Closed JonasAlbinus closed 2 months ago
Hi Jonas,
Thanks for the feedback. Yes, we are working on adding this feature. Should be available in the next release if everything goes well. Stay tuned.
Best,
Fengchao
Hi Fengchao,
Thanks for the quick feedback. Awesome to hear that you are already working on adding this feature. I look forward to trying it out and hope the new release comes soon.
Thanks, Jonas
Any progress updates on this feature or how to turn it on if already incorporated?
Hi @FriedLabJHU ,
Thanks for your interest in our tools. I was distracted by other projects recently. I will try to implement this month. Will let you know when it is ready.
Best,
Fengchao
Thank you for building great tools! The last question is, will the SILAC protein intensities utilize the MaxLFQ normalization?
This is one of things that we are discussing internally: using MaxLFQ or "convert" the log-ratio back to intensity.
Happy to hear your opinions and suggestions.
Thanks,
Fengchao
My first instinct is to use the "convert" method because it would be directly traceable to ion intensities. However, I could appreciate a MaxLFQ-like normalization if the normalization factor functions being minimized only included log-ratios from the respective SILAC channels, but it could require calculating up to three minimizations per protein for L, M, and H channels.
How do you suppose the contributions from unlabelled ions be incorporated into either method?
Best, Edgar
Hi Edgar,
Thanks for the suggestions. I think it might be the best to generate both types of intensity: MaxLFQ and the one "converted" from the log-ratio.
How do you suppose the contributions from unlabelled ions be incorporated into either method?
They won't be used in the label_quant
tables.
Best,
Fengchao
Hi Edgar,
We have a pre-released version that will report both top-N and MaxLFQ intensities for MS1 label quant. If you want to have a try, could you send an email to yufeATumich.edu (replace AT
with @
)?
Thanks,
Fengchao
The latest version has this feature implemented.
Thanks,
Fengchao
Dear Nesvilab,
Is it possible in the label_quant.tsv files to also get the Light, Medium and Heavy intensity instead of only the ratio?
I'm asking because I am doing a 3 channel pulsed SILAC experiment and I am interested in the fraction of each SILAC channel, e.g. Light fraction = Light / (Light+Medium+Heavy). I'm currently using the "combined_modified _peptide.tsv" output to extract each SILAC modified version of my peptides and then sum it up to protein level from there.
Kind regards, Jonas