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 *From:* [email protected] <[email protected]> *On Behalf Of *Debojyoti Pal *Sent:* Monday, October 2, 2023 9:57 AM *To:* spctools-discuss <[email protected]> *Subject:* [spctools-discuss] Feature request for LIBRA 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 -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To view this discussion on the web visit https://groups.google.com/d/msgid/spctools-discuss/89e5356d-8cb9-497d-9a74-367281a8c48fn%40googlegroups.com <https://groups.google.com/d/msgid/spctools-discuss/89e5356d-8cb9-497d-9a74-367281a8c48fn%40googlegroups.com?utm_medium=email&utm_source=footer> . -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To view this discussion on the web visit https://groups.google.com/d/msgid/spctools-discuss/f07444989b9f3979aa6c487d957afa15%40mail.gmail.com.
