Elhabashy Lab

You can choose to run the full CLAUDIO pipeline, or only a specific module. For details on the different modules, please consult the documentation.

Here you can upload your cross-linking mass spectrometry data in a comma separated value file (.csv).

Module 1 (Data Preparation) takes a raw XL-MS CSV file and prepares it for the subsequent structural and OPS analyses.

The input file must contain columns: "peptide1", "peptide2", "position1", "position2", "k_pos1", "k_pos2", "entry1", "entry2".

peptide1 and peptide2: Peptide sequences

position1 and position2: Starting positions of the corresponding peptide in protein sequence

k_pos1 and k_pos2: Position of the linked residue in the corresponding peptide

entry1 and entry2: UniProtID for corresponding protein.

If your CSV uses different header names, use the projections field to map your columns in this order: peptide1, peptide2, position1, position2, k_pos1, k_pos2, entry1, entry2.

You can leave the columns k_pos1 and k_pos2 empty if you do not have the information available, since they are only used if the peptide positions provided do not match the retrieved UniProt sequence and need to be validated.

Module 2 (Structural Analysis) takes the output of Module 1 (a .sqcs file) and performs a structural distance analysis by searching for 3D structures in RCSB-PDB and AlphaFold. It is recommended to run Module 1 first. If you are providing a custom input file, ensure it has the extension ".sqcs" and the required columns.

Module 3 (OPS Analysis) takes the output of Module 1 (a .sqcs file) and performs an ordered-pair statistics (OPS) analysis. It is recommended to run Module 1 first before using this module.

Module 4 (XL Classification) combines the results of Modules 2 and 3 to classify cross-links. It requires two input files: the structural distance output from Module 2 (.csv) and the OPS output from Module 3 (.csv).

The cross-linker parameters are used in the structural analysis to compute distances between cross-linked residues. They depend on the used cross-linker.

The linker minimum and linker maximum range are the lower and the upper limits that should be considered valid for the used cross-linker.

Cross-linking residues specify which residues the cross-linker binds to. It should be a comma-separated list of one-letter coded amino acids, optionally followed by two colon-separated specifiers for atom type (N, CA, C, O, CB) and position (0=anywhere, 1=N-terminus, -1=C-terminus).

ex.: "K:CB:0" — distance between lysine C-beta atoms at any position.

The e-value, query identity and coverage control the search query used to find structures from RCSB-PDB.

The e-value is the probability of finding a match by chance, in the range [0,1].

The query identity is the percentage of identical residues in the match, in the range [0,100].

The coverage is the percentage of the query sequence included in the match, in the range [0,100].

The resolution and pLDDT cutoff pose lower limits on the quality of 3D structures used.

The resolution cutoff is an upper limit on the resolution (Å) for RCSB-PDB structures.

The pLDDT is a per-residue confidence measure for AlphaFold models (range 0–100). Values above 70 indicate good quality.

If compute-scoring is enabled, an inter-interaction confidence score is computed in the range [0,1], where 1 indicates the highest confidence in observing an inter-link.

Euclidean strictness: a value subtracted from the euclidean distances for scoring (≥0, or leave the checkbox unchecked to exclude euclidean distances from scoring).

Distance maximum: an upper cap on distances during scoring.

Cutoff: threshold above which a cross-link is classified as an inter-link.

You can download your current settings in a file or upload a file with predefined settings.

Settings files store form parameters only. Uploaded data files are not included.