ScopeNovo

post-processor · Transformer (NAR)

ScopeNovo: post-processor · Transformer (NAR). Spectral-library reranking of π-PrimeNovo candidates

Spectral-library reranking of π-PrimeNovo candidates

Kind post-processor
Deep learning yes
Acquisition DDA
Family Transformer (NAR)

Code

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Reported comparisons (2)

The comparison tables this method’s own papers print, standardised: every value on a 0-1 scale, methods down the side, the measure and then the species across. These are numbers papers report about themselves and their baselines. They are not a leaderboard, and they do not compare across tables: each was produced by a different group, on the dataset named in its corner, with each baseline either retrained, run from released weights or quoted from another paper. Where the paper says which, it follows the method’s name (hover it for the sentence); most papers do not say. Bold is the best value in a column and underline the runner-up, our ranking rather than the paper’s own marks.

Table 1 (Nine-species · original (DeepNovo, 2017))

ScopeNovo: a De Novo Peptide Sequencing Method Using Spectrum-Spectrum Similarity to Refine the Prediction Accuracy, page 5: Comparison of de novo peptide sequencing methods on 9-species-V1 and 9-species-V2 benchmarks. For ScopeNovo we report two operating regimes: Setting 1 (External Library, spectrum-consistency reranking against a curated external spectral library), which characterizes the upper-bound performance attainable when high-quality external spectral resources are available; and Setting 2 (Self-Constructed Library), in which the reference library is bootstrapped entirely from high-confidence in-batch de novo predictions on the test data itself, placing ScopeNovo under the same resource assumptions as the baselines and yielding a direct comparison. In each column, the best value among the baselines and ScopeNovo (Setting 2) is in bold; ScopeNovo (Setting 1) is reported separately for reference and excluded from the bold comparison.

Nine-species benchmark
original (DeepNovo, 2017) 		Amino acid precision
Bacillus subtilis Candidatus Thiodiazotropha endoloripes Apis mellifera Homo sapiens Methanosarcina mazei Mus musculus Vigna mungo Solanum lycopersicum Saccharomyces cerevisiae Average
Casanovo 0.788 0.676 0.708 0.676 0.754 0.765 0.761 0.792 0.756 0.743
Casanovo V2 0.801 0.687 0.721 0.687 0.767 0.774 0.768 0.802 0.768 0.754
InstaNovo 0.802 0.656 0.718 0.691 0.756 0.742 0.794 0.774 0.767 0.745
ContraNovo 0.828 0.700 0.764 0.778 0.798 0.803 0.804 0.812 0.787 0.785
AdaNovo 0.858 0.798 0.767 0.690 0.804 0.778 0.878 0.818 0.791 0.798
RankNovo 0.807 0.771 0.880 0.784 0.838 0.823 0.876 0.846 0.828 0.827
π-PrimeNovo 0.840 0.715 0.767 0.725 0.799 0.797 0.823 0.822 0.795 0.789
ScopeNovo Setting 1 0.849 0.715 0.778 0.729 0.811 0.809 0.816 0.825 0.796 0.797
ScopeNovo Setting 2 0.844 0.722 0.774 0.732 0.806 0.809 0.829 0.828 0.798 0.795
Nine-species benchmark
original (DeepNovo, 2017) 		Peptide accuracy
Bacillus subtilis Candidatus Thiodiazotropha endoloripes Apis mellifera Homo sapiens Methanosarcina mazei Mus musculus Vigna mungo Solanum lycopersicum Saccharomyces cerevisiae Average
Casanovo 0.621 0.437 0.494 0.446 0.568 0.485 0.593 0.622 0.601 0.551
Casanovo V2 0.630 0.445 0.504 0.455 0.579 0.493 0.600 0.629 0.607 0.559
InstaNovo 0.652 0.459 0.535 0.515 0.595 0.525 0.635 0.635 0.618 0.582
ContraNovo 0.688 0.486 0.580 0.625 0.633 0.574 0.678 0.674 0.673 0.628
AdaNovo 0.753 0.638 0.620 0.494 0.671 0.546 0.797 0.684 0.660 0.660
RankNovo 0.765 0.592 0.642 0.621 0.688 0.595 0.765 0.720 0.726 0.687
π-PrimeNovo 0.725 0.532 0.602 0.575 0.654 0.572 0.701 0.701 0.703 0.650
ScopeNovo Setting 1 0.789 0.610 0.665 0.628 0.731 0.660 0.755 0.752 0.744 0.711
ScopeNovo Setting 2 0.749 0.572 0.643 0.624 0.690 0.637 0.733 0.732 0.721 0.684

The paper bolds the best of the baselines and ScopeNovo (Setting 2) only: 'ScopeNovo (Setting 1) is reported separately for reference and excluded from the bold comparison.' Bold and underline here rank every row, Setting 1 included; the paper's own marks were checked against its rule, and match it.

