Review on mass spectrometer sequencing

iTRAQ relative quantification:

Frequently Asked Questions

If you have other questions, do not hesitate to contact us.

How to install Scaffold?

  1. Access the Proteome Software website, at
  2. Click on « Download Scaffold » on the left side of the screen.
  3. Select Scaffold for Mac or PC.
  4. Save the installation file on the desktop of your computer.
  5. Execute (double-click on) that file and follow the installation steps.

How to visualize results in Scaffold?

This is a quick summary; the « Help » menu of the software contains all the details.

  1. Open the result file with a .sfd extention.
  2. On the left side of the screen, click on « SAMPLES » to get a list of proteins along with their accession numbers, molecular weights and the number of unique peptides.
  3. As a general rule, the minimum percentage of probability should be set to 50% at both protein and peptide levels (see menu on top of the program window).
  4. The display option (see menu on top of the program window) should be set to « unique peptides ».
  5. If you select a protein and click on « PROTEINS » on the left, its sequence will be shown along with all its identified peptides. If you select a particular peptide-spectrum match, you will get the MS/MS spectrum, fragmentation table or other relevant information depending on which tab has been selected in the lower part of the program window.
  6. You can come back to the protein list by clicking on « SAMPLES ».
  7. In addition to the protein list, this page also provides with links (to NCBI amongst others) to get extra information about the identified proteins.
  8. It is possible to export the results in a spreadsheet (compatible with Excel). Simply click on the menu « EXPORT » and select one of the available options.