Published June 19, 2026
| Version v1
Dataset
Open
InstaNovo prediction sample files for PDV import validation
Description
This dataset contains InstaNovo prediction CSV outputs generated from the MGF and mzML input files listed below for validating InstaNovo import support in PDV.
Input Files
| Format | Source URL |
|---|---|
| MGF | http://pdv.zhang-lab.org/data/download/test_data/msdata/SF_200217_U2OS_TiO2_HCD_OT_rep1.mgf.gz |
| mzML | http://pdv.zhang-lab.org/data/download/test_data/msdata/SF_200217_U2OS_TiO2_HCD_OT_rep1.mzML.gz |
The .gz inputs were downloaded from the URLs above and decompressed before running InstaNovo.
Generation
- Predictions were run on a
NVIDIA H100 80GB HBM3GPU.
The command table uses <input> and <output> placeholders for the concrete input and output paths inside the prediction runtime.
Prediction Files and Commands
| Input | Prediction file | InstaNovo software version | InstaNovo+ software version | InstaNovo checkpoint version | InstaNovo+ checkpoint version | Search method | Beams | Command / flags |
|---|---|---|---|---|---|---|---|---|
| mgf | SF_200217_U2OS_TiO2_HCD_OT_rep1.full.mgf.instanovo-1.0.0.transformer.model-instanovo-v1.0.0.denovo.greedy.beams-1.csv |
1.0.0 | - | v1.0.0 | - | greedy | 1 | python /opt/instanovo-versions/1.0.0/instanovo/transformer/predict.py 'data_path=<input>' model_path=/workspace/models/instanovo-v1.0.0.ckpt 'output_path=<output>' num_beams=1 save_beams=False batch_size=512 num_workers=4 denovo=True subset=1.0 fp16=True log_interval=1 device=cuda |
| mgf | SF_200217_U2OS_TiO2_HCD_OT_rep1.full.mgf.instanovo-1.0.0.transformer.model-instanovo-v1.0.0.denovo.beam-search.beams-5.save-beams.csv |
1.0.0 | - | v1.0.0 | - | beam search | 5 | python /opt/instanovo-versions/1.0.0/instanovo/transformer/predict.py 'data_path=<input>' model_path=/workspace/models/instanovo-v1.0.0.ckpt 'output_path=<output>' num_beams=5 save_beams=True batch_size=512 num_workers=4 denovo=True subset=1.0 fp16=True log_interval=1 device=cuda |
| mgf | SF_200217_U2OS_TiO2_HCD_OT_rep1.full.mgf.instanovo-1.1.0.transformer.model-instanovo-v1.1.0.denovo.greedy.beams-1.columns-predictions.csv |
1.1.0 | - | v1.1.0 | - | greedy | 1 | instanovo transformer predict -d '<input>' -o '<output>' -i instanovo-v1.1.0 --denovo num_beams=1 save_beams=False batch_size=512 num_workers=4 denovo=True subset=1.0 fp16=True log_interval=1 device=cuda |
| mgf | SF_200217_U2OS_TiO2_HCD_OT_rep1.full.mgf.instanovo-1.1.0.transformer.model-instanovo-v1.1.0.denovo.beam-search.beams-5.save-beams.columns-predictions.csv |
1.1.0 | - | v1.1.0 | - | beam search | 5 | instanovo transformer predict -d '<input>' -o '<output>' -i instanovo-v1.1.0 --denovo num_beams=5 save_beams=True batch_size=512 num_workers=4 denovo=True subset=1.0 fp16=True log_interval=1 device=cuda |
| mgf | SF_200217_U2OS_TiO2_HCD_OT_rep1.full.mgf.instanovo-1.1.0.instanovoplus.model-instanovoplus-v1.1.0-alpha.denovo.no-refinement.n-preds-1.csv |
- | 1.1.0 | - | v1.1.0-alpha | - | - | instanovo diffusion predict -d '<input>' -o '<output>' -p instanovoplus-v1.1.0-alpha --denovo --no-refinement -cn instanovoplus refine=False batch_size=512 num_workers=4 denovo=True subset=1.0 fp16=True log_interval=1 device=cuda |
