EasyPQP convert KeyError

[owentsai]

Hi, I'm trying to build a spectral library from fractionated DDA data. I spiked in Pierce retention time peptides for each fraction and followed https://github.com/Nesvilab/FragPipe/issues/506 to search for my spike-in peptides (I replaced K and R with B and J). I was able to identify most spike-in peptides in my psm.tsv.

However, the library generation step (easypqp convert) failed and it seems that easypqp can't process sequences with 'B' and 'J' when parsing the XML file. I got "KeyError: 'J'" (see log file). I am a bit lost on what to do next and I was wondering if there is a way to search for spike-in peptides without having to change the heavy label amino acid in the sequence database.

Thanks, Owen T.

log.txt

[guoci]

@owentsai please try the following modification of EasyPQP. Try running the following commands then rerun the library generation step.

pip uninstall -y easypqp
pip install git+https://github.com/guoci/easypqp.git@fragpipe_issue_760

[owentsai]

Hi @guoci thank you for the prompt response. I am still getting KeyError: 'J' but it stops on a different line in convert.py (see log_07132022_updated_easypqp.txt) log_07132022_updated_easypqp.txt

[fcyu]

Hi Guo Ci @guoci ,

Can you take a look again? I guess the bug is not fully fixed?

Thanks,

Fengchao

[guoci]

@owentsai I have just pushed a fix. Can you retry the commands in https://github.com/Nesvilab/FragPipe/issues/760#issuecomment-1183493986 again?

[owentsai]

Hi @guoci, thank you for working on it. I'm getting a different error message now (RuntimeError) but it seems like it's still related to the B and J modifications.

Owen log_20220715.txt

[guoci]

@owentsai this error originates from an external library (pyOpenMS). To resolve this, I will need to reimplement some code.

[owentsai]

@guoci thank you for working on it. In the meantime, is there a way to search for the heavy-labelled peptides without changing the amino acid residues in the sequence database?

[fcyu]

If you are using the isotope labelling like SILAC, you can always set them as variable modifications. Using the custom amino acids is just for reducing the search space.

Best,

Fengchao