Find valuable information.

Optimize your experiments to get the best results. We’ve compiled a detailed knowledge base of the top tips and tricks to meet your research needs.

View the relevant questions below:

Having problems with your experiment?  Visit our

Troubleshooting page

General

What kind of substances in my sample would interfere with mass spectrometry analysis?

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

What is the best way to remove small contaminants from my sample for mass spectrometry analysis?

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.

Can I use protein desalting columns for cleanup of peptide samples?

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.

What is the best way to remove detergents from my sample for mass spectrometry analysis?

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.

What kind of buffers and solutions are compatible with peptide clean-up and LC-MS?

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.

If I already removed small contaminants and detergents at the protein level, do I still need to desalt my peptides prior to mass spectrometry analysis?

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.

I have varying amounts of peptide in my mass spectrometry analysis samples. Is there a way I can determine peptide yield after sample clean-up?

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

For Research Use Only. Not for use in diagnostic procedures.

CMD SchemaApp code