| mgf | SF_200217_U2OS_TiO2_HCD_OT_rep1.full.mgf.instanovo-1.1.0.instanovoplus.model-instanovoplus-v1.1.0-alpha.denovo.refined-from-transformer-greedy.csv |
1.1.0 | 1.1.0 | v1.1.0 | v1.1.0-alpha | greedy | 1 | instanovo diffusion predict -d '<input>' -o '<output>' -p instanovoplus-v1.1.0-alpha --denovo --with-refinement -cn default 'instanovo_predictions_path=<transformer-greedy-output>' id_col=spectrum_id pred_col=predictions +pred_tok_col=predictions_tokenised +log_probs_col=log_probabilities +token_log_probs_col=token_log_probabilities batch_size=512 num_workers=4 denovo=True subset=1.0 fp16=True log_interval=1 device=cuda |
| mgf | SF_200217_U2OS_TiO2_HCD_OT_rep1.full.mgf.instanovo-1.1.3.transformer.model-instanovo-v1.1.0.denovo.greedy.beams-1.columns-preds.csv |
1.1.3 | - | v1.1.0 | - | greedy | 1 | instanovo transformer predict -d '<input>' -o '<output>' -i instanovo-v1.1.0 --denovo num_beams=1 save_beams=False batch_size=512 num_workers=4 denovo=True subset=1.0 fp16=True log_interval=1 device=auto |
| mgf | SF_200217_U2OS_TiO2_HCD_OT_rep1.full.mgf.instanovo-1.1.3.transformer.model-instanovo-v1.1.0.denovo.beam-search.beams-5.save-beams.columns-preds.csv |
1.1.3 | - | v1.1.0 | - | beam search | 5 | instanovo transformer predict -d '<input>' -o '<output>' -i instanovo-v1.1.0 --denovo num_beams=5 save_beams=True batch_size=512 num_workers=4 denovo=True subset=1.0 fp16=True log_interval=1 device=auto |
| mgf | SF_200217_U2OS_TiO2_HCD_OT_rep1.full.mgf.instanovo-1.1.3.instanovoplus.model-instanovoplus-v1.1.0.denovo.no-refinement.n-preds-5.csv |
- | 1.1.3 | - | v1.1.0 | - | - | instanovo diffusion predict -d '<input>' -o '<output>' -p instanovoplus-v1.1.0 --denovo --no-refinement -cn instanovoplus n_preds=5 refine=False use_basic_logging=True batch_size=512 num_workers=4 denovo=True subset=1.0 fp16=True log_interval=1 device=auto |
| mgf | SF_200217_U2OS_TiO2_HCD_OT_rep1.full.mgf.instanovo-1.1.3.instanovoplus.model-instanovoplus-v1.1.0.denovo.no-refinement.n-preds-5.verbose-prediction-columns.csv |
- | 1.1.3 | - | v1.1.0 | - | - | instanovo diffusion predict -d '<input>' -o '<output>' -p instanovoplus-v1.1.0 --denovo --no-refinement -cn instanovoplus n_preds=5 refine=False use_basic_logging=False batch_size=512 num_workers=4 denovo=True subset=1.0 fp16=True log_interval=1 device=auto |
| mgf | SF_200217_U2OS_TiO2_HCD_OT_rep1.full.mgf.instanovo-1.1.3.instanovoplus.model-instanovoplus-v1.1.0.denovo.refined-from-transformer-greedy.n-preds-5.csv |
1.1.3 | 1.1.3 | v1.1.0 | v1.1.0 | greedy | 1 | instanovo diffusion predict -d '<input>' -o '<output>' -p instanovoplus-v1.1.0 --denovo --with-refinement -cn instanovoplus 'instanovo_predictions_path=<transformer-greedy-output>' n_preds=5 use_basic_logging=True batch_size=512 num_workers=4 denovo=True subset=1.0 fp16=True log_interval=1 device=auto |
| mgf | SF_200217_U2OS_TiO2_HCD_OT_rep1.full.mgf.instanovo-1.1.3.instanovoplus.model-instanovoplus-v1.1.0.denovo.refined-from-transformer-greedy.n-preds-5.verbose-prediction-columns.csv |
