Modification chemistry should be designed with the synthesis, not added as an afterthought. Start with the modification service page, then use the articles below for dye, biotin and PEG decisions.
A useful modification brief names the chemistry, the residue or terminus, the spacer and the detection method. FITC, TAMRA and Cy5 are not interchangeable dyes; biotin with and without a spacer are not the same bait; PEG length changes both HPLC and mass spectra. Cyclization is a modification of connectivity, not a label, and belongs in the same planning conversation when the ring and the dye share a cysteine.
These guides are written for research reagents. They do not describe clinical PEGylation or diagnostic-kit manufacture. If the peptide is also an immunogen, read the antibody antigen-design notes before you lock a conjugation handle.