- LCMS chromatogram baseline is in the e6s
Poor solvents are leaving dirt in the system.
FIX or WORKAROUND
- Remove the column and replace it with a union.
- Put A and B lines from the ACQUITY into the alcohol mix, which is 25/25/25/25 water/isopropyl alcohol/methanol/acetonitrile and 0.2% formic acid (can go up to 1% formic acid).
- Flush the system by priming for five minutes, and then pump for at least two hours (preferably overnight) at a flow rate that gives at least 6,000-psi pressure.
- Prime and flush with fresh LC/MS-grade or Milli-Q water.
- Put on fresh LCMS-grade solvents that are used for the LCMS analysis. If the solvent bottles have not been cleaned recently, use the alcohol mix to clean out the bottles, and then rinse them well with fresh solvent.
- Attach a new column.
- Prime and flush out the water using the fresh solvents.
- Run the LCMS analysis again.