MassIVE-KB
training · DDA · 2 versions · 3 papers
| Kind | training |
| Acquisition | DDA |
| Organisms | Homo sapiens |
| Home | https://massive.ucsd.edu/ProteoSAFe/static/massive-kb-libraries.jsp |
A repository-wide spectral library of human peptide PSMs, large enough to train on and cited by version number. No single accession stands for it, which is why papers name it rather than an identifier.
Versions
v1
The version Casanovo’s original training set was drawn from. MassIVE titles MSV000081142 “MassIVE-KB Knowledge Base spectral library of Human HCD spectra” and names no version itself, so attaching it here rests on it being the original human HCD library rather than on the record saying so.
Where it lives:
- MassIVE · MSV000081142
v2
The later, larger release; papers that say only “MassIVE-KB” are ambiguous between the two.
No public address: this version is named in the literature but cannot be downloaded.
Used by (3)
- PowerNovo: de novo peptide sequencing via tandem mass spectrometry using an ensemble of transformer and BERT models (2024) peer-reviewed v1
- Introducing π-HelixNovo for practical large-scale de novo peptide sequencing (2024) peer-reviewed v1
- Introducing PandaNovo for practical large-scale de novo peptide sequencing (2023) preprint v1
Checkpoints trained on this (6)
| Method | Checkpoint | Version of this dataset | Size | Get it |
|---|---|---|---|---|
| Casanovo | v4.0.0 | v1 | — | GitHub release |
| Casanovo | v4.2.0 | v1 | — | GitHub release |
| Casanovo | v4.2.0 | v2 | — | GitHub release |
| RefineNovo | RefineNovo-30M | not stated | 388 MB | Google Drive · copy |
| π-PrimeNovo | MassIVE | not stated | 387 MB | Google Drive · copy |
| π-PrimeNovo | phosphorylation | not stated | 387 MB | Google Drive · copy |
Each link rests on stated evidence rather than a text match:
- Casanovo v4.0.0: trained_on: ‘MassIVE-KB v1’, from ProteoBench discussion 356
- Casanovo v4.2.0: trained_on: ‘~2M PSMs from MassIVE-KB v1 + v2.0.15’
- Casanovo v4.2.0: trained_on: ‘~2M PSMs from MassIVE-KB v1 + v2.0.15’
- RefineNovo RefineNovo-30M: the FILENAME, model_massivekb.ckpt; BEAM-Labs/denovo states no training set for it
- π-PrimeNovo MassIVE: trained_on: ‘MassIVE-KB’, with no version given
- π-PrimeNovo phosphorylation: INHERITED, not direct: fine-tuned from model_massive.ckpt, which was trained on MassIVE-KB. Its own fine-tuning set, 2020-Cell-LUAD, is not in this catalog
Methods on these papers (2)
- PowerNovo algorithm
- π-HelixNovo algorithm
Taken from the describing links only, so a paper that merely ran a tool on this data does not make that tool a method of it.