Open mobiusklein opened 7 months ago
This code path in v20 ignores the original LCMS file and just writes out data from the mzBIN file.
Yes, that is on purpose.
I see that your input seems to be from timsTOF? We never tested that, but I think I can let FragPipe read the uncalibrated.mzML for this case. But then, there will be no MS1 for the quantification.
BTW, the write sub mzML
checkbox is for a specific application, two-pass searching for the variant peptide analysis: https://fragpipe.nesvilab.org/docs/tutorial_two_pass_search.html. I am not sure if it is a good idea to use that option for other tasks.
Best,
Fengchao
Enabling writing sub-mzML fails with FragPipe v21 when the source MS data file is not an mzML file, but does work on v20.
The relevant snippet from the log file is:
The root cause is at https://github.com/Nesvilab/FragPipe/blob/cb80ec8d99349db5201ab9efecf3633bf70171d6/MSFragger-GUI/src/com/dmtavt/fragpipe/util/WriteSubMzml.java#L96-L110 which tries to unconditionally open the source LCMS file as an mzML file to later read out spectrum metadata to augment the data in the mzBIN file. This code path in v20 ignores the original LCMS file and just writes out data from the mzBIN file.