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 On Saturday, October 7, 2023 at 8:18:13 AM UTC+5:30 Eric Deutsch wrote: > 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:* spctools...@googlegroups.com <spctools...@googlegroups.com> *On > Behalf Of *Debojyoti Pal > *Sent:* Monday, October 2, 2023 9:57 AM > *To:* spctools-discuss <spctools...@googlegroups.com> > *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 spctools-discu...@googlegroups.com. > 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 spctools-discuss+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/spctools-discuss/ee4bfa37-bf2a-46d7-b747-6a84d1b034b8n%40googlegroups.com.
