The

high pH and high salt concentration facilitates the removal of cytosolic proteins. The washed membrane Torin 1 vesicles were resuspended using a pipette in 600 μl Tris-buffer containing high salt concentration of sodium chloride (10 MEK162 cell line mM Tris-HCl, 300 mM NaCl, pH 8) and stored at -80°C. Electron microscopy Electron microscopy was carried out to confirm that membrane vesicles were present and that no whole cells have been carried over prior to running the sample on the LPI™ FlowCells. Vesicle preparations (100 μl) were inactivated by adding Carson’s buffered formalin (Bios Europe Ltd) to give a final concentration of 1% (v/v) formaldehyde in the vesicle suspension. The inactivated suspension was made up to 1 ml with

distilled water and centrifuged at 48 000 g for 45 minutes. The supernatant was discarded and the pellet re-suspended in 25 μl distilled water. Five μl of re-suspended pellet was mixed with 5 μl 1% (v/v) potassium phosphotungstic acid (PTA) containing 0.05% (v/v) bovine serum albumin. A 400 mesh formvar-carbon coated copper EM grid was floated on the drop for several minutes and was then blotted by touching a piece of filter paper to the edge of the grid. Grids were examined in a Philips 420 transmission electron VS-4718 ic50 microscope. Operation of the LPI™ FlowCells – single trypsin digestion A solution containing outer membrane vesicles from S. Typhimurium (500 μl) was injected into the LPI™ FlowCell followed by incubation at room temperature for 1 h. This allowed the vesicles to attach to the membrane-attracting surfaces. The LPI™ FlowCell was rinsed with 2 ml of

10 mM Tris-HCl containing 300 mM NaCl at pH 8.0, followed by 2 ml of 20 mM ammonium-bicarbonate buffer (NH4HCO3), pH 8.0 and incubated at 37°C for 10 min. Seven hundred μl of 20 mM NH4HCO3 containing 5 μg ml-1 trypsin (sequencing grade, Promega) was injected into the LPI™ FlowCell and incubated at 37°C for 2 h. The resulting peptides ID-8 were collected from the LPI™ FlowCell by injecting 700 μl of 20 mM NH4HCO3, pH 8.0 at the inlet port and concomitantly capturing the eluted liquid at the outlet port. Fourteen μl of formic acid was added to the captured peptides to inactivate the trypsin and the sample was stored at -80°C for further use. Operation of the LPI™ FlowCells – multi-step digestion Trypsin was used for the first digestion step and the sample was digested for 30 minutes as described above for single trypsin injection. After elution of the peptides a second step digestion was performed on the captured stationary membrane vesicles in the LPI™ FlowCell. For the second digestion step, 700 μl of 20 mM NH4HCO3 containing 5 μg ml-1 of trypsin, pH 8.0 was injected into the LPI™ FlowCell and then incubated at 37°C for 1 h.