1.1.3 | 1.1.3 | v1.1.0 | v1.1.0 | greedy | 1 | instanovo diffusion predict -d '<input>' -o '<output>' -p instanovoplus-v1.1.0 --denovo --with-refinement -cn instanovoplus 'instanovo_predictions_path=<transformer-greedy-output>' n_preds=5 use_basic_logging=False batch_size=512 num_workers=4 denovo=True subset=1.0 fp16=True log_interval=1 device=auto |
| mgf | SF_200217_U2OS_TiO2_HCD_OT_rep1.full.mgf.instanovo-1.2.2.transformer.model-instanovo-v1.2.0.denovo.greedy.beams-1.normalized-columns.csv |
1.2.2 | - | v1.2.0 | - | greedy | 1 | instanovo transformer predict -d '<input>' -o '<output>' -i instanovo-v1.2.0 --denovo num_beams=1 save_all_predictions=False batch_size=512 num_workers=4 denovo=True subset=1.0 fp16=True log_interval=1 |
| mgf | SF_200217_U2OS_TiO2_HCD_OT_rep1.full.mgf.instanovo-1.2.2.transformer.model-instanovo-v1.2.0.denovo.beam-search.beams-5.save-all-predictions.normalized-columns.csv |
1.2.2 | - | v1.2.0 | - | beam search | 5 | instanovo transformer predict -d '<input>' -o '<output>' -i instanovo-v1.2.0 --denovo num_beams=5 save_all_predictions=True batch_size=512 num_workers=4 denovo=True subset=1.0 fp16=True log_interval=1 |
| mgf | SF_200217_U2OS_TiO2_HCD_OT_rep1.full.mgf.instanovo-1.2.2.instanovoplus.model-instanovoplus-v1.1.0.denovo.no-refinement.normalized-columns.csv |
- | 1.2.2 | - | v1.1.0 | - | - | instanovo diffusion predict -d '<input>' -o '<output>' -p instanovoplus-v1.1.0 --denovo --no-refinement -cn instanovoplus refine=False batch_size=512 num_workers=4 denovo=True subset=1.0 fp16=True log_interval=1 |
| mgf | SF_200217_U2OS_TiO2_HCD_OT_rep1.full.mgf.instanovo-1.2.2.combined.model-instanovo-v1.2.0.instanovoplus-v1.1.0.denovo.refined.save-all-predictions.csv |
1.2.2 | 1.2.2 | v1.2.0 | v1.1.0 | beam search | 5 | instanovo predict -d '<input>' -o '<output>' -i instanovo-v1.2.0 -p instanovoplus-v1.1.0 --denovo --with-refinement num_beams=5 save_all_predictions=True batch_size=512 num_workers=4 denovo=True subset=1.0 fp16=True log_interval=1 |
| mzML | SF_200217_U2OS_TiO2_HCD_OT_rep1.full.mzml.instanovo-1.0.0.transformer.model-instanovo-v1.0.0.denovo.greedy.beams-1.csv |
1.0.0 | - | v1.0.0 | - | greedy | 1 | python /opt/instanovo-versions/1.0.0/instanovo/transformer/predict.py 'data_path=<input>' model_path=/workspace/models/instanovo-v1.0.0.ckpt 'output_path=<output>' num_beams=1 save_beams=False batch_size=512 num_workers=4 denovo=True subset=1.0 fp16=True log_interval=1 device=cuda |
| mzML | SF_200217_U2OS_TiO2_HCD_OT_rep1.full.mzml.instanovo-1.0.0.transformer.model-instanovo-v1.0.0.denovo.beam-search.beams-5.save-beams.csv |
1.0.0 | - | v1.0.0 | - | beam search | 5 | python /opt/instanovo-versions/1.0.0/instanovo/transformer/predict.py 'data_path=<input>' model_path=/workspace/models/instanovo-v1.0.0.ckpt 'output_path=<output>' num_beams=5 save_beams=True batch_size=512 num_workers=4 denovo=True subset=1.0 fp16=True log_interval=1 device=cuda |
| mzML | SF_200217_U2OS_TiO2_HCD_OT_rep1.full.mzml.instanovo-1.1.0.transformer.model-instanovo-v1.1.0.denovo.greedy.beams-1.columns-predictions.csv |
1.1.0 | - | v1.1.0 | - | greedy | 1 | instanovo transformer predict -d '<input>' -o '<output>' -i instanovo-v1.1.0 --denovo num_beams=1 save_beams=False batch_size=512 num_workers=4 denovo=True subset=1.0 fp16=True log_interval=1 device=cuda |
