I need to compare between metal treated and untreated bacterial samples.We have LC-MS facility which determines only molecular weight.Thanks
Dear Abhishek,
As you are interested in the quantification of any proteins released in treated and untreated bacterial samples, you´ll need to know what proteins are being released. Usually protein identification is achieved based on the MW. An alternative way to identify proteins based on the Mw is by conducting gel electrophoresis.
When estimating the Mw, the advantage of LC-MS based methods over gel electrophoresis is that through LC-MS you can identify all and any post-translational modifications present in the proteins (oxidation, glycosilation, acylation, ubiquitylation, others).
Hope this helps,
Ana
Dear Ana,
Thank you very much for your answer.I get molecular weight data using LC-MS.How should I use these molecular weights to identify proteins?How will I be able to know the relative abundance of these proteins?Thanks
Hi Abhishek,
Normally what you get from LC-MS is the raw data containing the retention time, MZ and peak intensity information. You need to use some software to search these data in a the proteomic database specific to your microorganism, for example Protein Pilot. With the software, peaks are asigned to specific proteins and the statistical analysis of peak intensities will give you the relative abundances of different proteins of two conditions.
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