Make n_per_w spectrum filtering start from 0 m/z, and specify annotation / scoring losses per fragmentation type
Switch back to a 0.01 qvalue threshold for the PTM report. TODO - add option to specify threshold
Tidy up ModLS results display page
2+ charge state limit for ModLS fragment ions
Fragment ion calculation and PTM score changes. Types of losses to be calculated must be specified. ModLS speed-up: consider peak depths 1-10, but stop when increasing depth doesn't improve score; no need to worry about multiple matching, so don't sort peaks by intensity before matching
SINQ - update ion matching. Write per-group normalization coefficients to log file
Undo stupid decision to fork background threads for every database populate call in PepXML/ProtXML import.When DB can't keep up number of threads and connections explodes and things stop working.
Add sanity check for PepXML ProtXML import. Count of hits in XML should equal count in DB after impot