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Calibrating a PSD Spectrum
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Software User’s Guide 8-21
8
8.3.4 Creating PSD
Calibration Reference (.REF) Files
Overview You can manually create a calibration reference file by typing
masses in a text file as described in Section 5.3.3, Creating or
Modifying a Calibration Reference File (.REF).
You can also use the Ion Fragmentation calculator to generate
theoretical fragments and masses from the sequence for a
standard compound, then automatically save the masses and
associated information in a calibration reference file. For
detailed information on using the Ion Fragmentation calculator,
see Section 6.5, Using the Ion Fragmentation Calculator.
Using the Ion
Fragmentation
calculator to
create a
calibration
reference (.REF)
file
To create a PSD calibration reference file using the Ion
Fragmentation calculator:
1. From the Applications menu, select Ion Fragmentation
Calculator.
The Ion Fragmentation Calculator dialog box is displayed
(Figure 8-4 on page 8-8).
2. In the Sequence text box, type the amino acid sequence
of the standard compound. Use single-letter codes. Set
other parameters as needed. For parameter descriptions,
see Section 6.5, Using the Ion Fragmentation Calculator.
3. Select Monoisotopic from the Calculate fragment ion
masses as drop-down list.