DIA-Umpire crashes due to a FragPipe bug

[nicolasgrinberg]

Hi,

I am trying to run hybridDIA with 54 DIA folders and 57 DDA folders. I set a 3% FDR with group-specific FDR. I want to set the DDA folders as DDA+ but it keeps crashing unfortunately. Is it possible to use DDA+ with hybrid DIA? Thanks in advance,

Nico
log_2024-02-21_11-19-47.txt

[fcyu]

The error was from DIA-Umpire. @guoci can you take a look?

Thanks,

Fengchao

[nicolasgrinberg]

Hello, are there any news on this? Is it possible to use both DDA+ and hybrid DIA?

[fcyu]

Hi @nicolasgrinberg ,

The error is not about DIA+. It was thrown by DIA-Umpire (as the new title I have changed), which is before MSFragger starts. We are waiting for Guo Ci to take a look at the error because he knows DIA-Umpire the best. He might be busy at something else, so it might take a while.

Best,

Fengchao

[anesvi]

I looked at the log file and noticed a few things. DIA-Umpire crashed, as Fengchao pointed out. However, looking in more detail:

1. From a the file name, you are doing HLA peptidomics
2. Your DIA data is narrow window
   Processing DIA MS2 (mz range):1610.7758_1611.9757( 15/37495 )
   Is is Astral data? If so, we have a different workflow we can recommend that works well for Astral DIA data.
   I suggest you contact me directly via email.
   Best,
   Alexey

[anesvi]

So we determined there was a bug in FragPipe when DIA and DIA data were searched together and DDA specified as DDA+. Will be fixed in the next release.

[ds2268]

I looked at the log file and noticed a few things. DIA-Umpire crashed, as Fengchao pointed out. However, looking in more detail:

1. From a the file name, you are doing HLA peptidomics

2. Your DIA data is narrow window
   Processing DIA MS2 (mz range):1610.7758_1611.9757( 15/37495 )
   Is is Astral data? If so, we have a different workflow we can recommend that works well for Astral DIA data.
   I suggest you contact me directly via email.
   Best,
   Alexey

@anesvi can you elaborate more on the proposed Astral workflow that we can use with MSFragger-DIA? It would be great to have such information public (README?) for the wider audience to benefit. Thanks!

[fcyu]

Hi @ds2268 ,

You can use the existing built-in DIA related workflows, just not set the DDA data to DDA+ data type for now.

Best,

Fengchao

[ds2268]

Hi @fcyu.

Just to confirm: for the nDIA data, as collected for example here you suggest running the MSFragger-DIA workflow, as presented here?

The following was mentioned above: "Is is Astral data? If so, we have a different workflow we can recommend that works well for Astral DIA data."

[fcyu]

Correct. The DIA_SpecLib_Quant workflow performs better than the DIA_DIA-Umpire_SpecLib_Quant for Astral data.

Best,

Fengchao