Please exchange the column and emitter, or an attached column/emitter, and connect the emitter to the MS source. Verify proper connections up to, and at, the emitter.

Perform the following to achieve spray stability:

Ensure there are no sources of significant airflow on/near the MS source
Follow the MS vendor's procedure to clean the source region of the MS
Verify proper connections up to, and at, the emitter
Run a "Flow to column" script with a flow rate that closely resembles that of the method of choice
Optimize the source voltage by testing spray stability at ±50 V increments within the MS vendor's recommended range, and adjusting the position of the emitter (if possible)

Run 2-3 injections of the standard sample (HeLa or K562).

Do you observe peptides eluting at the correct retention times?

Peptides Elute Early or Late