IonQuant error in TMT16 workflow with Thermo raw but not mzml

[enonimos]

Hello, Thank you for all the updates in the new FragPipe v21. I was curious to test out the new TMT Integrator version that uses IonQuant. Running the default TMT16 workflow with ThermoRaw files, the analysis went almost to the end but I received a java ArrayIndexOutOfBoundsException error. I have attached my full log file.

When I use mzxml files, the same workflow completes successfully. So not a high priority, but given IonQuant should in theory allow using ThermoRaw directly, I thought my observation might be helpful.

Best, Todd

• Upload your log file log_2023-12-20_10-26-40.txt

[fcyu]

Hi Todd,

Thanks for the bug reporting. I guess IonQuant had some issue when extracting certain information from the raw file. Could you upload 2023Dec_37_F1.raw to https://www.dropbox.com/request/com7mlVE2vQB5J5hONBA ? I will take a look and fix the bugs if there are any.

Best,

Fengchao

[enonimos]

Thanks Fenchao. File uploaded.

[fcyu]

Thanks for your raw file. The parent scan number information is not available in the raw file. I have fix this bug. If you want to test the fixed version, please send an email to yufe AT umich.edu. I will probably release a new version in a few days, as well.

Best,

Fengchao

[enonimos]

Thanks for the diagnosis, I will wait for the new version. Todd

[prdawar]

Hello I also ran into this same error. Attached is the log file for the respective run. The issue was also fixed by providing a .mzml file to FragPipe instead of using .mzml file generated by FragPipe itself as described above log_2024-05-23_11-51-29.txt .

[fcyu]

Thank you for the feedback. We have fixed it and the next release will be available in a few days.

Best,

Fengchao

[fcyu]

Fixed in the latest version.

Best,

Fengchao