Evaluation of a 'plug and play' nanoflow liquid chromatography system for MS-based proteomic characterization of clinical FFPE specimens

Expert Rev Proteomics. 2023 Apr-Jun;20(4-6):87-92. doi: 10.1080/14789450.2023.2219844. Epub 2023 Jun 13.


Introduction: Proteomic analysis of formalin-fixed paraffin-embedded (FFPE) tumor tissue specimens has gained interest in the last 5 years due to technological advances and improved sample collection, as well as biobanking for clinical trials. The real-world implementation of clinical proteomics to these specimens, however, is hampered by tedious sample preparation steps and long instrument acquisition times.

Areas covered: To advance the translation of quantitative proteomics into the clinic, we are comparing the performance of the leading commercial nanoflow liquid chromatography (nLC) system (based on literature reviews), the Easy-nLC 1200 (Thermo Fisher Scientific, Waltham, MA, U.S.A.), to the Evosep One HPLC (Evosep Biosystems, Odense, Denmark). We measured FFPE-tissue digests from 21 biological replicates with a similar gradient on both of the LC systems while keeping the on-column amount (1 µg total protein) and the single-shot data-dependent acquisition-based MS/MS method constant.

Expert opinion: Overall, the Evosep One facilitates robust and sensitive high-throughput sample acquisition, making it suitable for clinical MS. We found the Evosep One to be a useful platform for positioning mass spectrometry-based proteomics in the clinical setting. The clinical application of nLC/MS will inform clinical decision-making in oncology and other diseases.

Keywords: Cancer research; clinical mass spectrometry; clinical proteomics; formalin-fixed paraffin-embedded (FFPE); label-free quantitation; nanoflow LC.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Biological Specimen Banks
  • Chromatography, High Pressure Liquid
  • Chromatography, Liquid / methods
  • Formaldehyde / chemistry
  • Humans
  • Paraffin Embedding / methods
  • Proteomics* / methods
  • Tandem Mass Spectrometry* / methods
  • Tissue Fixation / methods


  • Formaldehyde