LFQ intensities missing from peptides txt file?

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Murat Eravci

Hi Tarabryn,

to be honest, I have never used LFQ quantification on single peptide level, However there are a multitute of settings to define the calculation for LFQ.

Maybe, most important is to set the min peptide ratio for LFQ from 2 (default) to 1.

It also makes sense to disable the fast LFQ function.

Then set the type of peptides which should be considered for LFQ (i.e. Unique, Razor etc. and modified or unmodified only (depending on your experimental question.

I hope you can find the way to recover the LFQ values with the newer MQ versions.

Good luck!

Murat

Rohit Kumar Nadda

Hi,Tarabryn Shepherd Grismer , you will find this LFQ intensity columns in proteingroup.txt. Check there. Hope this answer your query.

Hediye Erdjument-Bromage

I am using MaxQuant version 2.2.0.0 and the peptide.text does contain LFQ intensities.

One more thing - when you pick your search parameters, the default, minimum peptide number for LFQ calculation is 2. So, for a given protein, if you have only 1 peptide that is identified, you may have value in the intensity column but not the LFQ column

Hediye.

I just saw that Murat Eravci already clarified the LFQ minimum number issue

Thank you Murat.

So it looks like it is the version of the software if your peptide count for protein IDs are more than 1.

Tarabryn Shepherd Grismer

Thanks for your insight! I may have to use the v2.2.0.0 then. I tried setting the LFQ min ratio to 1 and unfortunately it still didn't work, so I'm not sure if they just disabled it for the newer versions or what. Thank you again!