An acid/base extraction would probably work fairly well.  As auxin has a XlogP 3 of 1.4 even just defatting with a NP solvent would be likely to remove the chlorophyll while leaving the auxin unextracted.  The likeliest choice of NP would be something such as Toluene, Xylene, Pet ethers.  If working with fresh material lyseing the cells would help with the removal of chlorophyll, probably best to lyse prior to addition of NP to avoid emulsions.  A freeze/thaw cycle might work or L N2 then grind frozen material followed by addition of NP and seperation etc.

Leaf extracts can be easily treated with Dichloromethane several times to wash off chlorophyll and pigments, and as DCM is non-polar, it would not affect Auxins. Also, by better centrifugation speeds and allowing the extracts to stand at 4 C and -20 would help precipitate out the bulkier pigments like chlorophylls/ xanthophylls etc.

I am very grateful for the tips.

Certainly, they will be of great value and now I'm going to accomplish my tests!!

Hugs

I have actually been working on the quantification of Auxin and Cytokinins in plant tissues in relation to nutrient supplementation.  Have you attempted any analysis utilizing spectrophotometry? 

David,

I'm following the procedures described in:

Maren Müller and Sergi Munné-Bosch. 2011. "Rapid and sensitive hormonal profiling of complex plant samples by liquid chromatography coupled to electrospray ionization tandem mass spectrometry." http://www.plantmethods.com/content/7/1/37

The detection is ok. However, I have had some problems with chlorophyll that dirty the equipment and reduces the sensibility in time. Unfortunately, this problem was not so emphasized in the protocols and now we are fighting to reduce the pigment contamination without the loss of hormones, specially AIA.

I hope this information will help you.

Hug

I'm currently funding my own research so will be utilizing TLC, spectrophotometry, and bioasseys for now.  As I too am working with the quantification of Auxins, I will be utilizing the method I outlined for cleaning up the extracts.  One other concern is the effect extraction and handling will have on the auxin levels.  Especially when in solution it would be best to avoid exposure to UV light as well as red and blue as these are the wavelengths that are involved with decomposition of the auxin.  Amber glass, dim or filtered light (Incandescent and fluorescent can both put off wavelengths of concern) and rapid extraction/testing would be desirable. Also handling of samples prior to extraction is likely to have a very significant effect on IAA levels due to free radicals etc