- Introduction to proteomics
- Proteomics tools (e.g.: theoretical digestion: peptide mass)
- MASCOT (search engine from Matrix Science)
- Sequest (search engine from Thermo)
- GPM (search engines from Global Proteome Machine Organization)
- Scaffold (results visualization and validation)
Review on mass spectrometer sequencing
iTRAQ relative quantification:
- Protein and Biomarker Quantitation Using iTRAQ™ Reagents (pdf)
- Amine-specific Labeling Reagents for Multiplexed Relative and Absolute Protein Quantitation pdf
- Celebrating over 150 peer-reviewed publications (pdf)
Frequently Asked Questions
If you have other questions, do not hesitate to contact us.
How to install Scaffold?
- Access the Proteome Software website, at http://www.proteomesoftware.com/.
- Click on “Download Scaffold” on the left side of the screen.
- Select Scaffold for Mac or PC.
- Save the installation file on the desktop of your computer.
- 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.
- Open the result file with a .sfd extention.
- 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.
- 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).
- The display option (see menu on top of the program window) should be set to “unique peptides”.
- 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.
- You can come back to the protein list by clicking on “SAMPLES”.
- In addition to the protein list, this page also provides with links (to NCBI amongst others) to get extra information about the identified proteins.
- 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.