Reporting LC-MS data with Empower

[ManaJane]

To anyone comfortable with creating reports in Empower 2, specifically for MS data:

We recently purchased at Waters Acquity UPLC-TQD (triple quad MS) and are running it with Empower 2. I am trying to create a report method for my LC-MS data. I have the chromatograms I want appearing, as well as spectrum index plot, with show the extracted mass spectrum for a specific peak in my chromatogram. What I really would like is a table that lists the most abundant ions in a mass spectrum (you could set a threshold) extracted for a particular peak. The only way I have found to do this requires you to manually tell the table the peak retention times for which a mass spectrum is to be extracted. If you have lots of peak, you can imagine that this would be VERY time consuming. Does anyone know of an easier way to create a table like the one I described?

Thank you very much!

[carras]

We had the same problem about three years ago. Although I wasn't directly involved I gather that the whole thing was a complete and intractable mess. Even Waters had to admit that it was impossible and they installed Masslynx to process the TQD data. They said that Empower wasn't well tuned to mass data management, or words to that effect. Masslynx has its (many) shortcomings but its processing and presenting package is quite user friendly, compared with Empower, since it is designed specifically for mass data.
Good luck