Understanding Peptide Spectra

When interpreting the results of search engines it is important to:

• Look at the Scaffold probability, or SEQUEST or Mascot score
• Look at the sequence runs
• Consider the ion fragmentation chemistry
• Recognize the effects of different instruments
• Check that it all make sense

In the accompanying slide show, Karen Jonscher shows examples of valid peptide identitications and false ones and how you can tell the difference. She demonstrates that sometimes you need to know more than just the SEQUEST or Mascot score.

To manually verify that tandem mass spectra match the assigned peptides, you need a viewer that identifies the peaks in the MS/MS spectra. Scaffold's spectra viewer makes manually checking these matches easy .

Validating Sequence Assignments for Peptide Fragmentation Patterns

by Karen Jonscher, Ph.D.

pdf

(2.8 MB, 31 pages)

Power Point Format

(1.4 MB, 50 slides)

If you don't have Power Point, you can download Power Point Viewer.

Internet Explorer 6.0 format(If you use this, clicking the "Slide Show" button in the lower right corner plays the slide show. These slides will not display properly in other web browsers.)