Chapter 8 Viewing Voyager PSD Data

8

How the composite spectrum is generated

PSD calibration equation

The software does the following to generate a composite spectrum:

•Evaluates all segments in the .DAT file to determine if there are multiple segments acquired using the same PSD Mirror Ratio.

•If there are duplicates, selects the most recently acquired segment to include in the composite spectrum.

•Using the precursor ion mass and calibration constants from the PSD calibration in the .DAT file (see “PSD calibration equation” below), determines the region of each segment to include in the composite spectrum as illustrated in Figure 8-3 on page 8-7.

•Applies baseline correction and two-standard-deviation noise removal to the composite region of each segment.

•“Stitches” the composite regions together and displays the composite spectrum.

The equation that the Voyager software uses to calculate the mass for fragment ions is:

mf = (α R

 

+ β ) [( t

– t

 

) + γ (t

 

– t )2] +

α Ri + β

mp

i

p

f

 

α + β

 

 

 

f

 

 

p

 

 

where:

 

 

 

 

 

 

 

 

 

 

 

mf

=

Fragment ion mass

 

 

 

 

 

α , β, γ

=

Calibration constants

 

 

 

 

 

Ri

=

Mirror Ratio

 

 

 

 

 

 

 

 

tf

=

Fragment ion flight time

 

 

 

 

 

tp

=

Precursor ion flight time (at Ri = 1) calculated

 

 

 

during acquisition

 

 

 

 

 

mp

=

Precursor ion mass entered in PSD Acquisition settings

 

 

before acquisition, or changed in PSD Processing

8-6 Applied Biosystems