TABLE 1.

Advantages and disadvantages of current Oxi-Cys proteomic approaches.

Approach	Advantages	Disadvantages	References
SICyLIA	Simple protocol. Saves time and cost. Increased detection of low abundance oxidized Cys. High oxi-proteome coverage. Accurate quantitation.	Cannot distinguish different forms of reversible oxidized Cys. Need to control IAM reaction carefully to reduce the loss of deuterium in heavy IAM. Only two samples can be compared in a single experiment.	van der Reest et al., 2018
IodoTMT	Multiple samples (up to 6 samples per experiment).	Low selectivity. Antibody based purification.	Qu et al., 2014
cysTMTRAQ	Multiplexing analysis. Analyze both Oxi-Cys dynamics and protein-level changes in a single experiment. Can perform either Cys enrichment or not. Determine stoichiometry of redox modifications. High confidence and accuracy for oxi-Cys proteome analysis.	Costly and complicated protocol. Interference of both TMT and iTRAQ ion reporters cause ratio compression.	Parker et al., 2015
isoTOP-ABPP	Measure/monitor directly functions of enzymes in native biological systems. Exact sites of Cys reactivity. Low (μM) of IA used to allow differentiate the extent of alkylation. The isoTOP-ABPP ratio is independent with both peptide and protein abundances. Proteome-wide profiles of Cys reactivity in complex biological systems.	Incomplete precipitation of proteins after click chemistry (∼50% of total proteins). Low accurate characterization of too large or too short peptides. Combination of digested enzymes need to be used to increase proteome coverage. Limit in software that can be used for data analysis. Long protocol.	Weerapana et al., 2007; van der Reest et al., 2018
QTRP	High yield of biotinylated as click chemistry reaction performed on a peptide level.	Control concentration of IPM for alkylation.	van der Reest et al., 2018
DiaAlk	Measure directly S-sulfinylation and S-sulfenylation. High selectivity of S-sulfinated peptides/proteins.	Applicable for 2 biological samples only. Complicated sample preparation. Prolonged and costly protocol. Availability of chemicals. Many chemical reactions Not optimized to measure global level of S-sulinylated Cys directly in cells. Requires biotin based purification and photo-cleavage to release tags.	Akter et al., 2018
OxiMRM	Benefit for low abundance oxidized proteins. Detect/measure both reversibly and irreversibly oxidized Cys.	Two different alkylating steps. Many precipitation steps. Need specific antibodies. Low number of peptides detected.	Held et al., 2010
UPLC-pSRM	Label free approach. No affinity purification required. Detect/measure irreversibly oxidized Cys.	Underestimation of low abundance oxidized protein detection. Requires specific antibody for immunoaffinity purification. Prior knowledge of targets required.	Sherrod et al., 2012
Cys-DIA	High coverage of Cys proteome.	Only used with certain MS instruments. Need to run DDA to create customized database. Samples run individually does not support multiplexing. Need to purify Cys.	Tahir et al., 2020