Mascot: The trusted reference standard for protein identification by mass spectrometry for 25 years

Exercise DIS3


Study a SILAC quantitation experiment in Mascot Distiller. Drill down into the data to see how the quality thresholds are used to accept or reject individual peptide ratios. See the effect of changing various settings.


User access to the Matrix Science public web site

Install Mascot Distiller on your laptop by downloading the appropriate installer.

When Distiller is first launched, you will be prompted to register on-line and get a temporary 30 day licence by email. Use this serial number to register: 38EL-C6E7-U73R


The Analyst raw file and the Distiller project file need to be in the same directory. Open the project file in Distiller.

Press F1 to display the on-line help and go to the topic Quantitation Toolbox; Quick Tour: SILAC example. Follow this short tutorial to become familiar with how Distiller display quantitation results.


Right-click this link: Triple Encoding SILAC sample data.rov, and choose Save target as or Save link as.

Right-click this link: Triple Encoding SILAC sample data.wiff, and choose Save target as or Save link as.


  • If you cannot access the Matrix Science public web site, Distiller will ask whether you want to use the configuration information saved in the project file. Answer Yes.


  1. In hit 11, why does it say that LGGSAVISLEGKPL does not match to any component?
  2. Why are no quantitation results reported for hit 11?
  3. Try changing the quality thresholds to see whether other settings give more precise ratios
  4. Is normalisation appropriate for this data set?
  5. Select median normalisation in the format settings. Why does Distiller have to process the unassigned list?


Hints | Search results | Answers

Return to list of exercises