pNovo
algorithm · Graph / DP
First HCD-focused de novo
| Kind | algorithm |
| Deep learning | no |
| Acquisition | DDA |
| Family | Graph / DP |
Compared against in other papers (1)
3 tables from 1 paper that report this method as a baseline, newest first. The caveats of the comparisons above hold twice over: each paper ran, retrained or quoted this method its own way, so its number here is that paper’s claim, not a measurement of the method. Where a paper says which it did, the word follows the method’s name.
pNovo 3: precise de novo peptide sequencing using a learning-to-rank framework (2019) · 3 tables
Table2 (QE_HF_X2)
pNovo 3: precise de novo peptide sequencing using a learning-to-rank framework, page 5: Recall of top-1 peptides identified by different de novo sequencing algorithms
|
HeLa Q Exactive HF runs (pNovo 3) QE_HF_X2 |
Peptide recall |
|---|---|
| pNovo 3 | 0.383 |
| pNovo · quoted | 0.214 |
| PEAKS · quoted | 0.246 |
| Novor | 0.093 |
Table2 (QE_HF_X1)
pNovo 3: precise de novo peptide sequencing using a learning-to-rank framework, page 5: Recall of top-1 peptides identified by different de novo sequencing algorithms
|
HeLa Q Exactive HF runs (pNovo 3) QE_HF_X1 |
Peptide recall |
|---|---|
| pNovo 3 | 0.478 |
| pNovo · quoted | 0.298 |
| PEAKS · quoted | 0.322 |
| Novor | 0.109 |
Table2 (Nine-species)
pNovo 3: precise de novo peptide sequencing using a learning-to-rank framework, page 5: Recall of top-1 peptides identified by different de novo sequencing algorithms
| Nine-species benchmark | Peptide recall | ||||
|---|---|---|---|---|---|
| Vigna mungo | Mus musculus | Methanosarcina mazei | Saccharomyces cerevisiae | Apis mellifera | |
| pNovo 3 | 0.646 | 0.504 | 0.660 | 0.647 | 0.625 |
| pNovo · quoted | 0.429 | 0.257 | 0.424 | 0.477 | 0.367 |
| PEAKS · quoted | 0.443 | 0.249 | 0.424 | 0.500 | 0.380 |
| Novor | 0.174 | 0.097 | 0.191 | 0.191 | 0.137 |
Paper describing it
- pNovo: De novo Peptide Sequencing and Identification Using HCD Spectra (2010, Journal of Proteome Research, peer-reviewed)
Papers using it (3)
Applications and evaluations that ran this method. They are not counted among its authors below.
- PepExplorer: A Similarity-driven Tool for Analyzing de Novo Sequencing Results (2014, Molecular & Cellular Proteomics, peer-reviewed)
- NovoHCD: De novo Peptide Sequencing From HCD Spectra (2014, IEEE Transactions on NanoBioscience, peer-reviewed)
- A multi-edge graph based de novo peptide sequencing method for HCD spectra (2013, 2013 IEEE International Conference on Bioinformatics and Biomedicine, peer-reviewed)