Mass Spectrometry Sample Clean-Up Support—Getting Started

Salts, buffers, detergents, and other small molecules can interfere with liquid chromatography separation and mass spectrometer source ionization. 

For protein samples, Pierce Polyacrylamide Spin Desalting Columns (Cat. No. 89849 or 89862) can be used to remove salts and other small molecular weight contaminates. Acetone precipitation is recommended for low protein amounts provided you have at least 10 µg of sample. For peptide samples derived from protein digests, we recommend using Pierce Peptide Desalting Spin Columns, Pierce C18 Spin Tips or an in-line C18 trap column for sample clean-up.

No. Protein desalting columns (e.g., Zeba desalting columns) use size exclusion and have a molecular weight cut-off that is typically too high for peptide samples. Peptide desalting, on the other hand, uses reversed-phase chromatography resins (e.g., C18 resin) to bind peptides for salt removal during washing.

Detergents are more easily removed at the protein level using acetone precipitation, dialysis, or affinity capture using Pierce Detergent Removal Resin or HiPPR Detergent Removal Spin Columns.

Most organic solvents or volatile buffers are compatible with LC-MS. Water and acetonitrile with 0.1% formic acid is the most common solvent system for separation of peptide samples for mass spectrometry analysis. Trifluoracetic acid (TFA) is an alternative ion pairing agent for off-line peptide C18 clean-up or LC-UV analysis. We offer the following LC-MS grade reagents: 0.1% TFA, LC-MS water, acetonitrile, and TFA.

Yes. We recommend performing additional cleanup after protein digestion to remove any residual salts or partially digested proteins using Pierce Peptide Desalting Spin Columns, Pierce C18 Spin Tips or an in-line C18 trap column.

You can measure peptide concentration using our Pierce Quantitative Colorimetric Peptide Assay (Cat. No. 23275) or Pierce Quantitative Fluorometric Peptide Assay (Cat. No. 23290).