Bio-Rad EXQuest Spot Cutter User Manual
Page 327
PDQuest User Guide
10-4
In Step 3, the samples in the selected run are listed by microtiter plate well and sample
date. Click on a sample to select it.
In Step 4, the primary hits for each sample are listed in alphabetical order. The
number of peptides, percent coverage, molecular weight and pH are listed for each
protein. You can display the Joint Probability or MOWSE score for each hit by
selecting the appropriate option button at the bottom of the list.
Select the protein that you feel is the most likely identification, and click Apply to
import all the information into spot annotations in PDQuest.
Note:
The protein you select will be used as the name for the spot. (All the hits will be
included in a special annotation category called Hit Table.) If you change your
mind about the protein name, you can change the information directly in the Spot
Annotations dialog, or reimport the results with a different selection.
Click Protein Probe to launch the Protein Probe browser for each sample.
Annotation Categories Created
When you click Apply, the following annotation categories are created, and the mass
spec data for each spot is entered as an annotation in the appropriate category. (See
section 7.2.b, Annotation Categories for more information on annotation categories.)
•
Protein Name (The annotation entry in this category is the name of the protein
selected by you from the hit list).
•
Accession Number (The annotation entry in this category is the database number
keyed to the selected protein name. Note that some databases (e.g., Swissprot)
include accession numbers, while others do not. If the database used to identify
the protein does not have accession numbers, this category is not created.)
•
Hit Table (The annotation entry in this category is the entire list of proteins
identified for the spot.)
•
Protein Probe (This file name category provides a link to the Protein Probe file
for the spot.)
•
Mass Spec Score (Both the Joint Probability and MOWSE scores are listed.)