Protein aggregation in therapeutic products has become a major concern for the pharmaceutical industry and regulatory agencies. Protein aggregates can cause adverse patient immune responses and therefore are typically monitored throughout the formulation and production of bio-therapeutics. Monitoring aggregates by HPLC during production, storage and shipping is a part of the process of optimizing early formulations to minimize risk in clinical applications. Many clean-up techniques used to prepare cell culture samples prior to HPLC/UPLC provide incomplete clean-up, are time consuming, and waste precious sample. The presence of cellular debris remaining after sample preparation can lead to analytical instrument performance issues and will shorten column life. Here, we demonstrate how the use of Thomson Filter Vials for sample preparation allows for the analysis of low volume samples, processed in less time, with minimal sample loss and fewer transfer steps while extending column lifetimes and reducing HPLC/UPLC downtime.