Estimating quantification coverage

[khal3dj]

Hi, I am using FlashFLQ to quantify crosslinked samples (crosslinker is EDC, manually added to MetaMorpheus). I calibrated and searched the raw files using common modifications, and after adding custom EDC modifications I expect to see (present on unimod.org, but not in the built-in modifications lists). I would like to compare the overall identification coverage between the two different sets of modifications. Is there a straightforward way to judge? For example, does MetaMorpeus directly report on unidentified peaks? The allresults.txt files are helpful, but somewhat too ambiguous for me to paint an accurate picture. It could be that what I am looking for is there.

(thank you for the gift that is this software)

[rmillikin]

MetaMorpheus doesn't report unidentified peaks, but you could try summing all of the quantified+identified peptide intensities and compare these numbers between your two searches. I assume the search with EDC modifications would have a higher identified TIC.

Since EDC is a crosslinker and not a simple modification, have you tried the XL search to identified crosslinked peptides?