To determine whether the column, emitter, or attached column/emitter has to be replaced, please perform the following:

Disconnect the attached column/emitter or emitter from the MS source.
Run a "Flow to column" script with a flow rate closely resembling that of the method.
Once the HP pressure and flow rate have equilibrated, note the pressure.
For an emitter that can be detached: disconnect the emitter from the column and note the pressure once equilibrated. If the pressure drops more than 10 bar, the emitter has a blockage and needs to be replaced.
For an attached column/emitter or column: once equilibrated, compare the pressure to the method-specific application note. A significantly increased or decreased pressure requires the column/emitter or column to be replaced.

Run 2-3 standard sample injections. Do you observe peptides eluting?

No Peptides Elute