Lysine and Arginine Protein Post-translational Modifications by Enhanced DIA Libraries: Quantification in Murine Liver Disease

Aaron E. Robinson, Aleksandra Binek, Vidya Venkatraman, Brian C. Searle, Ronald J. Holewinski, George Rosenberger, Sarah J. Parker, Nathan Basisty, Xueshu Xie, Peder J. Lund, Gautam Saxena, José M. Mato, Benjamin A. Garcia, Birgit Schilling, Shelly C. Lu, Jennifer E. Van Eyk

Research output: Contribution to journalArticlepeer-review

6 Scopus citations

Abstract

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 trimethylation, 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 nonalcoholic steatohepatitis (NASH) mouse models. We report that 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.

Original languageEnglish
Pages (from-to)4163-4178
Number of pages16
JournalJournal of Proteome Research
Volume19
Issue number10
DOIs
StatePublished - Oct 2 2020

Keywords

  • acetylation
  • data-independent acquisition mass spectrometry (DIA-MS)
  • methylation
  • nonalcoholic steatohepatitis
  • peptidoforms
  • post-translational modifications
  • spectral library
  • succinylation

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