Chapter 8 Viewing Voyager PSD Data

8.3 Calibrating a PSD Spectrum
When to use this procedure

8

Overview of creating a PSD.CAL file

NOTE: Multi-point calibration yields higher mass accuracy than one-point calibration.

This section includes:

•Checking peak detection

•Calibrating

•Creating PSD .CAL files and applying to other data files

•Creating PSD calibration reference (.REF) files

•Changing the precursor mass

Use this procedure to:

•Generate a PSD calibration (.CAL) file from a known standard analyzed in PSD mode. You can then export the PSD .CAL file and include the PSD .CAL file in a PSD instrument settings (.BIC) file you use to acquire unknown PSD samples.

•Internally calibrate an unknown PSD data file by specifying known monoamino acid fragment ions as the peaks to match during calibration.

To create a PSD .CAL file:

•Acquire a peptide standard with a known sequence in PSD mode.

•Check peak detection as described in Section 8.3.1, Checking Peak Detection.

•Create a calibration reference (.REF) file as described in Section 8.3.4, Creating PSD

Calibration Reference (.REF) Files.

•Internally calibrate the PSD .DAT file as described in Section 8.3.2, Calibrating. Specify the calibration reference (.REF) file created in Section 8.3.4, Creating PSD Calibration Reference (.REF) Files, when calibrating.

•Export the calibration (.CAL) file from the PSD .DAT file to use when acquiring unknown samples in PSD mode.

8-10 Applied Biosystems