The assembly of trans-acting proteins on sequence-specific DNA cis-elements is crucial in the regulation of eukaryotic gene expression. Far upstream element binding proteins (FAB) are proteins that regulate the expression of the c-myc oncogene by binding to the far upstream element of the c-myc gene. The present study unambiguously identified the two human variants of FAB (FAB1, FAB2) in the medulloblastoma DAOY cell line and characterized their structure for the first time by tandem mass spectrometry independent of antibody availability and specificity. The study also tentatively assigned the third variant (FAB3) at the level of mass spectrometry, although tandem mass spectrometric analysis failed to corroborate the result. These findings open up an exciting possibility for discerning the cellular roles of FAB in tumor biology.