Yes, can use Ion 540 chips with an amplicon length of 243 bp. The 200 bp protocol, which is available for all chip sizes including Ion 540 and 550, can be used for amplicons up to 275 bp. Instead, the 400 bp protocol can be used only with Ion 510, 520, and 530 chips with amplicons lengths ranging between 125 and 375 bps.
Find additional tips, troubleshooting help, and resources within our Next-Generation Sequencing Support Center.