[SpectraST] Fix ETD z. ion mass calculation and charge-reduced precursor notation; update p-value calculation
[SpectraST] Override Peptide::setModByToken properly
[SpectraST] Re-revert to r8958
[SpectraST] Revert changes in SpectraST directory
[SpectraST] Revert changes in SpectraST directory
[SpectraST] Support ProForma delta mass format; New MappedProtein class to store associated prev/next AA; New PeptideUser class for PTMProphet
[SpectraST] Update annotation in mzPAF format, incl TMT tags/reporters. Adjustment to clustering algorithm for high-res data. Code cleanup.
[SpectraST] Fix bug of decoy generation from non-mzPAF annotated libraries; Set default fragmentation type to HCD (used to be CID, which is now becoming rare).