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pwilmart / TMT_analysis_examples

Examples of TMT data analyses using R. Links to notebooks and repositories. Also a few spectral counting analyses.
MIT License
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Example analysis of LFQ MS/MS data #2

Open Jokendo-collab opened 4 years ago

Jokendo-collab commented 4 years ago

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

pwilmart commented 4 years ago

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