Table 1 (Nine-species · revised (main))

ScopeNovo: a De Novo Peptide Sequencing Method Using Spectrum-Spectrum Similarity to Refine the Prediction Accuracy, page 5: Comparison of de novo peptide sequencing methods on 9-species-V1 and 9-species-V2 benchmarks. For ScopeNovo we report two operating regimes: Setting 1 (External Library, spectrum-consistency reranking against a curated external spectral library), which characterizes the upper-bound performance attainable when high-quality external spectral resources are available; and Setting 2 (Self-Constructed Library), in which the reference library is bootstrapped entirely from high-confidence in-batch de novo predictions on the test data itself, placing ScopeNovo under the same resource assumptions as the baselines and yielding a direct comparison. In each column, the best value among the baselines and ScopeNovo (Setting 2) is in bold; ScopeNovo (Setting 1) is reported separately for reference and excluded from the bold comparison.

Nine-species benchmark
revised (main) 		Amino acid precision
Bacillus subtilis Candidatus Thiodiazotropha endoloripes Apis mellifera Homo sapiens Methanosarcina mazei Mus musculus Vigna mungo Solanum lycopersicum Saccharomyces cerevisiae Average
Casanovo 0.923 0.787 0.776 0.856 0.828 0.806 0.854 0.874 0.865 0.881
Casanovo V2 0.843 0.799 0.788 0.865 0.836 0.813 0.867 0.882 0.875 0.865
InstaNovo 0.852 0.751 0.799 0.847 0.848 0.634 0.894 0.864 0.877 0.850
ContraNovo 0.863 0.802 0.817 0.909 0.864 0.830 0.903 0.881 0.883 0.865
AdaNovo 0.792 0.816 0.756 0.800 0.804 0.757 0.759 0.831 0.801 0.794
RankNovo 0.836 0.836 0.891 0.836 0.879 0.920 0.896 0.893 0.879 0.880
π-PrimeNovo 0.874 0.806 0.824 0.870 0.869 0.808 0.921 0.885 0.891 0.866
ScopeNovo Setting 1 0.885 0.822 0.839 0.884 0.882 0.841 0.931 0.897 0.900 0.885
ScopeNovo Setting 2 0.877 0.814 0.829 0.879 0.874 0.821 0.926 0.889 0.892 0.868
Nine-species benchmark
revised (main) 		Peptide accuracy
Bacillus subtilis Candidatus Thiodiazotropha endoloripes Apis mellifera Homo sapiens Methanosarcina mazei Mus musculus Vigna mungo Solanum lycopersicum Saccharomyces cerevisiae Average
Casanovo 0.687 0.522 0.579 0.662 0.656 0.522 0.645 0.730 0.738 0.682
Casanovo V2 0.693 0.532 0.587 0.670 0.661 0.531 0.654 0.737 0.743 0.683
InstaNovo 0.704 0.512 0.625 0.670 0.666 0.504 0.679 0.721 0.758 0.698
ContraNovo 0.709 0.533 0.615 0.759 0.698 0.567 0.722 0.729 0.725 0.701
AdaNovo 0.636 0.624 0.597 0.590 0.641 0.472 0.538 0.693 0.653 0.635
RankNovo 0.713 0.603 0.617 0.717 0.712 0.559 0.744 0.724 0.680 0.682
π-PrimeNovo 0.712 0.572 0.612 0.710 0.714 0.548 0.766 0.719 0.684 0.697
ScopeNovo Setting 1 0.748 0.664 0.669 0.762 0.772 0.664 0.816 0.771 0.702 0.737
ScopeNovo Setting 2 0.728 0.619 0.641 0.750 0.743 0.611 0.788 0.745 0.691 0.716

The paper bolds the best of the baselines and ScopeNovo (Setting 2) only: 'ScopeNovo (Setting 1) is reported separately for reference and excluded from the bold comparison.' Bold and underline here rank every row, Setting 1 included; the paper's own marks were checked against its rule, and match it.

Paper describing it

Authors (3)

Zhi Song, Zejian Ding, Lusheng Wang

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