pfindstudio / pdeep Goto Github PK

Hello，

First of all, I want to thank pFinders for providing so many convenient and practical software. You are really a great team.

Recently, I want to use the pDeep2 software to perform some verification on some suspected PSMs in our previous identification results. I encountered some problems in the process of doing it.
As a measure of similarity between predicted spec and real spec, does PCC have a threshold to distort true positives and false positives? For example, we will use the Andromeda score >100 as the threshold for MaxQuant identification in some cases.

If there is no such threshold yet, I may need to do some statistical testing to find a way out.

I would like to know whether the ProteomeTools data was used in the model training process corresponding to the-i Lumos, -e 0.30parameter in the current version (model-180921). This determines whether I can use this type of data from ProteomeTools as my data set for statistical testing.

Thank you.

Zhang Le

I saw in plabel files where neutral loss ions are included but I didn't see the prediction result for those ions. Are these ions considered in this version?

Dear pDeep Team,

I have two questions concerning pDeep2:
A) How can we add other modifications (like e.g. Propionyl)?
B) Is there a possibility to directly compare/calculate the Pearson Correlation between measured spectra (..mgf file) and the predictions?

Regards,
Bart

Is there a pre-trained model for EThcD? When I set mod_config = fconfig.EThcD_Config() the predictions were the same as with HCD.

In pDeep2 paper, we found that the PCC90 of the test data set, HPM: fetal gut, was quite high (87.5% in pDeep2 paper). Then we fixed a bug in https://github.com/pFindStudio/pDeep/blob/master/pDeep2/model/featurize.py, at line 252

252        if instrument not in self.instrument_feature:
253            inst_feature = self.instrument_feature[instrument.lower()]
254        else:
255            inst_feature = self.instrument_feature['unknown']

The correct code:

252        if instrument in self.instrument_feature:

After this bug was fixed, PCC90 of HPM: fetal gut decreased quite a lot, but PCC90 of PT25 became much better. To reproduce the results in pDeep2 paper, we could just modify the code at line 252 back.

There is no such a bug in pDeep3 repo, because it is already fixed in the initial commit.

Hi, I am not able to use pDeep for ETD data. pDeep only generating b and y ion. Can you please guide me on how I can generate c and z ion for ETD data.