Table 2.

Proteomics methods for SNO-peptide and SNO-protein quantification.

Method	Starting Materials	Advantages	Disadvantages	References
Direct MS Detection	Purified peptides and proteins	Rapid and direct detection of protein S-nitrosylation without the sample loss and artifacts from complicated derivatization steps.	Not suitable for the detection of proteins in complex mixtures; Not suitable for locating SNO-Cys in peptides containing multiple cysteines. Low throughput	[17–19]
ICAT	Proteins extracted from HeLa Cells & cerebellum	Enable the comparison of two samples in one experiment Enable simultaneous SNO-Cys localization and SNO-peptide quantification Amenable to multidimensional separation Suitable for large scale screening The cleavage step can remove biotins to produce simpler MS/MS spectra for SNO-Cys localization	The reagents are costly The throughput is relatively low compared to other multiplex proteomics methods	[6, 18, 21]
SILAC coupled with biotin switch	Proteins extracted from Jurkat cells	Enable the comparison of up to three cellular extracts in one experiment Enable simultaneous SNO-Cys localization and SNO-peptide quantification Enable detection of in vivo S-nitrosylation events Amenable to multidimensional separation & large scale screening	Not suitable for detection of protein from tissues and non-dividing primary cells The cell culture process for reagent incorporation is time consuming Biotinylated peptides contribute to complex MS/MS spectra, hinders automated SNO-peptide identification and SNO-Cys localization	[20]
SNO-CAP	Proteins extracted from rat cerebellum	Enable the comparison of two samples in one experiment Enable simultaneous SNO-Cys localization and SNO-peptide quantification Has similar SNO-Cys detection specificity as biotin-HPDP Amenable to multidimensional separation & large scale screening	Reagents are not commercially available Biotinylated peptides contribute to complex MS/MS spectra, hinders automated SNO-peptide identification and SNO-Cys localization	[21]
SNO-RAC	Proteins extracted from human embryonic kidney cells	Fewer steps than regular BST Efficient detection of high-mass SNO-proteins When coupled with isotopic or isobaric tag labeling, it allows the quantification of SNO-peptides from up to eight samples	Reagents are not commercially available MMTS, other disulfides and oxidized cysteines can also be released from the capture resins, thus could interfere with the identification and quantification of genuine SNO-peptides	[22]
TMT	Proteins extracted from human pulmonary arterial endothelial cells	Enable the comparison of six samples in one experiment Enable simultaneous SNO-Cys localization and SNO-peptide quantification Amenable to multidimensional separation & large scale screening	The reagents are costly The specificity of antibody enrichment of TMT tagged peptide is low.	[23]