pwiz: Quameter error when first spectrum is not MS1
We run Quameter in automation and it generally works well. However, we occasionally get a Thermo .raw file where the first spectrum (or spectra) is MS2, then later an MS1 spectrum appears, followed by more MS2 spectra. For data files that start with an MS2 spectrum, Quameter reports
Error processing ID-free metrics: error reading spectrum index 0 (No MS1 spectrum found before controllerType=0 controllerNumber=1 scan=1)
I found a workaround – update the default filter to include a scan range:
-SpectrumListFilters: "peakPicking true 1-;threshold absolute 0.00000000001 most-intense; scanNumber [14,1000000]"
However, it would be nice if Quameter could automatically skip the initial MS2 spectra and resume normal operation once an MS1 spectrum is found. If the entire file is MS2 spectra, it should report an error. Is this something that could be added?
About this issue
- Original URL
- State: closed
- Created 6 years ago
- Comments: 25 (16 by maintainers)
Also, we are looking into acquiring a Fusion Lumos dataset in the next few weeks that we can hopefully pare down to reasonably small file suitable for an additional test file. The hope is to include ETD, HCD, CID, EThcD, ETciD, and other scan type options in a single file, all available in a small scan range (i.e., < 200 scans). We’ll see what happens with it, we aren’t the instrument operators that would set it up.