Hi everyone,
I wonder if there is a general guidelines for selection of the right peptides in PRM-LC-MS/MS.
Many thanks in advance for your response(s).
Yes there are. You may want to search for literature containing e.g. "quantotypic peptides" and "proteotypic peptides". Plus, there are a number of reviews around this, starting with e.g. Lange et al., Mol Syst Biol. 2008;4:222. doi: 10.1038/msb.2008.61.
Literature reading is your friend.
Thanks so much for your kind response Christof!
Literature reading is of course OUR friend and so the list below is what I have found on this subject and used as guidelines in my research within the past one month.
1. Lange et al., 2008. Mol. Syst. Biol. 4:222
doi: 10.1038/msb.2008.61
2. Liebler and Zimmerman, 2013. Biochemistry 52, 3797−3806 . dx.doi.org/10.1021/bi400110b
3. Hoofnagle et al., 2016. Clin Chem. 62(1):48-69.
doi: 10.1373/clinchem.2015.250563.
4. Chiva and Sabido, 2017. J. Proteome Res. 3;16(3):1376-1380.
doi: 10.1021/acs.jproteome.6b00115.
I hope they can be of use for other researchers from different fields who might need a quick advice/support in quantitative proteomics research...
Dear Ozlem Yilmaz ,
if it is not an artificial protein and is already present in cells I would experimentally determine which of peptides are the best for PRM. You can perform and experiment by yourself or go through database such as PRIDE.
Trust me, experimental determination is always better.
Thanks so much for your response Michal,
We indeed run a preliminary experiment to identify the most abundant peptides for target proteins in our biological samples. And so we had a list of candidate peptides to start with. My question was on the optimal biochemical properties of these peptides to be considered for use in PRM and with the guidance of the overall literature above I found an answer to that question.
Thanks again and have a nice day.
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