Purpose: To understand the complexity of mass spectra.

1. Download Spectacular Mass Spec Viewer, unzip it to a directory.
2. Download the following data files:

Iontrap1, Iontrap2, Iontrap3, QTof1, QTof2, QTof3

3. Run java –jar Spectacular.jar
4. Open each file with a text editor to see the peak list. Copy paste the peak list to the viewer to view them.
5. Find the main differences between iontrap and qtof data.
6. Find some isotope peak clusters.
7. Find some charge 1, 2, and 3 ions, respectively.
8. Find a charge 1 peak and a charge 2 peak, so that they represent the same ion.
9. Observe the change of peak width (the width of a peak shape at half of the height of the peak) with respect to m/z value.

Purpose: To understand mass fingerprint method.

1. Download another spectrum file.

2. Use the viewer to observe the baseline of the spectrum.

3. This is the MALDI-TOF data for trypsin digestion of ADH_YEAST protein, of which the sequence is here.

4. Calculate some tryptic peptides of this protein, and try to match them with the peaks in the spectrum.

5. Use the Mascot mass fingerprint method at http://matrixscience.com/ to search for the protein. If the server refuses the submission, try to manually edit a small file with only the highest peaks and resubmit.