A systematic comparison of 4-[18F]fluorobenzaldehyde-O-(2-{2-[2-(pyrrol-2,5-dione-1-yl)ethoxy]-ethoxy}-ethyl)oxime ([18F]FBOM) and 4-[18F]fluorobenzaldehyde-O-[6-(2,5-dioxo-2,5-dihydro-pyrrol-1-yl)-hexyl]oxime ([18F]FBAM) as prosthetic groups for the mild and efficient 18F labeling of cysteine-containing peptides and proteins with the amine-group reactive acylation agent, succinimidyl-4-[18F]fluorobenzoate ([18F]SFB), is described. All three prosthetic groups were prepared in a remotely controlled synthesis module. Synthesis of [18F]FBOM and [18F]FBAM was accomplished via oxime formation through reaction of appropriate aminooxy-functionalized labeling precursors with 4-[18F]fluorobenzaldehyde. The obtained radiochemical yields were 19% ([18F]FBOM) and 29% ([18F]FBAM), respectively. Radiolabeling involving [18F]FBAM and [18F]FBOM was exemplified by the reaction with cysteine-containing tripeptide glutathione (GSH), a cysteine-containing dimeric neurotensin derivative, and human native low-density lipoprotein (nLDL) as model compounds. Radiolabeling with the acylation agent [18F]SFB was carried out using a dimeric neurotensin derivative and nLDL. Both thiol-group reactive prosthetic groups show significantly better labeling efficiencies for the peptides in comparison with the acylation agent [18F]SFB. The obtained results demonstrate that [18F]FBOM is especially suited for the labeling of hydrophilic cysteine-containing peptides, whereas [18F]FBAM shows superior labeling performance for higher molecular weight compounds as exemplified for nLDL apolipoprotein constituents. However, the acylation agent [18F]SFB is the preferred prosthetic group for labeling nLDL under physiological conditions.