The pierce datasheet suggests some alternate methods for elution at non-denaturing conditions.

https://www.piercenet.com/instructions/2160187.pdf

But have you tried to use SDS sample buffer without reducing agent to see whether you still have avidin release from beads?

In addition, there was another discusion in Researchgate regarding similar issue. May be it helps -

https://www.researchgate.net/post/Does_anyone_have_experience_with_elute_biotinylated_proteins_without_eluting_avidin_as_well/1

I don't know whether this idea will work.I've suggested it before. Maybe someone out there has tried it:

Try incubating the beads with a concentrated biotin solution (e.g. 10 mM) for several hours. The biotin should compete with the biotinylated protein-avidin interaction, releasing the protein into solution. To make a concentrated biotin solution, you have to add base to deprotonate the carboxylic acid group. At neutral pH, biotin is very soluble in water, up to at least 50 mM.

Thank you. I will try this out and will update with the result. 

Alternatively will it be any good if I use Glycine and EDTA at highly acidic pH to elute the samples ???

Have a look at this web page:

http://www.lifetechnologies.com/us/en/home/brands/product-brand/dynal/streptavidin-coupled-dynabeads/elution-of-the-streptavidin.html

I'm not sure what the purpose of the EDTA is in the elution conditions, but I think the formamide is there to interfere with hydrogen bonding, since I know it is also used to denature DNA.

Low pH would be unsuitable for use with EDTA, which would be insoluble.

I had good results by eluting peptides from streptavidin beads with H2O at 80 °C (5-10 minutes incubation). I analyzed the samples with LC-MS and obtained good results. Elution with SDS or GdmCl resulted in huge background.

You can check the Strep tag II / Streptactin beads manual from IBA.

They provide an elution buffer supplemented with desthiobiotin, which enables efficient elution at physiological conditions. I used this system and it worked very well. Should be similar for avidin biotin system (see IBA manual for reasoning). Alternatively, I also did 5 min 95°C in SDS-PAGE sample buffer, which also eluted my strep tagged protein very nicely, but I can't comment on biotin background as I did radio labeling of my protein of interest and thus did not see any background of non-labeled proteins (like avidin in your case). Also I did not do MS.

A colleague told me that self-made elution buffer using just biotin also worked for him (using the strep tag II, which is an engineered biotin analog). He used strep tag II and Streptactin beads (from IBA) to purify soluble proteins.

You can order all reagents separately from IBA. Streptactin beads should also work for biotin (IBA claims that affinity to biotin is significantly increased compared to ordinary biotin)

PS. May sound like it, but I have actually no working relationship to IBA. I simply used this system a lot and became a big fan of it.

Good luck!!

I am sharing the protocol that worked perfectly for me

1. Resuspend the samples in 1X SDS buffer.

2. Boil the samples for 5 minutes.

3. Centrifuge the tubes and load the supernatant.

4. Stain the gel with coomassie brilliant blue or Silver stain

Hey, in my case I just needed to run it on the gel itself so that i can cut few bands for amino acid sequencing. 

Alternatively once I know the protein sequence, my plan was to clone the gene and express the protein thereafter.

I guess the link added by Shapiro have the info to elute the proteins in native form.

Thanks

You may wash the beads with 8M urea to get rid of unspecific binders and digest on the beads. I am testing it now - hope it will work.

I haven't done it anytime. If it works with you please let us know. 

Thanks!