Cysteine modifications in cysteine-containing proteins are synthesized in vivo in several ways (see below). For example, oxidation reactions lead to disulfides or cysteine sulfonic acid. Pam3Cys is a cysteine modification found in bacterial proteins and is used for promoting immune stimulation.
For peptides used in proteomics experiments, cysteines are usually carbamidoylated. This can be done post synthesis using iodoacetamide, or by employing a suitable CAMC building block during synthesis.
Please also have a look at our PTM Reference & Kits for direct usage as reference material in mass-spectrometry based proteomics to support PTM proteomics.