Particles entering the chromatography system can block capillaries and valves, increase wear, and damage the column or system. Especially with aqueous solvents, algae and other microorganisms can grow and deposit in the system and block the solvent line filters. Blocked capillaries or filters can cause increased or unstable system pressure.

For optimum performance of the system, observe the following guidelines.

Solvent Quality and Filtration

  • Use high-quality high-purity solvents (filtered) and additives as required by the application, for example, UHPLC-grade or LCMS-grade. Filtered high-purity solvents are usually labeled accordingly by the vendor.

  • Use high-quality water for example, UHPLC-grade or LCMS-grade (0.2 µm filtered).

  • When you use water from water purification systems, polymeric contamination may occur if the purification system is not maintained properly.

  • When preparing salt solutions or buffers and preparation is complete, use membrane filtration (0.2 µm) to remove any particulate matter and to reduce microbial growth.

  • Use the appropriate solvent line filters as recommended by Thermo Fisher Scientific. Check the filter frits for permeability at regular intervals and replace them as necessary.

  • Use fresh, properly degassed solvents. Replace solvents at least on a weekly basis. Always replace the solvent in the reservoir completely. Do not "top up" solvents to avoid solvent composition changes or unwanted components building up in the reservoirs.

  • For longer seal lifetime, do not recycle or recirculate solvents.

  • Note the special properties of the solvents, such as viscosity, miscibility, boiling point, UV absorption, as well as the solubility of salts for all proportions during the gradient.

Solvent Reservoirs

  • Before filling a solvent reservoir, rinse the reservoir thoroughly with a high-purity solvent.

  • To reduce the growth of algae, use amber glassware. Use appropriate additives, for example, formic acid, for aqueous solvents.

  • Avoid the use of detergents when cleaning glassware. Rinse glassware used for LCMS applications (including graduated cylinders) with LCMS grade solvents prior to use, and label and store separately.

  • Do not use methanol from aluminum reservoirs.

Flushing after Operation

  • Flush out buffers and solutions that form peroxides.

  • Never leave buffers, salt solutions, or aggressive solvents in the system for a longer period without flow.

  • Before you change from a buffer or salt solution to organic solution, flush the system thoroughly with UHPLC-grade or LCMS-grade water.

  • Before you change solvents, make sure that the new solvent is miscible with the previous solvent. If the solvents are not miscible, flocculation may occur.

  • Switch between two immiscible solvents via an intermediate solvent, for example, isopropanol. Step by step, replace the first solvent by the intermediate solvent, then step by step replace the intermediate solvent by the new solvent.