Mass profiler professional v 14

Chromatography, mass spectrometry, SpectrumMill database search, and Profinder data extraction parameters were performed as described previously ^{33 (link)}. Briefly, immunoprecipitated acetyl-Lys peptides were analyzed via 6550 Q-TOF with a nano source (Agilent) using intensity-dependent CID MS/MS to generate peptide identifications and in MS-only mode for acetyl-Lys peptide quantitation. Pooled samples were used for generation of an accurate mass retention time library (AMRT) library, used for acetyl peptide identification in normal and AH samples run in MS-only mode for quantitation. Acetyl peptide extraction and alignment was exported to Mass Profiler Professional V.14.9 (Agilent) and peak area was used for quantitation. Acetyl peptides (quantified with 2 or more unique peptides) were normalized to the appropriate relative protein fold-change (FC) within each sample. Raw area abundances in each acetyl peptide sample were multiplied by the relevant FC normalization for the specific protein and sample. Statistical analysis was performed at the peptide level.