Issue with Missing Precursor Ions and Base Peak Intensity in MS² Data Analysis #687
Description
Dear community,
I am reaching out regarding an issue we have encountered while using MSdial for MS² data analysis.
On the experimental MS² spectra, when viewed with the "Exp. vs. Ref." option, we observed that the precursor ion is almost never present, even though this spectra is linked to the correct precursor, as seen in the "EIC of focused spot." Additionally, when checking the data with RawDataViewer, we encountered the same issue. Furthermore, we noticed that the ion considered as the base peak and the base peak intensity do not match; the base peak ion corresponds to the heaviest ion, while the base peak intensity is based on the most intense ion.
We are wondering if this issue arises from our data or if there may be a problem with the MSdial software's method of analysis. We have also observed that in the raw MS² spectra, some fragments, including the precursor ion and many other fragments, disappear after data extraction with MSdial, which significantly alters the original data and renders the results unusable.
I would appreciate your insights or any guidance on how we might resolve this issue.
Thank you for your time and assistance. I look forward to your response.
Best regards,
