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QuantSysBio / inSPIRE

in silico Spectral Predictor Informed REscoring
GNU General Public License v2.0
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Compability with MSFragger Output #22

Closed BenSamy2020 closed 1 year ago

BenSamy2020 commented 1 year ago

Greetings,

I would like to thank you for providing this cool and useful pipeline. I would like to check if this tool would be compatiable with FragPipe (MSfragger) output?

Regards, Ben

jamc1996 commented 1 year ago

Hi Ben,

Thanks for your interest in inSPIRE!

We have actually just added support for MSFragger pepXML output in inSPIRE 1.5 so good timing! The decoys PSMs should be labelled with 'rev_' at the start of the protein ID (I believe this is the default for fragpipe) and under advanced output options you should set Output max expect to 100.

Also for running inSPIRE please set rescoreMethod to percolatorSeparate in the config file.

Unfortunately inSPIRE 1.5 is not published on pip yet but you can still install it right away with the following steps:

Uninstall your existing installation:

pip uninstall inspirems

Clone the GitHub repo:

git clone https://github.com/QuantSysBio/inSPIRE.git

Change directory into inSPIRE:

cd inSPIRE

Install the cloned repo:

python setup.py install

Best wishes, John.

jamc1996 commented 1 year ago

Hi Ben,

I'm closing this issue as the version containing the fix (inSPIRE 1.5) is now published on pip meaning it can now be installled via the standard:

pip install inspirems==1.5

This does not impact you if you successfully installed inSPIRE manually via the instructions above.

Thank you for your help improving inSPIRE. We hope to hear from you again!

Best wishes, John.

BenSamy2020 commented 1 year ago

Greeting,

Sure thank you publishing the fixed version on pip.

Regards, Ben