I will assume then that you are separating your proteins by SDS-PAGE and wish to stain the gel to visualize the protein bands according to their molecular weight.

Certainly silver staining is the best in terms of sensitivity (down to about 0.3ng vs. > 7ng for coomassie). However, it is hazardous compared to regular coomassie staining.

Another option is SYPRO Ruby, which is a little more sensitive than silver staining (0.25ng vs. 0.3ng) but a) requires a specific filter for visualization and b) is similarly hazardous;

http://www.invitrogen.com/site/us/en/home/Products-and-Services/Applications/Protein-Expression-and-Analysis/Protein-Gel-Electrophoresis/Protein-Gel-Staining-and-Imaging.html

Another option is coomassie fluor orange, which can detect protein bands down to about 4ng;

http://www.invitrogen.com/site/us/en/home/Products-and-Services/Applications/Protein-Expression-and-Analysis/Protein-Gel-Electrophoresis/Protein-Gel-Staining-and-Imaging/Total-Protein-Visualization.html

At the end of the day you need to weigh multiple factors i.e. sensitivity, cost per gel, relative material hazard, and downstream application, if any. Only then can you come to a balanced solution for your specific needs.

Specific protein or generally protein like coomassie or silver?

Yes, you need to clarify the context and specificity of your question so we might better answer it effectively.

Its general protein (not any specific) ... still i need suggestions like which is better stain among standard coomassie R-250, colloidal coomassie G-250 or silver staining...

For standard routine stains we use silver stain. Also, Silver stain is more sensitive than coomassie. However, if you are planning to do spectrometry then use coomassie since silver stain is not compatible with spectrometry.

I will assume then that you are separating your proteins by SDS-PAGE and wish to stain the gel to visualize the protein bands according to their molecular weight.

Certainly silver staining is the best in terms of sensitivity (down to about 0.3ng vs. > 7ng for coomassie). However, it is hazardous compared to regular coomassie staining.

Another option is SYPRO Ruby, which is a little more sensitive than silver staining (0.25ng vs. 0.3ng) but a) requires a specific filter for visualization and b) is similarly hazardous;

http://www.invitrogen.com/site/us/en/home/Products-and-Services/Applications/Protein-Expression-and-Analysis/Protein-Gel-Electrophoresis/Protein-Gel-Staining-and-Imaging.html

Another option is coomassie fluor orange, which can detect protein bands down to about 4ng;

http://www.invitrogen.com/site/us/en/home/Products-and-Services/Applications/Protein-Expression-and-Analysis/Protein-Gel-Electrophoresis/Protein-Gel-Staining-and-Imaging/Total-Protein-Visualization.html

At the end of the day you need to weigh multiple factors i.e. sensitivity, cost per gel, relative material hazard, and downstream application, if any. Only then can you come to a balanced solution for your specific needs.

I would suggest colloidal coomassie staining for several days if you have enough protein to load onto the gel. Otherwise silver, which is much quicker but needs more bench work from your side.

coomassie is an oldie but goodie...mainly from invitrogen or you can make it your self...check current protocols

The sensitivity of silver staining is very good but the procedure is a little bit tedious. If the quality of protein extracted is good, simple staining method using the conventional CBB would be sufficient. CBB-R250 creates a sharper band but is difficult to be destained and is a little bit messy. CBB-G250 on the other hand is easier to be washed off.

I haven't performed a silver stain and therefore have not done a direct comparison myself but I have used the protocol from this paper for a modified CBB stain.

http://link.springer.com/article/10.1007%2Fs10529-007-9425-3

It uses the CBB-R250 and it gave me the best coomassie stained gel that I have ever seen, very crisp bands and definitely no problems with background staining.

CBB-250 i think is the best as it is user-friendly and at the same instance have good sensitivity with ease of destain.

it depends on the protein that should fxed and visualized

the best CB stain ever used...said to be MS compatible

it cost nearly nothing, no solvent smell and very easy

it is the home made equivalent of numerous (expensive) commercial stain