How much evidence do you need to make a peptide identification?
If you're using match between runs, if your identification is by "Match only" you are relying on your aligned retention time, mass and your isotopes to make that identification.
Is that enough?
MS1-only proteomics says черт возьми it is! (Google said that is how you say "hell yeah" in Moscow)
What if you had aligned retention time, and mass and some ion mobility hardware as well? Is that enough to make an identification?
Is that enough? It's certainly more.
What if you then toss in some sophisticated FDR based on machine learning?
Some of the work is performed on a FAIMS equipped Fusion Lumos, and some other files are from a QE HF.
This is one of an increasing number of studies that are questioning the foundations of "what makes a confident peptide identification?" and is definitely worth thinking about.
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