write sub-mzml files for timstof data

[jd690764]

- Upload your log file
(If a log file hasn't been generated, go to the 'Run' tab in FragPipe, click 'Export Log', zip the resulting "log_[date_time].txt" file to avoid truncation, then attach the zipped file by drag & drop here.)

- Describe the issue or question:

I was trying to follow the 2-pass workflow outlined on this page using timstof data, but I got an error at the write sub-mzml step (see attached log file). I found #1417, so I guess this feature doesn't yet work with timstof data. Just wanted to ask if you have any plans to make it work?

Thank you,
Janos

log_2025-12-11_15-37-40.txt.zip

[fcyu]

Yes, we plan to support it in the near future.

Best,

Fengchao

[jd690764]

Thanks, Fengchao! That's great - do you have a rough estimate when you might roll this out? Janos

…

On Thu, Dec 11, 2025 at 4:17 PM Fengchao ***@***.***> wrote: *fcyu* left a comment (Nesvilab/FragPipe#2592) <#2592 (comment)> Yes, we plan to support it in the near future. Best, Fengchao — Reply to this email directly, view it on GitHub <#2592 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ACP7QY2X5H6TJGTBYC4XLJT4BICSPAVCNFSM6AAAAACOZOCFI6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZTMNBUGM2DQNRVHA> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[fcyu]

I hope I will have time to implement it next year.

Best,

Fengchao

[jd690764]

Thank you!

…

On Thu, Dec 11, 2025 at 4:21 PM Fengchao ***@***.***> wrote: *fcyu* left a comment (Nesvilab/FragPipe#2592) <#2592 (comment)> I hope I will have time to implement it next year. Best, Fengchao — Reply to this email directly, view it on GitHub <#2592 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ACP7QYZNLCHEE2EDLGRHKDT4BIC7HAVCNFSM6AAAAACOZOCFI6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZTMNBUGM2TONBRGU> . You are receiving this because you authored the thread.Message ID: ***@***.***>