Have you tried, specifically "cysTRAQ" ?

Tambor, V., Hunter, C.L., Seymour, S.L., Kacerovsky, M., Stulik, J. and Lenco, J., 2012. CysTRAQ—a combination of iTRAQ and enrichment of cysteinyl peptides for uncovering and quantifying hidden proteomes. Journal of proteomics, 75(3), pp.857-867.

Or, for that matter, the more advanced hybrid approach from my former group of Professor Sixue Chen:

Parker, J., Balmant, K., Zhu, F., Zhu, N. and Chen, S., 2015. cysTMTRAQ—an integrative method for unbiased thiol-based redox proteomics. Molecular & Cellular Proteomics, 14(1), pp.237-242.

Both TMT and iTRAQ labels would be expensive to buy and use (I presume you are using label free techniques, right?) then the quantification would be robust!

Thanks,

Biswa

The amino properties of amino acids: Because amino acids contain the amino and carboxylic groups, they are considered bipolar, which acts as a acid or as a base and is called amphoteric, which loses and acquires a proton. If it is placed in strong acid solutions PH = 1 accept proton and charge (+) and if placed in solutions A strong base loses a proton and is emitted (-). At the electrostatic point (Pl-), the point is equal to (+) with (-) and PH.

Are you sure that your problems are a result of poor ionization, rather than loss of the peptide from solution through e.g. surface binding in your vials? If this is a problem, reduce and alkylate by all means - standard protocols with e.g. TCEP and iodoacetamide.