Harald Barsnes

I'm afraid that OMSSA is a quite old search engine that is no longer supported by the original developers. There may therefore be newer operating systems that are not able...

Hi Jacob, Thanks for the suggestion. However, all we are doing is using ThermoRawFileParser command lines of the following types: `ThermoRawFileParser.exe -i=C:\[...]\qExactive01819.raw -b=C:\[...]\qExactive01819.mzml -f=2 -e -x ` or `ThermoRawFileParser.exe -i=C:\[...]\qExactive01819.raw...

There are two trypsin versions included as defaults: "Trypsin" and "Trypsin_(no_P_rule)". It seems like it's the last one that you want? It includes the setting you list above, i.e. no...

> Still looking for the SearchCLI documentation on enzyme nomenclature. I'm not sure if we ever documented this properly. I had a look at https://github.com/compomics/compomics-utilities/wiki/IdentificationParametersCLI, but the closest I could...

Hi all, @bgruening I've discussed a bit with Kenneth and it seems like you should be able to link PeptideShaker and moFF by using the default PSM report from PeptideShaker....

Hi Marc, > You might want to try the compomics-utilities parser of mzID, can get you this piece of information fairly easily, might be quicker than trying to accommodate the...

> Well, moFF is mainly based on pandas dataframe and the name of the fields are also case sensitive. I m going to use a mapping function that change the...

> About passing data from PeptideShaker to moFF, I propose to export the result using one of the default export (at moment I do not remembar the name by heart)...

Yes, I think you should be able to do something like this: ``` DigestionParameters digestionPreferences = new DigestionParameters(); digestionPreferences.setCleavageParameter(DigestionParameters.CleavageParameter.enzyme); digestionPreferences.addEnzyme(enzymeFactory.getEnzyme("Trypsin")); SequenceIterator sequenceIterator = iteratorFactoryNoModifications.getSequenceIterator(yourSequence, digestionPreferences, 0.0, Double.MAX_VALUE); ```

Ah, sorry, forgot to add the semi-specific part. See the fourth line below. ``` DigestionParameters digestionPreferences = new DigestionParameters(); digestionPreferences.setCleavageParameter(DigestionParameters.CleavageParameter.enzyme); digestionPreferences.addEnzyme(enzymeFactory.getEnzyme("Trypsin")); digestionPreferences.setSpecificity("Trypsin", Specificity.semiSpecific); SequenceIterator sequenceIterator = iteratorFactoryNoModifications.getSequenceIterator(yourSequence, digestionPreferences, 0.0, Double.MAX_VALUE);...