.
Results
using
MPD
analysis
tools
may
differ
somewhat
from
those
reported
in
Rice
et
al.
(which
combine
males
and
females)
due
to
different
statistical
procedures.