Proteomics quantification of protein nitration

Abstract

Protein tyrosine nitration is a post-translational modification (PTM) that can occur in biological systems under conditions of oxidative stress. This PTM can impact protein structure and function and has been linked to diseases such as Alzheimer ' s disease, cardiomyopathy, and arthritis. In order to understand the role that 3-nitrotyrosine (3NT) plays in disease states, a better understanding at the macromolecular level is necessary. Proteomics is a powerful approach that can simultaneously measure hundreds to thousands of proteins in normal or diseased states and thus can be helpful in the analysis of 3NT-modified proteins. Recently, some attention has been focused on the development of proteomic workflows that provide enrichment, characterization, and relative quantification of 3NT-modified proteins. These approaches rely on gel electrophoresis, liquid chromatography, and mass spectrometry (MS) techniques. This review provides an overview of current proteomics approaches for 3NT-modified proteins and highlights current MS-based methods for quantification of this PTM.

Uncommon posttranslational modifications in proteomics: ADP‐ribosylation, tyrosine nitration, and tyrosine sulfation

“…Therefore, various efforts have been made to improve the identification and localization of Tyr nitration in a high throughput fashion. Several reviews have focused on the enrichment, chemical derivatization, proteomics, and bioanalytical approaches employed to detect 3‐nTyr and the biological and physiological roles of Tyr nitration (Bandookwala & Sengupta, 2020; Batthyány et al, 2017; Evans & Robinson, 2013; Tsikas & Duncan, 2014; Yeo et al, 2015; Zhan et al, 2015). In this section, we will discuss the latest developments in enrichment and advances in the MS/MS workflow to characterize the nitroproteome.…”

Pharmacokinetics and biotransformation of biopharmaceuticals

“…For an extensive evaluation of the applicability of HRMS for the analysis of plasma digests, we wanted to include multiple peptides. Since the three peptides LFDNAMLR (amino acids 9-16), SNLELLR (71-77) and FDTNSHNDDALLK (146)(147)(148)(149)(150)(151)(152)(153)(154)(155)(156)(157)(158) fulfilled all criteria, these were evaluated for further use, also because they represent different parts of the protein structure (C-terminal region, center and N-terminal region, respectively)…”

“…The high mass resolution of HRMS allows the application of a much narrower MEW, which can considerably reduce the number of tryptic peptides that are extracted during data processing. For an extensive evaluation of the applicability of HRMS for the analysis of plasma digests, we set up an LC-HR-MS/ MS method on a QTOF instrument with which we quantified three peptides, originating from rhGH after trypsin digestion: LFDNAMLR (amino acids 9-16), SNLELLR (71-77) and FDTNSHNDDALLK (146)(147)(148)(149)(150)(151)(152)(153)(154)(155)(156)(157)(158). After selecting the peptide precursor ions using a quadrupole with unit-mass resolution and subsequent collision induced dissociation, fragment ions were selected during data processing, on which the MEW was reduced from 0.5 to 0.01 Da.…”

“…De hogere massaresolutie van HRMS maakt het gebruik mogelijk van een veel nauwer MEW, wat het aantal tryptische peptiden dat wordt geselecteerd in de massaspectrometer sterk kan beperken. Voor een uitvoerige evaluatie van de toepasbaarheid van HRMS voor de analyse van plasmadigesten hebben we een LC-HR-MS/ MS methode opgezet op een QTOF instrument waarmee we drie peptiden kwantificeerden na digestie van somatropine met trypsine: LFDNAMLR (aminozuren 9-16), SNLELLR (71)(72)(73)(74)(75)(76)(77) and FDTNSHNDDALLK (146)(147)(148)(149)(150)(151)(152)(153)(154)(155)(156)(157)(158). Na selectie van de precursorionen van deze peptiden door een quadrupool met unit-mass resolutie en daarna fragmentatie, werden de productionen softwarematig geselecteerd uit het opgenomen spectrum, waarmee we het MEW verkleinden van 0.5 tot 0.01 Da.…”