I can't seem to find any universally-accepted method for measuring TMT or iTRAQ labelling efficiency. Some check just for any dynamic modifications at a peptide level; some compare fully labelled, to only N-terminally or lysine- (or, in the case of iTRAQ, the less efficient tyrosine-labeled); some do this at the level of peptide-spectral matches (PSMs)...
I'm running myself around in circles trying to find some satisfying way of doing it, just searching peptides with no missed cleavages and dynamic modifications, and filtering only those matches giving a 1% peptide FDR.
Does anyone have any ideas?
You can read this article:
https://www.researchgate.net/publication/221977274_Performance_of_isobaric_and_isotopic_labeling_in_quantitative_plant_proteomics?ev=prf_pub
I think that is a complete work about this issue.
Article Performance of Isobaric and Isotopic Labeling in Quantitativ...
Thanks! I have seen this paper and this was the method I was using so far as it makes most sense to me - however I've seen reviewers comment that this was not the most appropriate so I just want to make sure there is nothing I'm overlooking before arguing the case that this is a perfectly acceptable way of measuring labeling efficiency (which I think it is). But I was having trouble locating the paper again in my stack so thanks!
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