Hello,
I'm a new user of MaxQuant and need to look at proteins individually and for each of my sample.
I could see in the proteinGroups.txt output the scoring per protein but for all samples. And in the evidence.txt there is a score per sample but for each peptide, not protein.
Thank you for your help
Best
Julie
I think what you can do is get the sum of peptide scores for each protein. It's logical to use sum, not average for instance since more peptides give a higher confidence in protein score (I'm not sure if MaxQuant is also determining the score this way or not). This can be an arbitrary score value eventually but works with the same logic as I think you intend to use it for.
Note that the Score column in the evidence table is the Andromeda score for the best associated MS/MS spectrum.
- Badges
- Science topic
- Similar topics
- Biological Science
- Biochemistry
- Enzymology
- Enzymes