Compound Discovery
Compound Discovery builds analytes from a sample’s chromatogram. Open the method editor (Method → Edit method…) and use Add → Analyte…, or Open Compound Discovery when the method has no analytes yet.
Before you start
- File → Add samples… and add the data files.
- Select a sample (a calibration sample is a good choice).
- Open Edit method, then Compound Discovery.
- Deconvolute a range or the whole run.
- Create analytes from all.
The chromatogram
The top chart is the sample TIC. SCAN, SIM, and MRM choose the source. SCAN shows the full-scan chromatogram and discovers compounds from scan spectra. SIM uses SIM channels. MRM uses MRM channels. Turn on the source that matches the file. Existing analytes draws markers for names already in the method.
Drag a range on the chart. From and To are the start and end, in minutes. Deconvolute runs that range. Deconvolute all runs the whole chromatogram. If the TIC span is missing, the whole-run command reads every scan.
While it runs, a progress overlay covers the view. You can cancel it. Editing Corr. window, Min spec peak %, or Min ion intensity only saves the number until you run Deconvolute again. Co-elution is saved too; the SCAN run uses its own merge rule. See SCAN deconvolution.
The compound grid
Discovered compounds are listed in retention-time order. Columns include:
| Column | Meaning |
|---|---|
| RT | Apex time, minutes. |
| Area | Sum of the signal peak areas. |
| Width | Base-signal width at half height, minutes. |
| Signals | How many correlated ions or transitions. |
| Signal Name | m/z, or precursor → product for MRM. |
| Acq Name | Name from the acquisition method, matched by time and signal. |
| Source | SCAN, SIM, or MRM. |
| Height | Apex height of the base signal. |
| Lib Name | Name of the top library hit. |
| CAS | CAS of that hit. |
| Match, RMatch, Prob, PBM % | Library scores. See Library search. |
Remove selected compound drops a row from this list. It does not delete an analyte already saved in the method.
Creating analytes
Create analyte (on the detail) creates one analyte from the selected component. Update analyte writes the selected component onto an existing analyte. Create analytes from all creates an analyte for every compound, or for the selected rows when more than one row is selected.
The new analyte’s acquisition key is the sample’s key. A new quant uses Linear, origin Force, weighting Equal, unless the analyte is an ISTD, which uses Average of response factors. Qualifier percent starts at 100 until you update it. See Acquisition keys and Calibration curves.
Libraries chooses the ChemStation .L and MassHunter .mslibrary.xml files stored on the method.