My analysis involves the characterization of a DNA complex using a Finnigan LCQ Deca with the ESI source. Literature seems to suggest that LC/MS/MS of DNA with fewer than 20 base-pairs is possible. However, I am curious if anyone has been successful with a mixture of larger polynucleotides (100-1000 base pairs), as these standards are significantly less expensive. Although cheaper, a mixture of polynucleotides will present challenges in the data deconvolution step. I am open to any suggestions, including sample prep options.