FAM (5- or 6-carboxyfluorescein) and FITC (fluorescein isothiocyanate) are the two most common fluorescein-based labels attached to synthetic peptides. Both absorb near 495 nm and emit near 520 nm — standard FITC filter sets and the 488 nm laser line on any flow cytometer or confocal microscope.
Why the two are not interchangeable
The chemistry differs at the point of attachment. FITC reacts with a free amine to form a thiourea linkage, which is prone to slow hydrolysis and can degrade over months in solution. FAM is coupled as a carboxylic acid to form a stable amide bond, so FAM-labelled peptides are generally preferred where storage stability or quantitative work matters. Labels are normally placed at the N-terminus or on a lysine side chain, often via an aminohexanoic acid or PEG spacer so that the bulky fluorophore does not interfere with target binding.
Handling notes: fluorescein is markedly pH-sensitive, losing intensity below about pH 7, photobleaches quickly, and is light-sensitive from the moment the vial is opened — amber vials, foil and reduced illumination are standard. A labelled peptide's molecular weight and purity both shift relative to the unlabelled sequence, so read the COA for the conjugate rather than the parent.
Related terms and material
biotin label · I-125 radiolabel · HPLC. Reference material: labeled peptides. Further reading: labeled peptides guide.