Purified protein (1-2 μg) was acetone precipitated in lo-bind tubes (8:1 acetone:Ni-NTA eluate, -20 C overnight). Precipitated protein was centrifuged at 14,000 RPM in a microcentrifuge for 10 minutes, 4 oC. Acetone was removed, and the pellet was air dried at room temperature for 30 minutes. Proteins were denatured and reduced using 10 μl of reducing buffer containing 8 M Urea, 400 mM ammonium bicarbonate, and 10 mM TCEP at 50 oC for 5 min. Alkylation was performed at room temperature in the d
...ark by adding 5 μl 100 mM iodoacetamide in 50 mM Tris-HCl (pH 8.0) for 30 min. 45 μl of mass spectral grade water was added to alkylated samples. Digestion was performed with either trypsin (500 ng, 37 oC for 4 hours) or chymotrypsin (500 ng, 37 oC for 1 hour). Formic acid (5%, 7 μl) was added to digested samples, which were then sonicated for 20 minutes. Samples were desalted with Millipore C18 Zip Tip Pipette Tips (Millipore). After elution in 50% acetonitrile and 0.1% formic acid, samples were either diluted to 20-25% acetonitrile, 0.1% formic acid to a concentration of 10 ng/μl, or dried down using a speed-vac system and resuspended in 0.1% formic acid without acetonitrile before injection.
Approximately 10 ng of each sample was injected on a Q-Exactive Plus Orbitrap mass spectrometer (Thermo Fisher) with an Easy nano-LC HPLC system with a C18 EasySpray PepMap RSLC C18 column (50 μm x 15 cm, Thermo Fisher Scientific). A 30 or 40 min binary gradient solvent system (Solvent A: 0.1% formic acid in water and Solvent B: 90% acetonitrile, 0.1% formic acid in water) with a constant flow of 300 nl/min was used. Positive polarity mode was used with an m/z range of 350 to 2000 or 200 to 2000 at a resolution of 35,000 and automatic gain control set to 1 x 10^6. Higher-energy collisional dissociation–tandem mass spectrometry (HCD-MS/MS) was used on the top ten precursor ions in each full scan (collision energy set to 27%, 2 x 10^5 gain control, isolation window m/z 3.0, dynamic exclusion enabled, and 17,500 fragment resolution).[Show more]