Spectrum mill software package

Protein analysis of co-immunoprecipitation samples shown in Figure 1 were performed by mass spectrometry as described previously^{65 (link)}. Briefly, samples were digested with 1 μg trypsin in 50 mM ammonium bicarbonate (pH 7.8). Peptides were desalted using a SampliQ C18 (Agilent) cartridge and eluants were dried using a CentriVap Concentrator (Labconco) before resuspending the sample in water. Protein digests were analyzed by LC/MS on a Q Exactive Plus mass spectrometer (ThermoFisher Scientific) interfaced with a nanoAcquity UPLC system (Waters Corporation) equipped with a BEH dC18 column (Waters Corporation) and a C18 trapping column. Peptides were eluted using a linear gradient from 99% solvent A (0.1% formic acid in water (v/v)) and 1% solvent B (0.1% formic acid in acetonitrile (v/v)) to 40% solvent B over 60 minutes. The mass spectrometer was run in the positive ion mode and acquired in triplicate. Peak lists were generated from the LC/MS data using Mascot Distiller (Matrix Science) and searched using the Spectrum Mill software package (Agilent) against a species limited (human) Swissprot protein database. The spectral count for human Las1L and Nol9 are reported in Figure S1 along with representative spectra.