v.1.2.56-alpha

• Supports noncanonical amino acids (O, J, etc.)
• Major refactoring of code classes
• Improved readability of peptide formatting,
• AlphaPeptDeep all PTM support
• Improved RT/IM calibration, including with mass offsets
• Prints out spectra pred file location for PDV
• Supports new Koina MS2PIP models
• Better C terminal mod handling
• Fixed merging of libraries from multiple models

v1.2.38

• HTTP requests through Java rather than cURL
• Ion mobility features (delta IM loess; experimental IM value) can now be activated with useIM
• When doing calibration for RT/IM, file written with peptides used for calibration. Separate files are written for mass shifts and all others
• Separate figures are created with just mass offset peptides and those without, in addition to the joint one generated before
• Decreased memory usage while initializing mzML files

v1.2.31

Most up-to-date version since the Koina preprint

• Koina functionality with cURL requests and heuristic best model search
• Improved logging
• Updated RT calibration with bandwidth optimization and mass offset has separate calibration
• pred RT real units feature for Philosopher reporting of delta RT in real units
• png or pdf figure generation
• Improved multithreading and memory usage

v1.2.1

Release for Tools and Tech