Protein aggregates and other large particulates can be removed from samples that are being prepared for MMS typically by using a 0.2 um filter, or centrifuging to pellet the aggregates and use the supernatant. Removing large protein aggregates and particulates will help extend the lifetime of the flow cell as large aggregates can accumulate in the flow cell and slow the flow rate over time. If the flow rate slows, the options are to perform cleaning procedures or replace the flow cell with a new one.