I am struggling to figure out the relationship between proteins and phosphoproteins from LC-MS/MS datasets.
For example, if the protein concentration of a kinase is downregulated (due to any event), we can assume that the phosphorylation of its substrate should also be down. So, in the case of TiO2 enriched phospho-LC-MS/MS data, if the substrate is differentially downregulated, how we can identify whether it is due to protein concentration reduction or due to lack of phosphorylation?
Here the redundancy between kinase-substrate is ignored just to make explanation simpler.
And Is there any tool that take into considertion this aspect in system biology?
Merhaba Ayaz Anwar
You can also track the activity of a kinase through certain phosphorylations on other substrates, sites and proteins. a substrate can be phosphorylated by different kinases. Or its phosphorylation can be inhibited with different way.
There may be something during the preparation process that causes the loss of phospho sites. sampling and storage conditions may be effective. You can see the proteins (kinases and others) but the phosphorylations are gone.
The time frame is also important. Clearly proteins can be phosphorylated in very short time scales, much shorter time scales than proteins can be down (or up) regulated. Whether this is useful to you, depends on the kind of experiment you are running.
Further to the previous comment, I’m sure I’ve seen software recently that takes the entire phosphoproteome and then examines the kinases that contribute to the patterns observed. A quick Medline/Pubmed/Google Scholar search will pull them out.
Good luck,
Peter
Dear Mustafa Gani Sürmen , thank you for your insight. Certainly, protein-phosphorylation is a very complicated system, since, there are many redundant kinases are there and a large number of variables that affect the final outcome.
Peter G Hains, thank you for your valuable hint. At this moment, I am not interestd in timeframe (as the data have already been generated), though, we can not ignore this for later studies. However, I am looking for some tool that should take this into account. I am looking for some easy to use tool, if successful, i will update it here as well.
Nasreddin Hodja fell off the roof and soon the doctor came and said a few theoretical things for his treatment. but Hodja said to his friends I do not want a doctor, find someone who fell off the roof before.
I hope more details could provide more specific benefits.. from someone sharing same experimental conditions. or if you want to share some study details, i sent my email.
Hi, the analogy is very impressive. Yes, the details can be good for better understanding, however, I wanted it to be generalized for other studies as well. I sent you an email. Hope that will clarify the details.
Merhaba, thank you. I tried to answer. I hope it will be helpful.