Dataset: Data Independent Acquisition Proteomics

Emiliania huxleyi cells were grown to 72 hours in each treatment and 4 biological replicates from individual culture bottles were isolated for proteomics. Cells were pelleted using centrifugation and lysed with a sonicating probe. Proteins were reduced, alkylated, and digested with trypsin after being soubilized in 6M urea (see Nunn et al. 2016). All samples were desalted using NEST group desalting columns. Mass spectrometry was completed on Thermo Lumos with NanoAquity inline. Column was 75 micron ID, packed to 30cm with Dr. Maisch C18 packing material.

All DDA analyses were completed in single runs on the Lumos. 130 minute total run time, gradient 2-35% ACN in 90 minutes. OT resolution 120,000, scan range 375-1575, Rf lens 35%, AGC Target 7e5 MS2: charge state 2-5, Top 20 MS2, AGC targert 5e3, dynamic exclusion 30 s

DIA analyses were completed on each sample, and a pooled sample that included equal parts from each treatment and biological replicate were included. Library generation was completed with 6 GPFs covering the range of 400-1000 in 6 windows with 4 m/z isolation windows. Each sample was also analyzed with 90 minute gradient scan range of 400-1000 and covered isolation window of 8m/z.

Analyses performed by Brook L. Nunn and Miranda M Mudge at the University of Washington Proteomics Resource Center (https://proteomicsresource.washington.edu/).