Recent work to apply mass spectrometric methods to DNA analysis has led to the attachment of an electrophore to an oligonucleotide primer, with the purpose of investigating whether the advantages of electron capture ionization (increased ionization efficiency, reduced fragmentation) could be extended to larger molecules, such as Sanger sequence ladders. The stability of the electrophore-modified primers under conditions encountered during matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) was investigated. Four different electrophore labels were successfully attached to the 5' terminus of a 17-base, single-stranded oligodeoxyribonucleotide sequencing primer. The attached electrophore tags are robust under conditions used for sample preparation and MALDI-MS, and little or no fragmentation resulting from loss of the electrophore was observed. While no sensitivity enhancement was observed for the electrophore-labeled DNA, mass spectrometric conditions are discussed under which the electrophore labels could enhance the detection of DNA sequencing ladders.