Having difficulties with your experiment?

We are dedicated to your success. Get back on track. View our expert recommendations for commonly encountered problem scenarios.

View the relevant questions below:

Having problems with your experiment?  Visit our

Getting Started page

General

I have a low number of protein identifications from my protein digest sample. What can I do?

We recommend checking your mass spectrometry system performance using the Pierce HeLa Protein Digest Standard (Cat. No. 88328) to help determine if the problem is from the sample preparation or the LC-MS system.

I observe peptide retention time shifts in my liquid chromatography (LC) chromatogram. How can I check my LC performance?

We recommend using thePierce Peptide Retention Time Calibration Mixture (Cat. No. 88321). It provides synthetic heavy peptides to diagnose and troubleshoot your LC (liquid chromatography) system and gradient.

A database search of my peptide samples shows low and/or no identifications, but I have excellent signal in my chromatograph. What might be the problem?

Your mass spectrometry instrument may require calibration. We recommend recalibrating using one of our Pierce Calibration Solutions. Additionally, verify that correct search parameters were used for database searching (e.g., species, enzyme, fragment ions, mass tolerance, etc.)

After running the Pierce TMT11plex Yeast Digest Standard (Cat. No. A40938), I observe low signal to noise ratio and poor quantitative accuracy for the Tandem Mass Tag (TMT) reporter ions. What do you recommend?

Here are some recommendations:

  • Clean and recalibrate the mass spectrometry instrument using one of our Pierce Calibration Solutions.
  • Verify settings for liquid chromatography (LC) acquisition methods.
  • Fractionate TMT-labeled samples using the Pierce High pH Reversed-Phase Peptide Fractionation Kit (Cat. No. 84868) to reduce sample complexity.
My spray stability is erratic in my mass spectrometer, can you help?

Yes, we offer the Pierce Reserpine Standard for LC-MS (Cat. No. 88326) to guide in troubleshooting spray stability.

I’m struggling with mass spectrometry sample clean-up and feel that I’m losing peptides. Can you help me verify?

We recommend using the Pierce HeLa Protein Digest Standard (Cat. No. 88328) to test your sample clean-up method. Use it directly and also as a control co-treated with the sample to check for any loss of peptides.

Is there a way to evaluate the sensitivity of my triple quad mass spectrometry instrument?

Yes, Pierce Reserpine Standard for LC-MS (Cat. No. 88326) can be used to assess instrument sensitivity.

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