IonQuant no longer generate *_quant.csv files because they are useless intermediate files

[wyu]

Hi, I'm trying to get a LFQ workflow running for DDA run from our TimsTOF instrument. However, the output from IonQuant seems to be missing, even though the log file indicated a success IonQuant step.

What I'm looking for is *_quan.csv for each of the run that I usually get from my Thermo raw files. Are we expecting the same file from the TimsTOF run?

By the way, the Bruker native library shipped with the latest MsFragger 3.6 is not working. I had to bring back the version from v3.5 in order to complete the IonQuant step.

Thanks!
Wen

log_2022-12-11_17-46-47.txt

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[wyu]

Hi, I need to correct myself that the same problem is happening for the Thermo raw file with the latest IonQuant (v1.8.9).
log_2022-12-11_13-58-34.txt

In the prev version (v1.8.0), the Thermo raw files yield _quant.csv as expected.

Thanks!
Wen

[wyu]

Hi, looks like we have a temp workaround on this problem:

1. Download the temp patch of fragpipe jar as mentioned in another thread and replace the copy in the lib folder
2. Remove the ionquant 1.8.9 from the tools folder, and point the active version to 1.8.0 in the FragPipe GUI
3. replace the "ext/bruker" folder with the one from MsFragger 3.5 to avoid the error about Bruker native library.

I'll leave the ticket open for now till we have a more permanent solution.

Thanks!
Wen

[fcyu]

Hi Wen,

I think you got the questions wrong at the beginning. And then, tried to "fix" the problem in the wrong direction, which makes it looks complicated. Actually it is very simple.

Hi, I'm trying to get a LFQ workflow running for DDA run from our TimsTOF instrument. However, the output from IonQuant seems to be missing, even though the log file indicated a success IonQuant step.
What I'm looking for is *_quan.csv for each of the run that I usually get from my Thermo raw files. Are we expecting the same file from the TimsTOF run?

IonQuant no longer generates *_quant.csv files. They are intermediate files generated by old versions of IonQuant. The entries in those files are not 100% useful, and accurate. To prevent any misleading, I removed those files in the latest version. Please use psm.tsv, ion.tsv, peptide.tsv, protein.tsv, *_label_quant.tsv, and combined_*.tsv files.

By the way, the Bruker native library shipped with the latest MsFragger 3.6 is not working. I had to bring back the version from v3.5 in order to complete the IonQuant step.

I see no error messages regarding this issue from your log files. Can you upload the log file with the error message saying IonQuant couldn't read Bruker's files?

Hi, I need to correct myself that the same problem is happening for the Thermo raw file with the latest IonQuant (v1.8.9).
log_2022-12-11_13-58-34.txt
In the prev version (v1.8.0), the Thermo raw files yield _quant.csv as expected.

Again, IonQuant no longer generates *_quant.csv files. They are intermediate files generated by old versions of IonQuant. The entries in those files are not 100% useful, and accurate. To prevent any misleading, I removed those files in the latest version. Please use psm.tsv, ion.tsv, peptide.tsv, protein.tsv, *_label_quant.tsv, and combined_*.tsv files.

Hi, looks like we have a temp workaround on this problem:
Download the temp patch of fragpipe jar as mentioned in another thread and replace the copy in the lib folder
Remove the ionquant 1.8.9 from the tools folder, and point the active version to 1.8.0 in the FragPipe GUI
replace the "ext/bruker" folder with the one from MsFragger 3.5 to avoid the error about Bruker native library.

These "workaround" is not needed because you got the questions wrong. Please do not mislead users.

Best,

Fengchao

[wyu]

Hi Fengchao,

Thanks for looking into the issue!

We're depending on some of the columns from the _quan.csv" file for our data QC pipeline. Do you know if they can be found in the files you mentioned? The ion, psm, and peptide files mostly contain the "intensity" information as I can see.

Thanks!
Wen

retention_time_end, retention_time_begin, apex_retention_time, retention_time

[fcyu]

Hi Wen,

No, they are not in the tsv files.

Best,

Fengchao

[wyu]

Hi Fengchao,

Thanks for the clarification! Is there a way to have those files back in the future update? We're using FragPipe in headless mode for our data QC pipeline as it's much faster than MaxQuant.

Wen

[fcyu]

Hi Wen,

Yes, we are planning to write these information to the *.tsv files which have FDR filtered entries and also have MBR entries (the entries in the *_quant.csv are not FDR filtered and don't include the MBR ones). Will keep you updated.

Best,

Fengchao

[fcyu]

Hi Wen,

I would like to keep this issue open until I implement the requirement. An open issue can keep me noted.

Thanks,

Fengchao

[fcyu]

The latest IonQuant write the retention time and ion mobility information to the combined_ion.tsv file.

Best,

Fengchao