I got LC MS/MS data of two different species of animals, How I can calculate difference in protein concentration,when I compare same protein of both species.
Based on already obtained LC-MS data - impossible.
If you can generate new data it is doable and there is plenty of ways. We would need to have more details about protein, possiblity of generating labeled peptides, your mass spec set up, etc.
Your question is interesting but we would need more details regarding the dataset you obtained. For example, if you have LC-MS/MS data acquired in DDA mode, you may count the protein abundances by their spectral counts, and then normalize by estimating their NSAF ratio. Once done, you may compare the two datasets and compare the respective molarity of the proteins in both organisms, assuming that the characteristics of their detected peptides (number, ionizability, etc) are relatively similar. See Article Quick microbial molecular phenotyping by differential shotgu...
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Hi Udaybhanu Sirdeshmukh ,
I agree with both Jean Armengaud and Michal Gorka.
We might need a few details such as whether labeled or label-free method.
In the case of label-free, you can use spectral counts and normalize it using distributed NSAF or iBAQ values and then compare.
In the case of the label based such as TMT, iTRAQ, SILAC, you can use the protein intensities or the platform you use for searching such as Proteome Discoverer, can help you calculate fold change given the ration of interest provided by you.
Hope this helps!
Varsha
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