| mzML | SF_200217_U2OS_TiO2_HCD_OT_rep1.full.mzml.instanovo-1.1.0.transformer.model-instanovo-v1.1.0.denovo.beam-search.beams-5.save-beams.columns-predictions.csv |
1.1.0 | - | v1.1.0 | - | beam search | 5 | instanovo transformer predict -d '<input>' -o '<output>' -i instanovo-v1.1.0 --denovo num_beams=5 save_beams=True batch_size=512 num_workers=4 denovo=True subset=1.0 fp16=True log_interval=1 device=cuda |
| mzML | SF_200217_U2OS_TiO2_HCD_OT_rep1.full.mzml.instanovo-1.1.0.instanovoplus.model-instanovoplus-v1.1.0-alpha.denovo.no-refinement.n-preds-1.csv |
- | 1.1.0 | - | v1.1.0-alpha | - | - | instanovo diffusion predict -d '<input>' -o '<output>' -p instanovoplus-v1.1.0-alpha --denovo --no-refinement -cn instanovoplus refine=False batch_size=512 num_workers=4 denovo=True subset=1.0 fp16=True log_interval=1 device=cuda |
| mzML | SF_200217_U2OS_TiO2_HCD_OT_rep1.full.mzml.instanovo-1.1.0.instanovoplus.model-instanovoplus-v1.1.0-alpha.denovo.refined-from-transformer-greedy.csv |
1.1.0 | 1.1.0 | v1.1.0 | v1.1.0-alpha | greedy | 1 | instanovo diffusion predict -d '<input>' -o '<output>' -p instanovoplus-v1.1.0-alpha --denovo --with-refinement -cn default 'instanovo_predictions_path=<transformer-greedy-output>' id_col=spectrum_id pred_col=predictions +pred_tok_col=predictions_tokenised +log_probs_col=log_probabilities +token_log_probs_col=token_log_probabilities batch_size=512 num_workers=4 denovo=True subset=1.0 fp16=True log_interval=1 device=cuda |
| mzML | SF_200217_U2OS_TiO2_HCD_OT_rep1.full.mzml.instanovo-1.1.3.transformer.model-instanovo-v1.1.0.denovo.greedy.beams-1.columns-preds.csv |
1.1.3 | - | v1.1.0 | - | greedy | 1 | instanovo transformer predict -d '<input>' -o '<output>' -i instanovo-v1.1.0 --denovo num_beams=1 save_beams=False batch_size=512 num_workers=4 denovo=True subset=1.0 fp16=True log_interval=1 device=auto |
| mzML | SF_200217_U2OS_TiO2_HCD_OT_rep1.full.mzml.instanovo-1.1.3.transformer.model-instanovo-v1.1.0.denovo.beam-search.beams-5.save-beams.columns-preds.csv |
1.1.3 | - | v1.1.0 | - | beam search | 5 | instanovo transformer predict -d '<input>' -o '<output>' -i instanovo-v1.1.0 --denovo num_beams=5 save_beams=True batch_size=512 num_workers=4 denovo=True subset=1.0 fp16=True log_interval=1 device=auto |
| mzML | SF_200217_U2OS_TiO2_HCD_OT_rep1.full.mzml.instanovo-1.1.3.instanovoplus.model-instanovoplus-v1.1.0.denovo.no-refinement.n-preds-5.csv |
- | 1.1.3 | - | v1.1.0 | - | - | instanovo diffusion predict -d '<input>' -o '<output>' -p instanovoplus-v1.1.0 --denovo --no-refinement -cn instanovoplus n_preds=5 refine=False use_basic_logging=True batch_size=512 num_workers=4 denovo=True subset=1.0 fp16=True log_interval=1 device=auto |
| mzML | SF_200217_U2OS_TiO2_HCD_OT_rep1.full.mzml.instanovo-1.1.3.instanovoplus.model-instanovoplus-v1.1.0.denovo.no-refinement.n-preds-5.verbose-prediction-columns.csv |
- | 1.1.3 | - | v1.1.0 | - | - | instanovo diffusion predict -d '<input>' -o '<output>' -p instanovoplus-v1.1.0 --denovo --no-refinement -cn instanovoplus n_preds=5 refine=False use_basic_logging=False batch_size=512 num_workers=4 denovo=True subset=1.0 fp16=True log_interval=1 device=auto |
