I want to analyse whole protein from the plants.
I have isolated the proteins but there hplc analysis is not possible as they are not soluble is HPLC solvents like ACN,MeOH,IPA.What can be done?Also wide pore diameter columns are necessary?

Generally it's not a great idea to try to separate proteins via reversed phase as solvents are generally denaturing. You will find some reversed phase columns from Vydac based on silica which use C4 chemistry to minimize the solvent requirements but generally you are lots better off using ion exchange or HIC.

Such columns are widely available from a number of sources including Dionex, Waters, Agilent, Supelco, Pierce, Vydac, Tosoh Biosep and Amersham Biosciences, to name a few.

There is a world of difference between pure org. solvents like CH3CN, MeOH, etc. and their mixtures with water. The latter are extensively and very successfully used in RP (some unbelievably high resolution). Hearn and others have interesting reviews on this matter. Maybe I unwittingly added to the confusion on denaturing in an earlier chain. The only thing that needs to be avoided is denaturing which causes precipitation/coagulation. At very low protein conc. this doesn´t happen, you just increase retention. The chaotropic substances, used if you have to increase solubility or reduce retention, are also generally denaturing. It doesn´´t matter, unless you need to recover the proteins.

I m currently working on the protein profiling.I want to develope a HPLC pattern of whole protein(without clevage) and also peptide mapping by HPLC.
For whole protein sample solubility is a problem.Can you suggest something regarding solubility of proteins in RP solvents or buffers?
Also the clevage of protein using HCL is not fesible for me.So i m going for enzymatic clevage. Can you direct me to such protocols?

If your only purpose is protein profiling, use a reversed-phase column with a larger pore size (300A) and a gradient from water to a a high percentage (70%) of acetonitrile with 0.1% TFA in both components of the gradient. You will find several columns at our (Waters) website that will be good for this type of analysis. Symmetry300 C18 is an example. For peptide mapping, you can use the same principle. Several different columns are available. You will find comparisons of the performance of the different columns. You can see for yourself, which one work well for this type of analysis. There are actually several ones that perform equally well. If you contact me, I'll send you the examples.

If your objective is protein profiling, I still think you would be a lot better off doing your profiling work via ion exchange. As I mentioned above, reversed phase really isn't the preferred method for protein profiling although there are definitely some advocates of this method as indicated above. Since you mentioned solubility problems, exactly what type of sample are you working with? What strategies have you tried so far in order to solublize your proteins?

Chris, look at the analyses in proteomics. Ion sep is usually part of it, but ONLY part. Ion separation usually yields groups of proteins, rather sooner than later, one needs to separate down to individual proteins.