InstaNovo prediction sample files for PDV import validation

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 HBM3 GPU. 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.csv and prediction_manifest.json: prediction runner output manifests. SHA256SUMS: checksums for uploaded files.