Year Application Ind DeepNovo 2020 Detection of neoantigens 2021 De novo sequencing in metaproteomics ✓ 2021 Detection of neoantigens ✓ 2021 Detection of junction peptides ✓ 2021 Detection of shell proteins ✓ 2023 Detection of neuropeptides ✓ 2023 Detection of proteasome-generated spliced and non-spliced peptides ✓ 2023 Antibody sequencing ✓ 2023 Detection of short peptides ✓ 2023 Noncanonical antigen detection ✓ 2023 Detection of neoantigens 2024 Antibody sequencing ✓ 2024 Detection of neoantigens 2024 Detection of venom proteins ✓ DeepNovo 2022 Detection of antigen peptides in immunopeptidomics Peptide assignments for the MS/MS spectrum from the nine-species benchmark data with universal spectrum identifier mzspec:PXD003868:BY 04 heat 3:scan:28038. This spectrum is annotated as peptide "VFAIAN[+0.984]AFAK" in the original version of this dataset but was reannotated as "VFAIANAFAK" recently . The difference in peptide assignments originates from the fact that the precursor m/z corresponds to the first isotopic peak rather than the monoisotopic peak. Because isotope errors were not accounted for during the original labeling process, an erroneous deamidation was applied (a mass difference of 1.003 Da for the first isotopic peak versus 0.984 Da for deamidation). The mirror plot was generated using spectrum utils .