license: cc0-1.0
configs:
- config_name: data
data_files:
- split: XL_all
path: data/XL_all-*
- split: XL_inter
path: data/XL_inter-*
- split: XL_intra
path: data/XL_intra-*
- split: XL_Alkyne_BVSC
path: data/XL_Alkyne_BVSC-*
- split: XL_BS3
path: data/XL_BS3-*
- split: XL_DSBU_d12
path: data/XL_DSBU_d12-*
- split: XL_DSS
path: data/XL_DSS-*
- split: XL_DSSO
path: data/XL_DSSO-*
- split: XL_sulfo_SDA
path: data/XL_sulfo_SDA-*
- split: XL_TTD
path: data/XL_TTD-*
- split: XL_UCCL
path: data/XL_UCCL-*
- split: XL_VSD
path: data/XL_VSD-*
- split: XL_VTT
path: data/XL_VTT-*
dataset_info:
features:
- name: Data Source
dtype: string
- name: Crosslinker
dtype: string
- name: Accession A
dtype: string
- name: Accession B
dtype: string
- name: Residue A
dtype: int64
- name: Residue B
dtype: int64
- name: XL Type
dtype: string
- name: XL Distance
dtype: float64
splits:
- name: XL_all
num_bytes: 5702295
num_examples: 75038
- name: XL_inter
num_bytes: 1386289
num_examples: 17264
- name: XL_intra
num_bytes: 4316006
num_examples: 57774
- name: XL_Alkyne_BVSC
num_bytes: 6480
num_examples: 80
- name: XL_BS3
num_bytes: 278709
num_examples: 3793
- name: XL_DSBU_d12
num_bytes: 4446
num_examples: 57
- name: XL_DSS
num_bytes: 879796
num_examples: 12052
- name: XL_DSSO
num_bytes: 2720767
num_examples: 35352
- name: XL_sulfo_SDA
num_bytes: 996190
num_examples: 12610
- name: XL_TTD
num_bytes: 100302
num_examples: 1374
- name: XL_UCCL
num_bytes: 214306
num_examples: 2853
- name: XL_VSD
num_bytes: 287036
num_examples: 3932
- name: XL_VTT
num_bytes: 214182
num_examples: 2934
download_size: 1683784
dataset_size: 17106804
pretty_name: PRIDE Crosslinking Archive
PRIDE Crosslinking Archive
This dataset aggregates publicly available crosslinking mass spectrometry (XL-MS) datasets from the PRIDE repository. Each dataset is curated and categorized by crosslinking reagent a link type (inter-chain vs intra-chain). For intra-chain links where the protein can be mapped to a UniProt ID, each link is mapped onto the corresponding AlphaFold Database (AFDB) structure, and the Cα-Cα distance for the linked residue pair is reported.
The result is a standardized resource for analyzing XL-MS constraints across reagents and for benchmarking/evaluating integrative modeling pipelines.
Quickstart Usage
Install HuggingFace Datasets package
Each subset can be loaded into python using the Huggingface datasets library.
First, from the command line install the datasets library
$ pip install datasets
Optionally set the cache directory, e.g.
$ HF_HOME=${HOME}/.cache/huggingface/
$ export HF_HOME
then, from within python load the datasets library
>>> import datasets
Load datasets
To load one of the PRIDE_Crosslinking_Archive datasets, use datasets.load_dataset(...)
>>> dataset = datasets.load_dataset(
path="RosettaCommons/PRIDE_Crosslinking_Archive",
name="data",
data_dir="data"
)["XL_all"]
Dataset Details
Dataset Description
This dataset is a curated collection of crosslinking mass spectrometry (XL-MS) identifications sourced from PRIDE submissions and transformed into a consistent tabular format. Each record represents a single crosslink observation annotated with:
- Crosslinking reagent(e.g., DSS/BS3/DSBU, etc.)
- Crosslink type (inter-chain vs intra-chain)
- UniProt Accession IDs for each crosslinked protein
- Residue positions for the linked sites
- For intra-chain crosslinks, Cα-Cα distance, calculated from AlphaFold Database structures
Alongside the full, merged table, the dataset includes inter/intra-chain splits, as well as per-crosslinker splits (one split per reagent). These splits should make it easy to analyze reagent-specific distance distributions and restraint behavior without additional filtering.
Why AFDB distance mapping is included
A large fraction of downstream XL-MS analysis involves asking whether observed links are structurally plausible under a given model and/or what they imply about conformational states. By projecting intra-chain links onto AFDB structures, this dataset provides a standardized starting point for:
Comparing distance distributions across reagents
Identifying long-distance outliers that may indicate flexible regions or alternate conformations
Generating restraint sets for integrative modeling and benchmarking
Uses
This dataset is intended to be used as a benchmark/calibration set for integrative modeling workflows. Included crosslinks can be used as a constraint set to evaluate predicted or refined models (AlphaFold/AlphaLink/integrative models) by measuring what fraction of links fall below chosen distance thresholds. Long-distance outliers in this dataset can also be used to identify proteins/protein families in which contemporary structure prediction methods fail to recapitulate experimental observations.
Limitations
This dataset does not contain all of the identified crosslinks in the PRIDE repository. Only links with valid UniProt identifiers were included in this set.
Source Data
Crosslinks were obtained from the PRIDE Crosslinking Archive (PRIDE)
Dataset Curator/Dataset Card Author
Elijah Day (ehday@ucla.edu)