Protein extraction was done as previously described [44 (link)]. 150 μg of total worm protein from three biological replicates of each light-SILAC sample was mixed with one aliquot (150 μg of total worm protein) of heavy-SILAC sample and digested with trypsin as previously described [44 (link)].
Peptide samples were pre-fractionated by hydrophilic interaction liquid chromatography (HILIC) on an Agilent 1200 series HPLC system using a YMC-pack polyamine II column (250 mm × 3 mm ID, particle size 5 μm, pore size 12 nm) at a flow rate of 0.5 ml/min into 26 fractions (pooled to 11 final fractions). The previously described [44 (link)] buffer composition and elution gradient profile was used with the total run time reduced to 60 min.
Peptide samples were pre-fractionated by hydrophilic interaction liquid chromatography (HILIC) on an Agilent 1200 series HPLC system using a YMC-pack polyamine II column (250 mm × 3 mm ID, particle size 5 μm, pore size 12 nm) at a flow rate of 0.5 ml/min into 26 fractions (pooled to 11 final fractions). The previously described [44 (link)] buffer composition and elution gradient profile was used with the total run time reduced to 60 min.
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