The column is nonpolar on the other hand the vitamin b12 is polar, should I always use this method or not
B12 analysis can be performed spectrophotometrically (see old versions of the AOAC). HPLC can be used to resolve Vitamin B12. However, since it is difficult it will depend on the expected concentration and the sample matrix. Do an internet search first, including the websites for Agilent.com , Waters.com , Phenomenex.com , Restek.com .... (remember the chromatograms you view are HIGH concentrations and DO NOT contain interferences from potential sample matrices).
Vitamin B12 analysis in tablets using HPLC is certainly possible because concentrations are relatively high and the matrix is not compicated. However, determination in food products can be very difficult, because at very low concentrations it is "sticky". Difficult to liberate from the matrix and it also tends to stick to components of your HPLC system (e.g. tubing and column)
I agree with Bruce and Kees, it depends on the matrix and the concentration of B12. If you have a fluorescense detector this paper might be of interest to you: J Chromatogr A. 2000 Sep 8;891(2):243-7.
doi: 10.1016/s0021-9673(00)00724-x. H B Li 1 , F Chen, Y Jiang
Determination of vitamin B12 in multivitamin tablets and fermentation medium by high-performance liquid chromatography with fluorescence detection
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