Chapter 6 Using Tools and Applications

6

4. Enter m/z values in the m/z ratio list by doing any of the

following:

 

 

• Right-click-drag over a peak in the spectrum to

 

add the m/z and the associated charge state.

 

• Double-click the line to display the Elemental

 

Target Mass dialog box, type the m/z and the

 

associated charge state, then click OK.

 

 

• Click

to add a line to the list, then

 

 

double-click the line to display the Elemental

 

 

Target Mass dialog box, type the m/z and the

 

 

associated charge state, then click OK.

5.

 

Specify the Tolerance to use. The Tolerance value entered

 

 

is directly used as the window for elemental comparisons,

 

 

and is also multiplied by 2 and used as the window for

 

 

isotope peak comparison (because related isotope peaks

 

 

will usually have lower mass accuracy than monoisotopic

 

 

peak). Setting Tolerance too low can result in a falsely low

 

 

Isotope Match Score (see page 6-6).

6.

Specify the Mass Type to calculate.

7.

 

If the displayed Mass Peak Resolution is not appropriate

 

 

for this calculation, change the setting in Peak Detection.

 

 

For more information, see Section 3.2.4, Peak Detection

 

 

Parameter Descriptions.

8.

Specify the Result Type (Elemental, Amino Acid,

 

 

Carbohydrate, DNA, or RNA).

9.

Specify the Max Number of Results for each m/z entered

 

 

in step 4.

 

 

 

 

 

 

NOTE: Max Number of Results is per m/z entered, not

 

 

total number of results generated for the calculation.

 

 

 

10.

 

Set limits as described in:

 

 

• “Setting limits for existing elements” on

 

 

page 6-7

6-4 Applied Biosystems