How to process multiple MS runs in one WIFF/WIFF2 file using MS-DIAL

[vv1175]

Hi, I accidentally stored multiple MS runs in a single WIFF/WIFF2 file using SCIEX instruments. I tried converting the file using ABF converter, but it outputs only one ABF file. I tested both WIFF and WIFF2 formats but only a single ABF file is generated in both cases.

MS-DIAL seems unable to distinguish the runs before and after ABF conversion, and I’m unable to process each run individually.

I’m wondering:

1. Can MS-DIAL recognize and separate individual runs from a single WIFF/WIFF2 file?
2. Is there a way to force ABF converter to output separate ABF files for each run?
3. Any recommendation on alternative ways to separate the data?

Would appreciate any suggestions or workarounds to properly analyze these samples in MS-DIAL.
Thanks!

[JacobRPrice]

I'm running into a similar issue. I have used MSConvert to split up the .wiff file into multiple .mzML files. That said, I haven't been able to get MSDIAL to finish an analysis with those split up .mzML files. The process seems to be getting hung up on a single sample after all others have completed. @vv1175 were you able to come up with a solution?