Human colorectal peptides
were subjected to basic-pH reverse-phase
HPLC fractionation. Mixed and labeled peptides were solubilized in
buffer A (5% ACN, 10 mM ammonium bicarbonate, pH 8.0) and separated
on an Agilent 300 Extend C18 column (5 μm particles, 4.6 mm
i.d., and 20 cm in length). Using an Agilent 1100 binary pump equipped
with a degasser and a photodiode array (PDA) detector, a 50 min linear
gradient from 18% to 45% acetonitrile in 10 mM ammonium bicarbonate
pH 8 (flow rate of 0.8 mL/min) separated the peptide mixture into
a total of 96 fractions. The 96 fractions were consolidated into 24
samples, acidified with 10% formic acid, and vacuum-dried. Each sample
was redissolved with 5% formic acid/5% ACN, desalted via StageTip,
dried via vacuum centrifugation, and reconstituted for LC–MS/MS
analysis.
All LC–MS experiments were performed on a Velos-Orbitrap
Elite mass spectrometer (Thermo Fischer Scientific) coupled to a Proxeon
nLC-1000 (Thermo Fisher Scientific) ultra high-pressure liquid chromatography
(UPLC) pump. Peptides were separated on a 75 μm inner diameter
microcapillary column. The tip for the column was pulled in-house
and the column was packed with approximately 0.5 cm of Magic C4 resin
(5 μm, 100 Å, Michrom Bioresources) followed by 25 cm of
Sepax Technologies GP-C18 resin (1.8 μm, 120 Å). Separation
was achieved by applying a 3–22% ACN gradient in 0.125% formic
acid over 165 min at ∼300 nL/min. Electrospray ionization was
enabled by applying a voltage of 2.0 kV through an IDEX high-pressure
fitting at the inlet of the microcapillary column. In the case of
the two-proteome mixture, the linear gradient was shortened to 70
min.
were subjected to basic-pH reverse-phase
HPLC fractionation. Mixed and labeled peptides were solubilized in
buffer A (5% ACN, 10 mM ammonium bicarbonate, pH 8.0) and separated
on an Agilent 300 Extend C18 column (5 μm particles, 4.6 mm
i.d., and 20 cm in length). Using an Agilent 1100 binary pump equipped
with a degasser and a photodiode array (PDA) detector, a 50 min linear
gradient from 18% to 45% acetonitrile in 10 mM ammonium bicarbonate
pH 8 (flow rate of 0.8 mL/min) separated the peptide mixture into
a total of 96 fractions. The 96 fractions were consolidated into 24
samples, acidified with 10% formic acid, and vacuum-dried. Each sample
was redissolved with 5% formic acid/5% ACN, desalted via StageTip,
dried via vacuum centrifugation, and reconstituted for LC–MS/MS
analysis.
All LC–MS experiments were performed on a Velos-Orbitrap
Elite mass spectrometer (Thermo Fischer Scientific) coupled to a Proxeon
nLC-1000 (Thermo Fisher Scientific) ultra high-pressure liquid chromatography
(UPLC) pump. Peptides were separated on a 75 μm inner diameter
microcapillary column. The tip for the column was pulled in-house
and the column was packed with approximately 0.5 cm of Magic C4 resin
(5 μm, 100 Å, Michrom Bioresources) followed by 25 cm of
Sepax Technologies GP-C18 resin (1.8 μm, 120 Å). Separation
was achieved by applying a 3–22% ACN gradient in 0.125% formic
acid over 165 min at ∼300 nL/min. Electrospray ionization was
enabled by applying a voltage of 2.0 kV through an IDEX high-pressure
fitting at the inlet of the microcapillary column. In the case of
the two-proteome mixture, the linear gradient was shortened to 70
min.