Update ProteinPilot - stop using Excel macros, improved visuals and better PTM analysis

ProteinPilot 5 is much the same now as in version 4, visuals are not publication quality, it is incredibly fiddly to add in custom PTMs, compare PTM abundance, or even some standard ones (editing xml files) with no options for changing thresholds for viewing the data after the analysis is complete.  It's reliance on Microsoft Excel (itself a poor piece of software for speed and resource hogging on even the fastest PC with 64GB RAM) is a huge problem.  It takes considerable time to open FDR results files, and if you active the in-depth results it can take several minutes to open each of the complex Macro driven spreadsheets that reclaculate constantly on opening.  I still believe PP needs a local software version as moving software to the cloud has a lot of resistance due to versioning/changes not being notified. Recently we have been using PEAKS studio which is much easier to use, great visuals and options for data sorting, exporting and PTM analysis.