Lars Nilse comments

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                                            Lars Nilse

Pweave does not recognize imported module

I encountered the same problem. [This fix](https://github.com/mpastell/Pweave/issues/102#issuecomment-506536800) helped. Thanks @sbuller.

Storing and exporting non-Unimod modifications (e.g. from MSFragger)

@timosachsenberg Does [this exception](https://github.com/OpenMS/OpenMS/blob/develop/src/openms/source/FORMAT/MzTab.cpp#L275) look familiar? Any idea why the `mod_identifier_` could be `null`? I will check tomorrow on `develop`.

Storing and exporting non-Unimod modifications (e.g. from MSFragger)

@Matthias313 Here the probable reason for the crash. ``` lars@SchillingLinux:~/Desktop/test$ IDFileConverter -in MFA175.pepXML -out MFA175_NEW.idXML Progress of 'Loading...': Non-fatal error while loading 'MFA175.pepXML': No modification description given. Trying to define...

Storing and exporting non-Unimod modifications (e.g. from MSFragger)

MSFragger output [MFA175.pepXML](https://www.dropbox.com/s/or58bgf0vmwunrz/MFA175.pepXML?dl=0).

Storing and exporting non-Unimod modifications (e.g. from MSFragger)

Nothing close to `202.0413` is in `UniMod`. We need to talk to the MSFragger developers what this is. Only then can we make full use of the MSFragger output.

Storing and exporting non-Unimod modifications (e.g. from MSFragger)

Unknown mods are not allowed in `mzTab`, right? So we cannot report full `MSFragger` results in `mzTab`.

Storing and exporting non-Unimod modifications (e.g. from MSFragger)

`V(MOD:00756)KLGC(Carbamidomethyl)SFSGKP` is the culprit. The sequence corresponds to this section in `pepXML`. ``` ```

Storing and exporting non-Unimod modifications (e.g. from MSFragger)

During `pepXML` to `idXML` conversion, `115.0633` turns to `MOD:00756`. Why?

Storing and exporting non-Unimod modifications (e.g. from MSFragger)

The only close mass is `115.0667` of Unimod `#866`. But in this case I would expect `ICPL:13C(6)2H(4)` and not `MOD:00756`. @hendrikweisser @cbielow Any comments from the `pepXML` experts?

Storing and exporting non-Unimod modifications (e.g. from MSFragger)

@timosachsenberg Guess this is it. https://github.com/OpenMS/OpenMS/blob/develop/src/topp/MzTabExporter.cpp#L742 `MOD:00756` is a PSI-MOD (thanks @enetz), but `mzTab` allows only Unimod.