Example analysis of LFQ MS/MS data

[Jokendo-collab]

Do you have example analysis of LFQ MS/MS data?

[pwilmart]

Hi Javan,
I seemed to have missed your question. No, I do not have any MaxQuant MS1 feature intensity quantitative examples. I have made some progress off and on, but have not set aside the time to finish it up. I do not really like the whole LFQ normalization scheme. It seems wacky to me. I have been working on an "evidence.txt" file parser so that I can take the MQ PSMs through my protein inference algorithm and compute feature sums. Then I could start playing with notebooks and seeing how normalization methods compare, what the summarized data looks like (intensity distributions, CV distributions, etc.), and statistical testing sensitivity, etc. It takes a lot of hours of focused effort to make these pipelines and analyses.
Cheers,
Phil