One may say it depends on your compound of interest but, in general, which one would be a better choice all together in terms of labour, yield loss, possibility of multi solvent usage?
For example, I am afraid of column chromatography during, overnight auto collection of fractions. What if the auto collector got struck and lose everything? On the other hand, I am afraid of SPE cartridges with possibilities of multi solvent system. What is your opinion?
Like you mentioned, it depends on your compound. In addition, how pure is the compound? Do you know which compounds you are purifying? In my opinion (please note it is only my opinion!) SPE is better for purifying known compounds that don't have closely eluting impurities, and are good for known compounds. This is why one mostly sees SPE as the clean-up steps for analytical procedures. So if you are purifying a known compound, SPE may work very well for you.
I find column chromatography works better until I know which compound(s) is active in my extract. Once I know which compound I want, I may be able to simplify the purification so an SPE procedure may be more suitable, depending on impurities and how they elute. Once on the SPE cartridge, there is a possibility of solvent savings.
As for over night runs, I find that using one of the automated flash chromatography systems run fast enough that I don't need to do over night runs. They are very well suited for natural products. Alternately, I suspect you might be using one of the "shuttle" type fraction collectors, which i find are prone to jamming. A find a fraction collector that uses an overhead arm tends not to jam, but these require tubing to the fraction collector, where the shuttle fraction collectors can be simply be placed under the column.
As for multi solvent usage, flash chromatography works very well. I use a technique I term "wide polarity range chromatography" for natural products.
Conflict of interest notice: I do work for Teledyne ISCO which makes the items I link to below.
Wide polarity range chromatography:
http://www.isco.com/WebProductFiles/Applications/101/Poster_and_Paper_Reprints/Wide%20Polarity%20Range%20Flash%20Purifications.pdf
Automated flash chromatography applications in natural products:
http://www.isco.com/WebProductFiles/Applications/101/Poster_and_Paper_Reprints/Purification_of_Phenolic_Flavonoids.pdf
http://www.isco.com/WebProductFiles/Applications/101/Poster_and_Paper_Reprints/Facile_Isolation_of_Carotenoid_Antioxidants.pdf
http://www.isco.com/WebProductFiles/Applications/101/Poster_and_Paper_Reprints/Isolation_and_Purification_of_Alkaloids_with_SCX_Columns.pdf
Links to the flash chromatography systems and fraction collectors:
http://www.isco.com/products/products2.asp?PL=10110
http://www.isco.com/products/products2.asp?PL=10160&image=Chromatography3.jpg
Depends on your purpose. If you are creating a screening library, I would do both (split crude into two equal weights and do silica and C18). While this might double your wells, you will have avoided the problem of having similar structural families co-eluting all the time and masking your bioactivity of interest. If its for purification purposes only, then C18-SPE is usually better. Good luck!
Columns for chromatography can be big or small, according to the amount of material which needs to be loaded onto the column. There are columns which have autofraction collector. Pharmacia biotech supplies both and these are also battery operated, if any high electric supply interruption occurs then in such a condition. These columns will prpve more feasible and applicable. SPE cartridges with possibilities of multi solvent system need extra care because every time you have check over laps in sample collections, or fractionation. You can avoided this problem by manual collection of eluting fractions to obtain desirable bioactivity.
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