added S3 as.data.frame methods
refactored ProteinGroup creation

cleared structure and changed to use environment for protein group table
added lower bounds for fitting of  scale parameter of Tlsd
simplified .as.vect to use the setNames function
improved formatting of properties.R file
fixed import of MzIdentML - should work now for Mascot and ProteomeDiscoverer
upped to version 1.7.1
Merge branch 'ptm' into devel