My runs show far fewer ions than I would expect; what might have caused this?
At Import Data, as soon as your runs are imported, you’ll be presented with an ion intensity map view of the data and also a summary in the About this run box in the top right hand corner; this allows you to quickly assess the quality of your data before you start your analysis, an outcome of which might be that your runs show far fewer ions than you were expecting.
Possible reasons for this include:
- Data collected using an inappropriate ionisation mode
- Data collected using the wrong polarity mode
- Sample decomposition
- Sample hasn’t reached the ionisation source
- Insufficient volume of sample injected
- Other hardware issues
Alternatively, if you believe that the data file should contain a higher number of ions, but that Progenesis hasn’t imported it correctly, you might want to try reducing the strength of the filtering applied at import.