Please perform the following steps:

Disconnect the column from the emitter (if applicable) and the MS source
In a clean solvent bottle, mix mobile phase B (acetonitrile with 0.1% formic acid) with isopropanol in a 1:1 ratio
Place solvent lines A and B in solvent bottle with the above solution
Perform a full solvent exchange with this solution (15 iterations)
Run 3 system and column wash scripts (with only the column, or column with an attached emitter, connected)
Place solvent lines A and B back in solvent bottle A and B
Perform a full solvent exchange with solvent A and B (15 iterations)
Reconnect the column to the emitter (if applicable) and the MS source
Perform three LC-MS runs with acetonitrile rinsed tips - only follow step one of tip protocol (RINSE)

Do you still observe contamination in your chromatograms?

Contamination Issues