use FlashLFQ for estimates of PTM occupancy

smith-chem-wisc / MetaMorpheus

Proteomics search software with integrated calibration, PTM discovery, bottom-up, top-down and LFQ capabilities

MIT License

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Open trishorts opened 5 years ago

trishorts commented 5 years ago

rather than PSMs.

lonelu commented 5 years ago

A peptide may have a very different intensity than the peptide with modification. Depend on what the mod is.

lonelu commented 5 years ago

I agree this will be easier to code and the result may be more accurate than counting PSMs.

acesnik commented 5 years ago

I'm very interested in this!

I wonder if we could estimate the difference in ionization efficiency based on comparing all unmodified <-> singly modified peptide intensity ratios.