| mzML | SF_200217_U2OS_TiO2_HCD_OT_rep1.full.mzml.instanovo-1.1.3.instanovoplus.model-instanovoplus-v1.1.0.denovo.refined-from-transformer-greedy.n-preds-5.csv |
1.1.3 | 1.1.3 | v1.1.0 | v1.1.0 | greedy | 1 | instanovo diffusion predict -d '<input>' -o '<output>' -p instanovoplus-v1.1.0 --denovo --with-refinement -cn instanovoplus 'instanovo_predictions_path=<transformer-greedy-output>' n_preds=5 use_basic_logging=True batch_size=512 num_workers=4 denovo=True subset=1.0 fp16=True log_interval=1 device=auto |
| mzML | SF_200217_U2OS_TiO2_HCD_OT_rep1.full.mzml.instanovo-1.1.3.instanovoplus.model-instanovoplus-v1.1.0.denovo.refined-from-transformer-greedy.n-preds-5.verbose-prediction-columns.csv |
1.1.3 | 1.1.3 | v1.1.0 | v1.1.0 | greedy | 1 | instanovo diffusion predict -d '<input>' -o '<output>' -p instanovoplus-v1.1.0 --denovo --with-refinement -cn instanovoplus 'instanovo_predictions_path=<transformer-greedy-output>' n_preds=5 use_basic_logging=False batch_size=512 num_workers=4 denovo=True subset=1.0 fp16=True log_interval=1 device=auto |
| mzML | SF_200217_U2OS_TiO2_HCD_OT_rep1.full.mzml.instanovo-1.2.2.transformer.model-instanovo-v1.2.0.denovo.greedy.beams-1.normalized-columns.csv |
1.2.2 | - | v1.2.0 | - | greedy | 1 | instanovo transformer predict -d '<input>' -o '<output>' -i instanovo-v1.2.0 --denovo num_beams=1 save_all_predictions=False batch_size=512 num_workers=4 denovo=True subset=1.0 fp16=True log_interval=1 |
| mzML | SF_200217_U2OS_TiO2_HCD_OT_rep1.full.mzml.instanovo-1.2.2.transformer.model-instanovo-v1.2.0.denovo.beam-search.beams-5.save-all-predictions.normalized-columns.csv |
1.2.2 | - | v1.2.0 | - | beam search | 5 | instanovo transformer predict -d '<input>' -o '<output>' -i instanovo-v1.2.0 --denovo num_beams=5 save_all_predictions=True batch_size=512 num_workers=4 denovo=True subset=1.0 fp16=True log_interval=1 |
| mzML | SF_200217_U2OS_TiO2_HCD_OT_rep1.full.mzml.instanovo-1.2.2.instanovoplus.model-instanovoplus-v1.1.0.denovo.no-refinement.normalized-columns.csv |
- | 1.2.2 | - | v1.1.0 | - | - | instanovo diffusion predict -d '<input>' -o '<output>' -p instanovoplus-v1.1.0 --denovo --no-refinement -cn instanovoplus refine=False batch_size=512 num_workers=4 denovo=True subset=1.0 fp16=True log_interval=1 |
| mzML | SF_200217_U2OS_TiO2_HCD_OT_rep1.full.mzml.instanovo-1.2.2.combined.model-instanovo-v1.2.0.instanovoplus-v1.1.0.denovo.refined.save-all-predictions.csv |
1.2.2 | 1.2.2 | v1.2.0 | v1.1.0 | beam search | 5 | instanovo predict -d '<input>' -o '<output>' -i instanovo-v1.2.0 -p instanovoplus-v1.1.0 --denovo --with-refinement num_beams=5 save_all_predictions=True batch_size=512 num_workers=4 denovo=True subset=1.0 fp16=True log_interval=1 |
Files
*.csv: individual full prediction CSV outputs. File names include the input format, InstaNovo package version, model/checkpoint, and prediction/refinement options.prediction_manifest.csvandprediction_manifest.json: prediction runner output manifests.SHA256SUMS: checksums for uploaded files.
Files
prediction_manifest.csv
Files
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md5:03a7641792742312a1b843ebd084edfd
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- Is derived from
- Publication: 10.1038/s42256-025-01019-5 (DOI)