PD-Nodes 2.0

• MSFragger-PD node in PD v2.5 and v3.0
• Compatible with MSFragger v3.8 and Philosopher v5.0.0
• Add a new software tool, AutoMod, for possible PTM discovery. More information at: https://github.com/ICMOL/AutoMod

PD-Nodes 1.2.0

• Compatible with MSFragger v3.7 and Philosopher v4.8.1

PD-Nodes 1.1.0

• New dll and workflows available for PD v2.5
• Compatible with MSFragger v3.3 and Philosopher v4.0.0

PD-Nodes 1.0.7

• Allow up to 16 dynamic modifications

PD-Nodes 1.0.6

• Fix a bug of one MS/MS spectrum with multiple precursor charge states

PD-Nodes 1.0.5

• New dll and workflows available for PD v2.4
• A new parameter (deisotoping) in the MSFragger node
• Compatible with MSFragger v2.3 and Philosopher v2.1.1

PD-Nodes 1.0.4

• Allow multiple processing workflow (please see the PD-Nodes website (https://github.com/Nesvilab/PD-Nodes/blob/master/README.md) for detailed instructions
• Support for new options introduced in MSFragger 2.0
• Log MSFragger and Philosopher(PeptideProphet) output messages in PD job queue
• Add a drop-down bottom for enzyme selection in MSFragger node

PD-Nodes 1.0.3

• Support RAW files (Compatible with MSFragger-20190628 or later version)
• Add fragment annotation
• Automatically allocate memory usage if not specified

PD-Nodes 1.0.2

• Add new MSFragger parameters

  1. calibrate_mass = 2
  2. precursor_mass_mode = selected
  3. fragment_ion_series = b,y
  4. report_alternative_proteins = 0

• Update MSFragger parameters

  1. shifted_ions -> localize_delta_mass
  2. shifted_ions_exclude_ranges -> delta_mass_exclude_ranges

PD-Nodes 1.0.1

• MSFragger-PD.dll for PD v2.2 and v2.3
• Delete temp folder after each process