Reduction of Allergenic Potential in Bread Wheat RNAi Transgenic Lines Silenced for CM3, CM16 and 0.28 ATI Genes
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A peer-reviewed article of this Preprint also exists.
Kalunke, R.M.; Tundo, S.; Sestili, F.; Camerlengo, F.; Lafiandra, D.; Lupi, R.; Larré, C.; Denery-Papini, S.; Islam, S.; Ma, W.; D’Amico, S.; Masci, S. Reduction of Allergenic Potential in Bread Wheat RNAi Transgenic Lines Silenced for CM3, CM16 and 0.28 ATI Genes. Int. J. Mol. Sci. 2020, 21, 5817. Kalunke, R.M.; Tundo, S.; Sestili, F.; Camerlengo, F.; Lafiandra, D.; Lupi, R.; Larré, C.; Denery-Papini, S.; Islam, S.; Ma, W.; D’Amico, S.; Masci, S. Reduction of Allergenic Potential in Bread Wheat RNAi Transgenic Lines Silenced for CM3, CM16 and 0.28 ATI Genes. Int. J. Mol. Sci. 2020, 21, 5817.
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Commenter: Sabrina Geisslitz
The commenter has declared there is no conflict of interests.
this is a very interesting study and the manuscript is well written. Taken together, the study should be published. Nevertheless, there are some suggestions for the Proteomics part, which has to be improved.
1. It is absolutely essential to publish your Proteomics data online, e.g. using Panorama and ProteomeXchange or tools of Sciex. In my opinion, today this is a very important requirement and give your publication more background, reliability and confidence. If you decide to not make your data public availably, you have to justify your decision.
2. I think it is incorrect to remove non-unqiue peptides/proteins and only use peptides, which are unique. This is because, that there a lot of entries for ATIs, which are either quite similar or are even equal. If you ignore all these proteins, you lose huge amounts of information. The protein of 0.28 (X2KYP9, in SM) has an identity of 98% to the reviewed 0.28 (X2KYP9). So, why did you decided to mention X2KYP9 and no other isoforms of 0.28?
3. No 0.19 is listed. According to Detlef Schuppan, this is the most bioactive ATI (with CM3). I am not a genomics expert, but I think, if the specific genes are changed, this might also have an effect on other proteins, as you indicate for the HMW-GS. I think, 0.19 is not listed, because you only consider unique peptides and 0.19 has no unique peptides. The fold-change (maybe there is an increase???) of 0.19 should be considered and this might be a very interesting issue!
4. You have to include the identified peptides. The information about the coverage is not sufficient for proteomics studies. This is because that you identified 17 peptides for X2KYP9. However, if I do an in-silico digest of this protein, there are only 15 peptides (https://web.expasy.org/cgi-bin/peptide_cutter/peptidecutter.pl), of which only 11 peptides have a MS compatible length. This is really strange! Thus, it is necessary to publish your data online and give a list of identified peptides.
5. Last, absolute quantitation would be a perfect tool to express the proteins quantity and change in mg/g. Our new method (absolute quantitation of 13 ATIs per SIDA and LC-MS/MS) is currently under revision. A collaboration either for the current study or for a new small publication would increase the significance of your work.
I would be very happy, if you contact me for further discussion or if you need further information about publication of your MS data.