---
license: other
license_name: embl-ebi-terms-of-use
license_link: https://www.ebi.ac.uk/about/terms-of-use/
configs:
- config_name: default
  data_files:
  - split: train
    path: dataset-phospho-train-*.parquet
  - split: validation
    path: dataset-phospho-valid-*.parquet
  - split: test
    path: dataset-phospho-test-*.parquet
dataset_info:
  features:
  - name: sequence
    dtype: string
  - name: precursor_charge
    dtype: int64
  - name: precursor_mz
    dtype: float64
  - name: mz_array
    sequence: float64
  - name: intensity_array
    sequence: float64
  - name: experiment_name
    dtype: string
tags:
- biology
size_categories:
- 1M<n<10M
---


# Dataset Card for InstaNovo-P finetuning data

The dataset used for fine tuning InstaNovo-P is comprised of a collection of reprocessed PRIDE projects in [Scop3P](https://pubs.acs.org/doi/10.1021/acs.jproteome.0c00306). (For a list of the projects, see [Dataset Sources](https://huggingface.co/datasets/InstaDeepAI/InstaNovo-P#dataset-sources)). 

- **Curated by:** Jesper Lauridsen, Pathmanaban Ramasamy
- **License:** [EMBL-EBI terms of use](https://www.ebi.ac.uk/about/terms-of-use/)

## Dataset Details

### Dataset Description

The dataset originally contains 4,053,346 PSMs. To only fine-tune on high confidence PSMs, the dataset is filtered at a confidence threshold of 0.80, reducing it to 2,760,939 PSMs, representing 74,686 unique peptide sequences. Most of the data is of human origin, except for [PXD005366](https://www.ebi.ac.uk/pride/archive/projects/PXD005366) and [PXD000218](https://www.ebi.ac.uk/pride/archive/projects/PXD000218), which contain a mix of human and mouse. All PSMs that were used to train the model contained at least one phosphorylated site, while 169, 114 PSMs
( 6%) contained oxidated methionine. 

### Dataset Structure

To partition the fine-tuning dataset into training, validation and test, [GraphPart](https://academic.oup.com/nargab/article/5/4/lqad088/7318077), an algorithm for homology partitioning, was applied on the set of unique peptide sequences. GraphPart was set to use [MMseqs2](https://www.nature.com/articles/nbt.3988) with a partitioning threshold of 0.8 and a train-validation-test ratio of 0.7/0.1/0.2 . Of the 74,686 unique sequences, 390 were removed by GraphPart, reducing the total number of PSMs to 2,691,117 in a 2,008,923/232,641/449,553-split, although during training, a random subset of only 2% of the validation set was used in order to reduce computation.

### Dataset Sources

PRIDE Accession codes used for training, validation and test sets:

* [PXD006482](https://www.ebi.ac.uk/pride/archive/projects/PXD006482) (1)
* [PXD005366](https://www.ebi.ac.uk/pride/archive/projects/PXD005366) (2)
* [PXD004447](https://www.ebi.ac.uk/pride/archive/projects/PXD004447) (3)
* [PXD004940](https://www.ebi.ac.uk/pride/archive/projects/PXD004940) (4)
* [PXD004452](https://www.ebi.ac.uk/pride/archive/projects/PXD004452) (5)
* [PXD004415](https://www.ebi.ac.uk/pride/archive/projects/PXD004415) (6)
* [PXD004252](https://www.ebi.ac.uk/pride/archive/projects/PXD004252) (7)
* [PXD003198](https://www.ebi.ac.uk/pride/archive/projects/PXD003198) (8)
* [PXD003657](https://www.ebi.ac.uk/pride/archive/projects/PXD003657) (9)
* [PXD003531](https://www.ebi.ac.uk/pride/archive/projects/PXD003531) (10)
* [PXD003215](https://www.ebi.ac.uk/pride/archive/projects/PXD003215) (11)
* [PXD002394](https://www.ebi.ac.uk/pride/archive/projects/PXD002394) (12)
* [PXD002286](https://www.ebi.ac.uk/pride/archive/projects/PXD002286) (13)
* [PXD002255](https://www.ebi.ac.uk/pride/archive/projects/PXD002255) (14)
* [PXD002057](https://www.ebi.ac.uk/pride/archive/projects/PXD002057) (15)
* [PXD001565](https://www.ebi.ac.uk/pride/archive/projects/PXD001565) (16)
* [PXD001550](https://www.ebi.ac.uk/pride/archive/projects/PXD001550) (17)
* [PXD001546](https://www.ebi.ac.uk/pride/archive/projects/PXD001546) (17)
* [PXD001060](https://www.ebi.ac.uk/pride/archive/projects/PXD001060) (18)
* [PXD001374](https://www.ebi.ac.uk/pride/archive/projects/PXD001374) (19)
* [PXD001333](https://www.ebi.ac.uk/pride/archive/projects/PXD001333) (20)
* [PXD000474](https://www.ebi.ac.uk/pride/archive/projects/PXD000474) (21)
* [PXD000612](https://www.ebi.ac.uk/pride/archive/projects/PXD000612) (22)
* [PXD001170](https://www.ebi.ac.uk/pride/archive/projects/PXD001170) (23)
* [PXD000964](https://www.ebi.ac.uk/pride/archive/projects/PXD000964) (24)
* [PXD000836](https://www.ebi.ac.uk/pride/archive/projects/PXD000836) (25)
* [PXD000674](https://www.ebi.ac.uk/pride/archive/projects/PXD000674) (26)
* [PXD000680](https://www.ebi.ac.uk/pride/archive/projects/PXD000680) (27)
* [PXD000218](https://www.ebi.ac.uk/pride/archive/projects/PXD000218) (28)

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17/25
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26. Publication pending
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