Bio-Rad EXQuest Spot Cutter - Manual (Page 238)

Analysis Sets and Annotations
7-11
here is you are given a view of which spots will be included or excluded from the
analysis set.
Do you want to look for a protein whose quantitation went up under the experimental
conditions as compared to the control? If so, click the Above Upper limit button.
A represents all matched spots in sample A and B represents the corresponding
matched spots in sample B. Comparisons are made using spot quantity only.
Positional comparisons, etc., are not possible.
The comparison is performed as follows: A threshold value is established by
multiplying and/or dividing A by the factor you specify. B is then compared to the
threshold.
For example:
• If you ask to create a set by clicking on the Above upper limit button and enter a
factor of 2.0, the set will include spots whose quantity in B is at least twice that of
the corresponding spot in A.
• If you click on the Above Upper Limit button and enter a factor of 0.5, the set
will include spots whose quantity in B is greater than half the quantity of the
corresponding spot in A.
• Clicking on the Below Lower Limit button and entering a factor of 0.5 (-2.0 fold)
will find spots whose quantity in B is less than half the quantity of the
corresponding spot in A.
• Creating a set by clicking on Below lower limit and entering a factor of 0.33 (-3.0
fold) finds all the spots whose quantity in B is less than one-third the quantity of
the same spot in A.
• If you are interested in finding the spots whose quantitation has significantly
changed either way (either increased or decreased), select the Outside limits
option. The proteins found in this test have increased in quantitation above the
upper limit or decreased below the lower limit. If you enter an upper limit of 2.0
and a lower limit of 0.33 you will find spots whose quantity in B is more than
twice the quantity in A or less than one-third the quantity in A.
• To find spots whose quantitation in B has not changed significantly from A, click
on the Between limits button. Enter factors to define the upper and the lower
limits. If, for example, you enter an upper bound factor of 1.10 (+1.1 fold) and a
lower bound factor of 0.90 (-1.1 fold), the analysis set will include spots whose
quantity in B is between 10% up or 10% down relative to the quantity of those