Comments (3)
Thank you for providing the .mzML file. We will look into this
from informed-proteomics.
This has to do with a conflict between how scans are referenced internally, and the waters function:scan id format. Internally (because this was originally written with a focus on Thermo .raw data) we reference the scans using an integer, and so working with Waters data with duplicate scan numbers with different functions is problematic, as least in setting up the internal references to individual scans. There are several options for compensating for this, but I don't know enough about waters functions/scans to choose one that will reasonably represent the data file. I can see that your data has 4 functions, where functions 1 and 4 are MS1, and functions 2 and 3 are MS2. Can you give us more information about the 4 functions? Also, I noticed that it is IMS (or TW-IMS) data; you are venturing into uncharted territory with MSPathFinder...
from informed-proteomics.
from informed-proteomics.
Related Issues (20)
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from informed-proteomics.