I am using a MALDI-TOF-TOF(Bruker autoflex) to gain the PMF spectrums by using the H/L mixture samples,the SILAC labels is Lys0,lys4,Arg0,Arg6.The mass difference between the heavy peptide and light peptide should be 4,6,8,10,12,Am I right？I want to find the H and L peptide peak from the PMF,but It's hard to find the difference.I know how to analysis the H/L ratio by using the maxquant,but the question is how to analysis the H/L ratio or SILAC labelling efficiency by PMF from MALDI-TOF-TOF.I need some suggestions.
Any other suggestions are most welcome!
Regards.
Hi,
The incorporation efficiency of labeled amino acids can be estimated from the analysis of a labeled (heavy) sample only (so not in a mixture of heavy and light): if you analyze the heavy sample by itself, you have to look for signals of the unlabeled (light) version of the peptide to allow a (rough) calculation of labeling efficiency.
Assuming you use trypsin to generate peptides, the difference between heavy and light peptides can indeed be 4, 6, 8, 10 or 12 (or higher), depending on the number of missed cleavages (digestion efficiency) and KP/RP sequences in your peptides.
Hope this helps!
Hello Tingting Li,
In addition to what Eef has said, please look at the peptides.txt file generated by Maxquant. You will need to look at both of the arginine and lysine containing peptides. A helpful description of determining labelling efficiency can be found at this web page:
http://www.biochem.mpg.de/221777/SILAC
Under the section "Examination of SILAC labeling efficiency"
Kind regards,
Peter
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