Data Processing Tools

Internal calibration

To (re)calibrate data using internal calibration standard choose Internal Calibration [Processing → Internal Calibration…] icon from application main menu. In the top right peaklist click to the peak you want to use and type reference value. List of predefined reference points can be also used. Double-clicking the peak, the skip/use value can be changed.

Calibration type can be set to either Linear fitting or Quadratic fitting. Using Calculate button, relevant constants are calculated and calibration plot can than be seen (View plot button). Press Apply button to recalculate spectrum and/or peaklist data.

internal calibration dialog

Internal calibration dialog.

Statistical calibration

Statistical Calibration [Processing → Statistical calibration…] icon, sometimes called "self-calibration" is a special method for peptide mass spectra only. It does not need any external reference points since it is based on the fact that monoisotopic masses of peptides are distributed in a very regular way and decimal fraction of peptide mass can be calculated with sufficient accuracy just by multiplying their integral part by factor 1.00048. These calculated values are then used as reference points. Even for this method, linear or quadratic fitting can be used. It is highly recommended to check calibration plot before applying calculation to data.

This calibration type, however, has two main limitations summarised further on. It can be used for peptides only; any non-peptide contamination or modification have disturbing effect and this method can not be used. Double-clicking the peak in list, skip/use value can be changed. Using statistical calibration, only small mass shifts within 0.5 Da can be corrected.

statistical calibration dialog

Statistical calibration dialog.

calibration plot

Calibration plot.

Spectrum crop

A simple Crop Spectrum tool [Processing → Crop Spectrum…] can be used to choose relevant part of spectrum and/or peaklist and discard the rest. This feature is useful especially in cases of MALDI-TOF MS data to delete unnecessary parts like matrix clusters etc.

Undo processing

All of the above mentioned function can be undone if the result is not what you want. Simply choose Undo Processing [Processing → Undo Processing] from main menu.