Owing to its high sensitivity and throughput, the MBAS assay is a convenient approach to quantify residual SDS. However, this method is prone to interferences, most notably from anionic com- pounds which can ion pair with the cationic methylene blue dye. As an example, employing the FASP II protocol, the MBAS assay revealed an apparent level of SDS depletion between 45 and 60%. Such values are suspiciously poor, given that over 99% SDS must be depleted for samples to be compatible with LC–MS. The FASP II pro- tocol was repeated, omitting the addition of TFA (used to quench trypsin). From the test solutions, MBAS reported an average 99.6% of the SDS to be depleted. This value would appear more reasonable, though it may still be possible that other interfering compounds skew the analysis. Given the non-selective nature of a colorimetric assay, we sought to develop a more reliable assay to quantify trace levels of SDS from protein-containing solutions.