S-Nitrosylation is a redox-based protein post-translational
modification in response to nitric oxide signaling and is involved
in a wide range of biological processes. Detection and quantification
of protein S-nitrosylation have been challenging
tasks due to instability and low abundance of the modification. Many
studies have used mass spectrometry (MS)-based methods with different
thiol-reactive reagents to label and identify proteins with S-nitrosylated cysteine (SNO-Cys). In this study, we developed
a novel iodoTMT switch assay (ISA) using an isobaric set of thiol-reactive
iodoTMTsixplex reagents to specifically detect and quantify protein S-nitrosylation. Irreversible labeling of SNO-Cys with the
iodoTMTsixplex reagents enables immune-affinity detection of S-nitrosylated proteins, enrichment of iodoTMT-labeled peptides
by anti-TMT resin, and importantly, unambiguous modification site-mapping
and multiplex quantification by liquid chromatography–tandem
MS. Additionally, we significantly improved anti-TMT peptide enrichment
efficiency by competitive elution. Using ISA, we identified a set
of SNO-Cys sites responding to lipopolysaccharide (LPS) stimulation
in murine BV-2 microglial cells and revealed effects of S-allyl cysteine from garlic on LPS-induced protein S-nitrosylation in antioxidative signaling and mitochondrial metabolic
pathways. ISA proved to be an effective proteomic approach for quantitative
analysis of S-nitrosylation in complex samples and
will facilitate the elucidation of molecular mechanisms of nitrosative
stress in disease.