Calibrating a PSD Spectrum

8.3.4Creating PSD

Calibration Reference (.REF) Files

Overview

Using the Ion Fragmentation calculator to create a calibration reference (.REF) file

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.

To create a PSD calibration reference file using the Ion Fragmentation calculator:

1.From the Applications menu, select Ion Fragmentation

Calculator.

8

 

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.

Data Explorer™ Software User’s Guide

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