carbohydrate is usually analyzed with phenol/sulfuric acid method, as Xiomara suggested. Protein can be estimated with the Lowry method.

Thanks for your answers. The problem is i also have hematite nano particles in my EPS. these particles are very difficult to separate by centrifugation. And their presence is altering the colorimetric analysis. As for sterilization. I donot sterilize polysaccarides. I isolate them in sterile conditions, and keep them in same. Also I have not observed any contamination.

maybe the interference comes from iron III released from hematite when you add sulfuric acid. You can measure the Fe concentration, e.g, by AAS after acidification, and then a calibration curve can be figured out to compensate the Fe effect.

I have many samples.. and would like to have a method which help in easy analysis. and dialysis will involve a lot of complications.

Detailed composition of carbohydrate and protein in EPS is difficult being a dynamic function of microbial community especially the carbohydrate. you can try flourimetry for protein and phenol-sulphuric acid for carbohydrate (chances of error is quite high). I hope this may help you.