%0 Journal Article %A Aaron E. Robinson %A Aleksandra Binek %A Vidya Venkatraman %A Brian C. Searle %A Ronald J. Holewinski %A George Rosenberger %A Sarah J. Parker %A Nathan Basisty %A Xueshu Xie %A Peder J. Lund %A Gautam Saxena %A José M. Mato %A Benjamin A. Garcia %A Birgit Schilling %A Shelly C. Lu %A Jennifer E. Van Eyk %T Quantitative Method for Assessing the Role of Lysine & Arginine Post-Translational Modifications in Nonalcoholic Steatohepatitis %D 2020 %R 10.1101/2020.01.17.910943 %J bioRxiv %P 2020.01.17.910943 %X Proteoforms containing post-translational modifications (PTMs) represent a degree of functional diversity only harnessed through analytically precise simultaneous quantification of multiple PTMs. Here we present a method to accurately differentiate an unmodified peptide from its PTM-containing counterpart through data-independent acquisition-mass spectrometry, leveraging small precursor mass windows to physically separate modified peptidoforms from each other during MS2 acquisition. We utilize a lysine and arginine PTM-enriched peptide assay library and site localization algorithm to simultaneously localize and quantify seven PTMs including mono-, di-, and tri-methylation, acetylation, and succinylation in addition to total protein quantification in a single MS run without the need to enrich experimental samples. To evaluate biological relevance, this method was applied to liver lysate from differentially methylated non-alcoholic steatohepatitis (NASH) mouse models. We report altered methylation and acetylation together with total protein changes drive the novel hypothesis of a regulatory function of PTMs in protein synthesis and mRNA stability in NASH.Competing Interest StatementThe authors have declared no competing interest.PTMsPost translational modificationsNASHNon-alcoholic steatohepatitisMSMass spectrometryDDA-MSData dependent acquisitionDIA-MSData independent acquisitionsIPFInference of peptidoformsSAMeS-AdenosylmethionineLCLiquid chromatographyMat1aMethionine Adenosyltransferase A1GnmtGlycine N-methyltransferaseFLRFalse localization rateSCXStrong cation exchangeFDRFalse discovery rateSILStabile isotopically labeledTICTotal ion currentRTRetention timefmFemtomolesAUCArea-under-the-curve %U https://www.biorxiv.org/content/biorxiv/early/2020/06/05/2020.01.17.910943.full.pdf