- need some way of highlighting select peptide for manual verification
- Add the tricks in this paper for improved +2 and >+3 
  performance on ETD and ETCaD (http://pubs.acs.org/doi/abs/10.1021/pr100648r)

- add some sort of isotope distribution model
- serialize search results
- add smoothing of XICs  (average peaks between -1 +1 time points)
- add breaking of smoothed XICs (where there is a dip due to isomers)
- improve peptide level output
- use duty cycle to set XIC parameters
- in isotope mode when there are multiple conditions, create ID'd isotope pair
  lists in separate files for each condition (this is not handled well currently)
- output isotope pairs with NO ids (for mass/rt inclusion list)
- output grouped monoisotopic XICs with NO ids for label-free asw well 
- modify reports.R and internal correlation generation to ignore
  modified peptides
- in _summary.txt output isotope labeled correction
- handle out of memory errors more gracefully!!!!
- add additional enzymes AspN, etc
- report loading error for SILAC data
- report XICs that were not sequenced 
  report XICs sequence but no ID
- add function to compute coverage for each protein in protein_meta
- address resize bug and tabs for gui
- add option to load entire range
- fix output bug for additional tables
- add better error handling 
    - cover all places were use input comes in mzXML, pview.xml, pepXMls, etc.
    - fasta file errors
    - parameter inconsistencies especially among
      fixed and variable modifications as well as custom isotopes
    - switch to using combo boxes and spin boxes for most paramters
      *DO NOT TRUST THE USER*
- run tools that report/look for memory leaks
- generate different branches for each condition, replicate set, scan number in the tree view
- create a thread when saving output data to disk


- for group 1 vs. group 2 plots show quartiles 1st and 3rd (of each group) as bars on the plot

- validate all input data, mzXML, pview.xml, pepXML, and fasta files, complain if not OK (use exceptions here)
- add protein/per accession coverage computation
- add default parameter sets for instrument types to configuration GUI
- create a installer for windows version http://nsis.sourceforge.net/ (best option)
- add report stats on what's left in data (dataset_summary.txt)
- report pairs not assigned an ID
- add a QTOF parameter setting option (drop down box)
