Automatic peptidoform scoring

[julia-broadbent]

Hi, I have generated a spectral library with generic scoring, max 2 variable modifications, Ox(M) and Ac(N-term) selected. I got the warning message WARNING: peptidoform scoring enabled because variable modifications have been declared; to disable, use --no-peptidoforms

Just want to clarify - does this mean that whenever I generate a spectral library or run an analysis with these settings, it will not make a difference whether I select generic or peptidoform scoring, because peptidoform will automatically be enabled if I leave the default generic setting?

[vdemichev]

Hi Julia,

Correct. That said, if tht's undesirable and you do not wish to localise these modifications (and in most cases this is not needed), you don't need to declare them as variable at the raw data analysis stage.

Best,
Vadim