Excluding mono-link from search

[b-sundberg]

Hello,

I am using pLink to look for cross-links due to oxidation (e.g. diTyr, diTrp).

In this context, the idea of searching for mono-linked peptides seems a bit non-sensical. Is there an option to opt out of the mono-link search?

Thanks in advance!

[NorthblueM]

Hi,

Sorry, there's currently no such switch. However, you don't need to worry, because even with the monolink parameter set, it will barely affect crosslink identification, as monolink and crosslink are handled in separate workflows in pLink.

Additionally, you may consider temporarily setting the MonoMass to 0, in which case a monolink will essentially be treated as a regular peptide. Or set it to a very large value (e.g., 10,000), which exceeds the peptide mass restriction, so no candidate monolinks will be generated. However, be sure to modify MonoComposition accordingly, because pLink performs an internal mass validation based on the specified composition.

Best!