MRM peak integration

[cobbolds]

Hi, I was trying to use an SRM library to extract some mzXML files I acquired off an Eclipse (Thermo), targeted MS2. The idea was to use one of the MS2 ions for quantification but when I use an SRM library (for example, a single MS1 species, fragmented and one MS2 ion defined), the MS2 target ion looks incomplete (scans missing) and low intensity compared to visualising the same MS2 ion extracted via Thermo Freestyle.

I think it is likely that I am doing something wrong, but I am not sure how best to go about doing this successfully. I am converting the .raw files with MSConvert into mzXML using the vendor peak-picking for MS1.

Thanks in advance for any suggestions.

Simon

[PMSeitzer]

Thanks @cobbolds for your interest in maven.
In terms of SRM data, in recent years MAVEN has been optimized to work with Sciex 7500 data. It's possible that there are some differences between the instrument you're using and the 7500 which are causing the problem.
If you're using SRM data, You could try to view your data in the Widgets -> SRM List or Widgets -> SRM Transition List from the program's main drop-down menu.

I'm not sure why the EIC widget is showing a truncated form - perhaps you could try opening your file in a newer version of MAVEN? The latest version is 2.10.21
https://github.com/eugenemel/maven/releases/tag/2.10.21
In the program options, under Instrumentation, you can set the Q1 and Q3 tolerance values - if these are set at 0 there could be some floating point rounding errors which could be excluding some of the intensity you're seeing. You can access this window by clicking the Options button from the main window toolbar.