Feature request for LIBRA

[Debojyoti Pal]

Dear TPP team

I would like to point out that one of the most important aspects of iTRAQ/TMT quantification is proper normalization. Many studies have demonstrated the crucial importance of global spectrum level normalization i.e. normalization of the whole data by the respective total intensity of each channel (Huang et al., 2020, Mol Cell Proteomics 19(10), 1706–1723). Unfortunately, this very simple normalization is missing in LIBRA. 

I would request the TPP team to please incorporate this feature in the LIBRA tool, so that intensity of each channel can be normalized with respect to the total intensity of each channel. For example, if total intensity of channel A is 100000 and channel B is 120000, then each reading in channel B should be multiplied by 100000/120000. 

Please incorporate this feature into the tool. It will dramatically increase the accuracy of quantification when we compare it to validation methods. Multiple studies have already pointed this out.

Regards

Debojyoti

[Eric Deutsch]

Hi Debojyoti, we will see if we see if we can add that feature to Libra, but you’re probably best off exporting the data from Libra to MSstatsTMT, which you cite below, itself. It has many nice features in addition to normalization, and so a good workflow would be to compute the raw TMT values with Libra and then export to MSstatsTMT and do all your normalization and comparisons there.

 

Regards,

Eric

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[Debojyoti Pal]

Dear Eric

Yes, I have considered that. I am using iTRAQ though and hence I was hoping the features could be implemented in Libra. I don't think I can use iTRAQ data in MSStatsTMT, but I will recheck. Thank you for the suggestions.

Regards,

Debojyoti