For tandem mass spectrometry (LC-MS/MS) analysis, native BLF and the fractions collected from the benzamidine column over five repeats were separately resolved on SDS-PAGE gels and stained as described. The protein bands were excised as 1-mm
3 cubes, washed with 100 mM NH
4HCO
3 for 20 minutes, and destained in 25 mM NH
4HCO
3 in 50% acetonitrile that was then replaced with 100% acetonitrile for dehydration at 37°C under vacuum (CentriVap; Labconco, Kansas City, MO). The gel cubes were rehydrated with 10 mM dithiothreitol for 1 hour at 37°C to chemically reduce disulfide bonds, followed by alkylation with 25 mM iodoacetamide at room temperature for 1 hour. After three rinses in ultrapure water (MilliQ; Millipore, Bedford, MA), then once with 25 mM NH
4HCO
3 and twice with acetonitrile, next the cubes were again dehydrated as described. In-gel digestion was performed by the addition of 50 ng sequencing grade modified trypsin (Promega, Madison, WI), per cube, in cold 50 mM NH
4HCO
3, followed by incubation at 37°C overnight. The supernatant of the digest was pooled and dried under vacuum with the gel extracts obtained from one 20-minute incubation with 20 mM NH
4HCO
3 and three 20-minute incubations with 50% acetonitrile/5% formic acid. Samples were further cleaned with zip tips (C18; Eppendorf, Hamburg, Germany) in accordance with the manufacturer's instructions. These were analyzed with a mass spectrometer (LTQ-FT Ultra; Thermo Electron, Bremen, Germany). Peptides were first separated by nano-LC with a high-performance liquid chromatography (HPLC) system and autosampler (UltiMate 3000; Dionex, Amsterdam, The Netherlands). Samples were concentrated and desalted onto a precolumn (micro C18; 500 μm × 2 mm; Michrom Bioresources, Auburn, CA) with 0.05% heptafluorobutyric acid at 20 μL/min. After a 4-minute wash, the precolumn was switched (Valco 10-port valve; Dionex) into line with an in-house built fritless nano C18 column. The HPLC mobile phase consisted of a mixture of buffer A (2% acetonitrile and 0.1% formic acid) and buffer B (80% acetonitrile and 20% formic acid). Peptides were eluted from the column along a linear gradient of 2% to 50% buffer B over 30 minutes followed by a 100% buffer B wash over 1 minute at a flow rate of 300 nL/min. LTQ-FT was operated, as described previously.
27 Peak lists were generated using MASCOT Daemon/extract_msn (Matrix Science, London, UK), with default parameters and were submitted to the database search program MASCOT.
28