I would first try the method with dialysis above, you may want to have a specific molecule weight cutoff to ensure other molecules that may be soluble will not pass through the membrane. Alternatively (or subsequently), you may want to consider liquid liquid extraction...maybe DMSO and H20 (just a guess). The sugars should be soluble in water whereas other unwanted additives may go into the DMSO. Then using your water fraction, you could try lectin binding, or other forms of glycan enrichment prior to LC-MS analysis. Hope this helps generate some ideas.
I would suggest gel filtration using a Sephacryl S-100 column or equivalent with sterile water as mobile phase. This will do a better job of separating the oligosaccharides from low molecular weight saccharides than dialysis. Identify fractions with carbohydrate by phenol-sulfuric or any of the reducing sugar assays.
Diafiltration using a tangential-flow setup will simultaneously remove low-MW oligosaccharides and concentrate the high-MW polysaccharides. The polysaccharides can then be isolated more readily by ethanol or acetone precipitation. If you have reason to suspect anionic polysaccharides, or just feel like checking for them, they can be precipitated with a quaternary detergent such as CETAB or Cetavlon.
Just so we are all talking about the same compounds, do you want to isolate polysaccharides (as your question states) or small oligosaccharides (3-10 conjugated monosaccharides)? Do you want to include disaccharides? Do you want to identify any charged polysaccharides? Are you looking for natural oligo- or polysaccharides or are you looking for contaminants put in by unscrupulous dealers?
We purify polysaccharide from bacterial broth by addition of 3 volume ice cold Iso-propanol to 1 volume broth and incubating overnight at 4o C. The precipitate is centrifuged and dried in oven. This is then dissolved in dH2O and dialysed (10000 MWCO) against dH2O to remove all the contaminating monosaccharides and oligosaccharides.
Your method 1 should be fine. You do not have to heat to 40C. But it will take a little longer at lower temperatures. The better your vacuum, the faster you get rid of the solvent.
You can also use 100% ethanol at later steps to help remove the last traces of water. You may also find good results with isopropanol.
Things to watch out for: 1. di- and tri-valent cations in solution. These accelerate the Lobry de Bruyn–van Ekenstein transformation. This degradation of the reducing terminal is accelerated by higher pH and heat.
Also watch for extra acidity. During concentration of samples, slight amounts of acid can be concentrated and lead to acid hydrolysis of the polysaccharide. Keeping teh temperature down will help.
There is already literature that states that the amount of polysaccharides in honey, while always small (
I want to remove carbohydrates from my proteins sample. Is it possible to use ethanol or any solvent mentioned above, because what i think it might affects the functionality of proteins. Any suggestions on this, please.
Depending on the type of carbohydrate you want to purify,after using Sephacryl S-100 gel filtration,the fractions can be pooled and the dialysed with dialysis membranes of various MWCO.It is good to start with lower MWCO for example 3,500,then 6-8000 MWCO ,12-14000MWCO and so on.In this way smaller molecules leave the membranes first. @