diff --git a/vignettes/IV-benchmarking.Rmd b/vignettes/IV-benchmarking.Rmd index f8e42e8bc..63c2e220b 100644 --- a/vignettes/IV-benchmarking.Rmd +++ b/vignettes/IV-benchmarking.Rmd @@ -37,12 +37,12 @@ The benchmarking dataset was built using [https://zenodo.org/record/5186176](htt It contained positive and negative MS^2^ spectra of multiple ion species ([M+H]^+^, [M+Na]^+^, [M+H~4~N]^+^, ...) coming from different mass spectrometers. In positive mode, -It was filtered to 22,251 spectra, representing 12,482 structures without stereo. -Of those, only 16,136 spectra (72.5%) corresponded to structures present in the library we used to annotate. +It was filtered to 27,789 spectra, representing 17,822 structures without stereo. +Of those, only 15,005 spectra (54.0%) corresponded to structures present in the library we used to annotate. In negative mode, -It was filtered to 7,472 spectra, representing 6,587 structures without stereo. -Of those, only 5,025 spectra (67.4%) corresponded to structures present in the library we used to annotate. +It was filtered to 12,060 spectra, representing 9,112 structures without stereo. +Of those, only 6,282 spectra (52.1%) corresponded to structures present in the library we used to annotate. ## Best 500 candidates ### Positive diff --git a/vignettes/benchmark_comparison_neg.svg b/vignettes/benchmark_comparison_neg.svg index 647bbfcf4..ebb324ee1 100644 --- a/vignettes/benchmark_comparison_neg.svg +++ b/vignettes/benchmark_comparison_neg.svg @@ -1 +1,177 @@ -OriginalTaxo informed0.000.250.500.751.000.000.250.500.751.00ScoreDensityAOriginalTaxo informed0102030405001020304050RankDensityBAnnotationCorrectIncorrect \ No newline at end of file + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +Original + + + + + + + + + +Taxo informed + + +0.00 +0.25 +0.50 +0.75 +1.00 +0.00 +0.25 +0.50 +0.75 +1.00 +Score +Density +A + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +Original + + + + + + + + + +Taxo informed + + +0 +10 +20 +30 +40 +50 +0 +10 +20 +30 +40 +50 +Rank +Density +B +Annotation + + +Correct +Incorrect + + diff --git a/vignettes/benchmark_comparison_pos.svg b/vignettes/benchmark_comparison_pos.svg index 9e5cbfbb1..7af404536 100644 --- a/vignettes/benchmark_comparison_pos.svg +++ b/vignettes/benchmark_comparison_pos.svg @@ -1 +1,177 @@ -OriginalTaxo informed0.000.250.500.751.000.000.250.500.751.00ScoreDensityAOriginalTaxo informed0102030405001020304050RankDensityBAnnotationCorrectIncorrect \ No newline at end of file + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +Original + + + + + + + + + +Taxo informed + + +0.00 +0.25 +0.50 +0.75 +1.00 +0.00 +0.25 +0.50 +0.75 +1.00 +Score +Density +A + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +Original + + + + + + + + + +Taxo informed + + +0 +10 +20 +30 +40 +50 +0 +10 +20 +30 +40 +50 +Rank +Density +B +Annotation + + +Correct +Incorrect + + diff --git a/vignettes/benchmark_full_neg.svg b/vignettes/benchmark_full_neg.svg index d7c94b3e0..178dfd0ee 100644 --- a/vignettes/benchmark_full_neg.svg +++ b/vignettes/benchmark_full_neg.svg @@ -1 +1,56 @@ -02550751000100200300400500RankCorrect candidates [%]nameMS2 onlyMS2 taxo informedMS2 taxo informed + MS1 completionMS2 taxo informed + MS1 completion + larger library \ No newline at end of file + + + + + + + + + + + + + + + + + + + + + + + + +0 +25 +50 +75 +100 +0 +25 +50 +75 +100 +Rank +Correct candidates [%] +name + + + +MS2 only +MS2 taxo informed +MS2 taxo informed + MS1 completion + + diff --git a/vignettes/benchmark_full_pos.svg b/vignettes/benchmark_full_pos.svg index b8b21cd14..7659c6849 100644 --- a/vignettes/benchmark_full_pos.svg +++ b/vignettes/benchmark_full_pos.svg @@ -1 +1,56 @@ -02550751000100200300400500RankCorrect candidates [%]nameMS2 onlyMS2 taxo informedMS2 taxo informed + MS1 completionMS2 taxo informed + MS1 completion + larger library \ No newline at end of file + + + + + + + + + + + + + + + + + + + + + + + + +0 +25 +50 +75 +100 +0 +25 +50 +75 +100 +Rank +Correct candidates [%] +name + + + +MS2 only +MS2 taxo informed +MS2 taxo informed + MS1 completion + + diff --git a/vignettes/benchmark_zoomed_neg.svg b/vignettes/benchmark_zoomed_neg.svg index e391a7f2e..6ee6c40a5 100644 --- a/vignettes/benchmark_zoomed_neg.svg +++ b/vignettes/benchmark_zoomed_neg.svg @@ -1 +1,57 @@ -010203040500510152025RankCorrect candidates [%]nameMS2 onlyMS2 taxo informedMS2 taxo informed + MS1 completionMS2 taxo informed + MS1 completion + larger library \ No newline at end of file + + + + + + + + + + + + + + + + + + + + + + + + +0 +25 +50 +75 +100 +0 +10 +20 +30 +40 +50 +Rank +Correct candidates [%] +name + + + +MS2 only +MS2 taxo informed +MS2 taxo informed + MS1 completion + + diff --git a/vignettes/benchmark_zoomed_pos.svg b/vignettes/benchmark_zoomed_pos.svg index 9c2ebf2c9..ead9a41b5 100644 --- a/vignettes/benchmark_zoomed_pos.svg +++ b/vignettes/benchmark_zoomed_pos.svg @@ -1 +1,57 @@ -010203040500510152025RankCorrect candidates [%]nameMS2 onlyMS2 taxo informedMS2 taxo informed + MS1 completionMS2 taxo informed + MS1 completion + larger library \ No newline at end of file + + + + + + + + + + + + + + + + + + + + + + + + +0 +25 +50 +75 +100 +0 +10 +20 +30 +40 +50 +Rank +Correct candidates [%] +name + + + +MS2 only +MS2 taxo informed +MS2 taxo informed + MS1 completion + +