RP columns, such as C18, are most commonly used for good reasons. They are easy to use, more familiar to most chromatographer, readily available, etc. Thus I agree with Tom that RP columns should be the first choice to consider when encountering a new separation challenge. On the other hand, C18 columns have limitations, such as not fully compatible with aqeuous mobile phase, not suited for separating highly hydrophilic analytes, and limited selectivity range. Mixed-mode columns provide remedies to these shortcomings.
In my opinion, the main benefit of mixed-mode column is adjustable selectivity, which provides greater flexibility in method development. Although mixed-mode columns have lots of potentials and can be considered (at least in theory) to be a repalcement to many other HPLC columns, considering the long history and much familarity of RP columns, I believe it is more useful for most chromatographers to use mixed-mode columns as the complementary or "niche" columns. You will find mixed0mode columns can do magics when the RP columns fail to produce desirable result.
At Dionex, we develop each mixed-mode column to address specific analytical challenges, such as Acclaim Trinity P1 (a RP/SCX/WAX trimode column) for pharmacutical counterion and API analysis, Acclaim Mixed-Mode WAX-1 for organic acids and a broad range of anoinic molecule analysis, Acclaim Surfactant for a a variety of surfactants (anionics, cationics, nonionics and amphoterics) analysis, and etc. All these applications can't be fully addressed by any other types of HPLC columns alone.
In terms of method development, good understanding of retention mechanism is essential. When using a mixed-mode column, the sparation process in the column may be a complex one, but the developed method can be very simple.
The following link and sources will provide more information on Acclaim Trinity P1:
1.
http://www.dionex.com/en-us/webdocs/707 ... 239-02.pdf
2. X. Liu, C. Pohl, J. Sep. Sci. 33 (2010) 779–786.
3. K. Zhang, L. Dai, N. P. Chetwyn, J. Chromatogr. A 1217 (2010) in press.
4. B. N. Tran, R. Okoniewski, R. Storm, R. Jansing, K. M. Aldous, J. Agric. Food Chem. 58 (2010) 101 – 107.
For other mixed-mode columns from Dionex, please check:
http://www.dionex.com/en-us/products/co ... 71735.html