Creating an Extracted Ion Chromatogram

4.2.2Creating a Constant

Neutral Loss (CNL) Chromatogram

This section includes:

•Overview

•Applications

•Labeling spectrum peaks with mass difference (optional)

•Procedure

•Example

Overview

Applications

To rapidly screen for the presence of mass differences corresponding to loss of specific fragments, you can create a Constant Neutral Loss (CNL) extracted chromatogram.

When you generate a Constant Neutral Loss Extracted ion chromatogram, the software constructs a chromatogram that contains signal only for spectra that contain peaks separated by the specified mass difference. To construct a Neutral Loss Extracted ion chromatogram, the software:

•Compares each mass in the peak list to every other mass in the peak list and derives mass differences.

•Takes the total signal of any pairs of peaks that generated the mass difference and includes it in the chromatogram, if any mass difference corresponds to a mass difference plus tolerance specified.

You can generate a CNL extracted chromatogram:

4

 

•To determine if a fragment of known mass is present

•To increase sensitivity of a trace by including signal from both the parent and one or more fragment ions

For LCMS data, a CNL extracted chromatogram is useful to identify eluting components with a given neutral loss.

For other types of data, a CNL extracted chromatogram is useful to screen samples for a given mass difference. For example, create a CNL extracted chromatogram to survey a peptide digest for the presence of peaks separated by a glycosyl residue, as you might see in a digest containing glycopeptides.

Data Explorer™ Software User’s Guide

4-9