Kingfisher HDX-MS v2.0

Interactive HDX-MS analysis, visualization, and structural mapping.

Developed by JuaNolan at Washington University in St. Louis

This application supports HDX-MS data import, statistical comparison, functional fitting, visualization, structural mapping, and export of final results.

HDX-MS Statistics Kinetics Woods plots 3D mapping Export

Example CSV Example FASTA

Overview

Documentation by section

Select a section below to view the corresponding guide.

Choose a guide:

Contact

For questions, suggestions, or support:

Juan P Rincon
Nolan McLaughlin

Data import and experiment details

Upload your HDX-MS CSV file and FASTA file, then define the experimental design used for your dataset.

Select exported CSV file from HDExaminer

Browse...

Check an option if you are NOT using HDExaminer output file

WATERS/DynamX output file

Custom .csv output file

Select FASTA file

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Number of protein states

Number of labeling times

Significance level

Number of replicates per labeling time

Number of residues that can't withhold deuteration:

1 2

Labeling times in seconds (separated by commas):

Download a test .csv file here

Download a test FASTA file here

Statistical analysis

This panel displays hybrid significance volcano plots and, when clustering is enabled, histograms of normalized differences.

Quick overview of peptide-level statistical outcomes for the selected comparison.

Volcano plot

Use zoom and hover to inspect peptide-level differences interactively.

Optional clustering

Check to cluster the data

Select color for strong effects:

Select color for intermediate effects:

Export options

Histogram of normalized differences

Functional data analysis

Fit kinetic models to peptide uptake curves, visualize fitted profiles, and compare states using forest and Manhattan plots.

Select the desired equation to fit the data:

Input initial parameters:

Provide starting values for non-linear fitting. Good starting values can improve convergence and reduce failed fits.

Parameter a:

Parameter b:

Parameter d:

Parameter p:

Displays the full qFeatures-derived exchange matrix across all samples and timepoints.

Download Heat map

Inspect fitted uptake curves and forest plots for individual peptides. Use the selector below to move between peptides.

Select peptide:

Download kinetic plot

Compares peptide-level statistical evidence across the selected labeling timepoint.

Select labeling time:

Download Manhattan plot

Global Woods plot

Shows residue coverage and significance across all peptides in a single global view.

Select color for peptides with increased flexibility:

Select color for peptides with increased protection:

Woods plot by timepoint

Displays peptide-level ΔHX values along the sequence for one labeling time at a time.

Digestion efficiency

Summarizes peptide coverage, average peptide length, and redundancy across the sequence.

Peptide length distribution

Distribution of peptide lengths observed in the current digestion dataset.

Peptide map

Visualizes peptide coverage across the protein sequence, with both a compact overview and the full stacked peptide layout.

Summary peptide map

Compact overview of total sequence coverage and peptide stacking.

Detailed peptide map

Detailed stacked peptide map across the protein sequence.

Display and export options

Select color for peptides:

Uptake plots

Display uptake curves for the selected peptide, compare protein states, and customize the plot appearance.

Plot settings

Color palette

Solarized

Chalk

Dust

Line thickness

Font size

Axis settings

Y min

Y max

Additional display options

Extra display controls will appear here when available.

Show all protein states

Selected peptide uptake profile

Use the peptide selector in the sidebar to switch peptides. The plot updates automatically.

3D Structure

Visualize significant peptides on a protein structure, compare FASTA and PDB sequence alignment, and export screenshots or PyMOL scripts.

1. Load structure

2. Visualization settings

Cluster colors

3. Export

Save a screenshot of the current view or export a PyMOL coloring script.

Color legend

Default significance mode

No significant change

Mixed behavior

Increased flexibility

Increased protection

If clustering mode is enabled, colors indicate effect strength rather than protection/deprotection.

Tip: rotate the structure with the mouse, zoom with the wheel, and use the offset to align residue numbering.

Sequence alignment preview

Compare the FASTA sequence with the shifted PDB sequence. The amino acid offset will move the PDB sequence accordingly.

Export results

Download the full analysis workbook and export the generated plots for reporting or publication.

Frequently Asked Questions

Common questions about Kingfisher.

About

Project background, contributors, and supporting information.