v2.0.5

v2.0.5 implements bug fixes from v2.0.0

• fix glyco crash if localization not run in MSFragger
• prevent crash if unknown glycans in database
• add support for additional glycan database types

other changes:

• Upgrade batmass-io to 1.28.5
• Added output list of glycans for IonQuant
• Add charge state column to global.diagmine.tsv
• Change in output structure

This release includes two files.

ptmshepherd-2.0.5.jar does not include dependencies and can only be run within FragPipe
ptmshepherd-2.0.5_CLI.jar includes dependencies and can be run as a standalone Java program from the command line.

v2.0.0

Implements Multiattribute Glycan Identification and FDR Control for Glycoproteomics

Implements Diagnostic Feature Mining (manuscript in preparation)

This release includes two files.

• ptmshepherd-2.0.0.jar does not include dependencies and can only be run within FragPipe
• ptmshepherd-2.0.0_CLI.jar includes dependencies and can be run as a standalone Java program from the command line.

v1.1.1

Bux fixes from v1.1.0

• Fixed missing scan when loading MGFs in rare cases
• Properly deletes some old files when running using data from previous run in CLI mode

v1.1.0

Released with Fragpipe v16.0

• Smart Unimod mapping embedded in psm.tsv
• Bug fixes for MGF spectra reading where crash would occur with specific number of spectra in file

v1.0.0

Originally released with FragPipe v15.0, late release for archival purposes.

• new output files
• cleaner output formats
• ability to direct output
• major bug fixes
• added compatibility for low-resolution MS2
• added minimum PSM filter for reported peaks
• CLI usability improvements, config and annotation file printing

v0.3.5

Added custom modlist parameter
Fixed "shepherd.config not found" error when run in FragPipe on Linux systems

v0.3.5-alpha

addition of custom_modlist parameter

v0.3.4

Update README.md

v0.2.13

fixed version name