One possibility for you would be to evaluate how the abundance of proteins in your sample change in response to a stimulus. By understanding which proteins respond, either through abundance changes or through changes in their posttranslational modifications, you can understand more about the biology. There are a number of ways in mass spectrometry that you can track abundance changes. One way is to use protein labeling (e.g. itraq, silac or neucode). You can also do label free quantification. Two tools that do very good quantitative analysis of proteomics data are maxquant and MetaMorpheus with FlashLFQ. If you are interested in following changes in posttranslational modification assays, you can use an enrichment strategy for specific types (e.g. phosphorylation or acetylation) or you can do a global PTM analysis. The G-PTM-D task in MetaMorpheus will discover PTMs in unenriched samples, which makes the technique very accessible. Here are a couple papers from our group that may help you along.

Li, Q., M. R. Shortreed, C. D. Wenger, B. L. Frey, L. V. Schaffer, M. Scalf and L. M. Smith (2017). "Global Post-Translational Modification Discovery." J Proteome Res 16(4): 1383-1390.

Millikin, R. J., S. K. Solntsev, M. R. Shortreed and L. M. Smith (2018). "Ultrafast Peptide Label-Free Quantification with FlashLFQ." J Proteome Res 17(1): 386-391.

Good luck with your research.

What do you mean you have "identified certain proteins"?

Are the proteins up/down regulated?

Do you know the reason why?

Is it because the proteins are different in controls vs treatments?

You want to know the answer to a question you dont even know

I wish to express my opinion. The 2DE method and the Western blotting method are notorious methods especially to hydrophobic proteins using polyacrylamide gel (PAG) electrophoresis (please see file, IEF for hydrophobic proteins). And I must have to apply to the soluble proteins in the sexual differentiatin study (please see file; Tremalla 2D-EP). Further, LC-MS is also a notorious method, which gives no quantitative results (personal communication from Shimadzu Co. to me when working at The University of Tokyo, Tokyo, Japan). Then, I must have to develop a new HPLC-Surf-SEC method, which has been better working than SDS-PAGE. Furthermore, notorious ELISA (RIA) and PCR methods are not quantitative at all to me. Immunogloulins and heat-stable (?) DNA and/or RNA polymerases (DdDP and/or DdRP) are surely using the protein-enzymes, which have multiple-substrates capacity (please see file; Multiple Hydrolase LIP).

Therefore, I recently have to develop the new quantitative proteomics of the PDMD (protein-direct-microsequencing-deciphering) method, which uses the famous Edman-degradation method (please see file; HepG2 fucoidan).

Thank you so much Kou Hayakawa , Michael Shortreed for your suggestion

Dear Leonardo Pantoja Munoz I have not published this results and hence i have not specified the name of the protein and that's why i have specified as certain protein