Ok, I try to explain it better.

You asked how to analyze SDS gel bands, right?

You can obtain two type of information: how intense (concentrate) is your band or what it is.

For example: if you KNOW what your band is andyou have a standard for comparison, you can scan your gel and digitally compare the two bands (unknown sample and standard or control band). This way you can assess the concentration of your target. And if you have more than a sample, you can build diagrams and so on..

On the other hand, you can cut your band, extract the target from the gel and the analyze it with another technique (e.g. a MS/MS approch). This will tell you WHAT isthat band.

An example: you make a cell lysate. Then you ran a SDS gel. You cut the band you are interested in and then you extract the protein. You run a LC-MS/MS protocols (too long to explain now) and at the end you can say "My band is this protein". You can also try to quantify the protein in your band (ad enjoy the tons of problems related to that :-P)

Now, you wrote "In literature the data are presented as diagrams".

Can you make an example? paste the title of an article.

well, you can scan your gel and then analyze the band intensity. Or you can cut the bands and extract the material from the gel for further analytical techniques.

If I can ask, why did you run the SDS gel in the first place? And what do you mean with "In literature the data are presented as diagrams"?

Maybe link an article so that we can look it up together.

I couldn't understand what you want to know. Can you be more clear about this?

Ok, I try to explain it better.

You asked how to analyze SDS gel bands, right?

You can obtain two type of information: how intense (concentrate) is your band or what it is.

For example: if you KNOW what your band is andyou have a standard for comparison, you can scan your gel and digitally compare the two bands (unknown sample and standard or control band). This way you can assess the concentration of your target. And if you have more than a sample, you can build diagrams and so on..

On the other hand, you can cut your band, extract the target from the gel and the analyze it with another technique (e.g. a MS/MS approch). This will tell you WHAT isthat band.

An example: you make a cell lysate. Then you ran a SDS gel. You cut the band you are interested in and then you extract the protein. You run a LC-MS/MS protocols (too long to explain now) and at the end you can say "My band is this protein". You can also try to quantify the protein in your band (ad enjoy the tons of problems related to that :-P)

Now, you wrote "In literature the data are presented as diagrams".

Can you make an example? paste the title of an article.

Dear Fabrizio

Thanks a lot for your excellent explanation. Recently I try to setup the SDS PAGE, so maybe my question was not clear enough. But you competently understand my question. I will try your suggestions.

About presented data as diagram:

http://www2.unibas.it/parente/fuzzy.html

Dear Keysson

In fact, as I told in previous comment, I am new in this test. I could setup the page recently. But I do not what must I do with proteins bands on gel and how I can use this bonds to get data.

Fabrizio explained the procedure and I found out what is the matter and initially what I must do.

do you have any additional suggestions?

My study field is immunology and I need SDS PAGE for antigenic proteins detection.

So I think you will use immunoblotting and you need SDS PAGE just for seperating your sample and transferring to a membrane.

Dear Naşit

You are right. I just wonder how can I use the presented bands on SDS PAGE for get some reportable data. But as you said, for immunologic aims we must follow the test to blotting.

The most convinient data presentation is the picture of your gel and, if relevant, dencitometric analysis.

Dear Reza,

If you want to give the results of western-blot, it's not necessary and also not possible to demonstrate the SDS-PAGE photograph since you don't stain your gel prior to transferring to a membrane. You can present your western-blot results as a photograph of your membrane. Your imaging depens on your staining protocol (eg. chemiluminescent, radioactive etc.) If you want to make qualitative comparison only, the photo of a membrane would be enough. But for quantitative comparisons, you must perform densitometric analyses as Natalia said. You can use various programs for this purpose: licensed software packages which does it automatically or some freely available image processing programs (such as ImageJ, a java-based application).

If you want to give the results of your SDS-PAGE, you must take an image after staining your gel. This figure would be informative in must cases and you discuss your band pattern in the text. Also you can make quantitation by the methods I mentioned above. You can perform various statistical tests once you obtain the density values of your bands using a software. Some licensed softwared does some tests (such as PCA, cluster, densitometric analysis) automatically.

Dear Naşit

Thank you very much. Your answer was perfect.

Te$ekurler hocam.

Hi all,

Sorry to for the question but what is the densitometric analysis? Is it the quantitative analysis for western blotting?

Yes.

So the system have sort of WB band colour measurement or something? Sorry I'm just not very clear of the protocol.

You can apply TMB solution on your membrane, which will result in color development (it's an expansive method), or perform an ECL reaction with detection by special film. In the latter case you will get black-grey bands. In both cases you should scan the membrane or the film and to analyze the strength of the signal of you bands using special software (mentioned in earlier comments)

I see..thanks a lot Natalia!