Address issue where a peptide with a low xcorr identified in a very poor/sparse spectrum would be assigned a good E-value. This is due to the majority of matched xcorr scores being "0" so any poor scoring match looks like a good outlier. Thanks to D. Shteynberg for reporting the issue.
Add "scale_fragmentNL" parameter entry which scales (multiplies) the neutral loss mass value by the number of modified residues in the fragment. Feature requested by A. Keller.
Add contributions of fragment neutral loss peaks in preliminary (Sp) score; previously they only applied to the cross-correlation score.
Correct bug where the fragment neutral loss peak was not analyzed if the primary fragment peak was not matched.
Fix minor typo in command line help. Thanks to M. Riffle for contributing the fix.