PEAKS support and various fixes/improvements

[ArthurDeclercq]

Improvements

• Added support for PEAKS mzid identification files!.
• Retention time predictor calibrates now for each raw file independently resulting in more accurate calibrations.

Bugfixes

• MaxQuant pipeline: Carbamidomethyl is not listed as default fixed modification anymore, as this could not be overridden. Searches without carbamidomethyl as fixed modification are now supported. However, carbamidomethyl now always needs to be specified explicitly if applicable!
• When parsing MGF files, all lines ending on 0.0 (including lines ending on 10.0) were removed, instead of only 0 intensity peaks. This is now fixed.

Refactoring and minor changes

• PIN pipeline: Allow mass shift modification labels with + sign (e.g. R.IM[+15.99492]MAR.D).
• PEAKS and MaxQuant pipelines: Precursor charge from ID file now overwrites CHARGE in MGF file. (Identification and instrument precursor charges do not always match; identification charge should be prioritized).
• Plotting module can only be run when Percolator is run as part of MS²Rescore.
• If no decoy PSMs are present, MS²Rescore raises an error and stops.
• Removed obsolete mgf option from maxquant_to_rescore configuration.