Does Map peptide needs to be conjugated to a carrier protein and if so what carrier is best? My concern here is steric hindrance if peptides themselves are conjugated to the beads. The aforementioned paper suggested that BSA was better than KLH, as KLH caused higher non-specific reactivity.
It is not necessary to use carrier protein. BSA and OVA are good carrier proteins use for assay development. As for carboxylated polystyrene Luminex beads for conjugation, one important point is that you have to optimize the conjugation condition for carrier protein-peptide conjugate, because after conjugation the amine groups on carrier protein are consumed by peptides which makes it difficult to be conjugate to the beads as well. In this case, you either have to use a different beads with different functional groups or they have to control the conjugation degree of the peptide to carrier protein.
Another method to avoid carrier protein conjugation is to consider adding a spacer (such as a PEG spacer) to the N-terminus of peptides with terminal amine group (which can be done by peptide synthesis) for conjugation to the beads, this method also works very well and peptide still can be conjugated to the carboxylated polystyrene Luminex beads.