To load the macro,

Load the Mascot.frm onto VBA editor.

In ModRunVBA5, paste the following in the code:

Public Sub Run_Mascot()

Dim Form As New frmMascot

Form.Show

End Sub

You should be able to run this macro.

Mascot Search

Use the Mascot Toolbox to perform a protein database search of mass values from a peptide digest or a PSD spectrum.

Preparing the mass values

Before using the Mascot Toolbox:

1. In the Data Explorer software, smooth the data, perform a baseline correction, then de-isotope.

2. If needed, use Advanced Peak Detection parameters to adjust peak detection ranges and thresholds to screen out noise in low mass regions and detect peaks in high mass regions.

3. Set the % Base Peak Intensity or % Max Peak Area in peak detection until the unwanted noise peaks are removed from the Spec Peak list.

Performing the search

1. In the Toolbox Palette dialog box, click Mascot Toolbox.

2. If you have a local copy of Mascot, replace the URL of the Matrix Science web site with the URL of Mascot on your intranet. For example: http://localhost/mascot

3. Click:

· Peptide Mass Fingerprint¾If you are examining peptide data from a protein digest.

· MS/MS Ions Search¾If you are examining PSD data.

4. Enter the Parent Ion mass if you are searching PSD data.

5. Click Copy Peaks, and the Spec Peak list for the data file is copied to a new Mascot search form in your web browser.

6. Go to the Mascot search form and, if necessary, modify the search parameters. Note that the charge state of the precursor is set to 1+ (MH⁺) in the Query field, which over-rides the default setting elsewhere in the form.

7. Submit the form to start the search. After the database search is complete, the results will be displayed in the web browser.