Casanovo v5.1.0

5.1.0 - 2025-10-22

Changed

• Avoid redundant spectrum encoding during database mode to speed up PSM scoring.
• accelerator: "auto" is overwritten to accelerator: "cpu" on Apple Silicon devices due to MPS compatibility issues.
• Removed reverse_peptides from the configuration since decoding from the C-terminus to the N-terminus yields better results.
• Log a warning if residues in the user configuration are not present in the tokenizer alphabet.
• The full ProForma sequences of predicted peptides are reported in the op_ms_run[1]_proforma of the output MzTab file for backwards compatibility.

Fixed

• Inline mass modifications are now specified separately from the sequence column in the modifications column of the output mzTab file, as per the mzTab specification.