PepFoot is intended for analysis and discovery in peptide footprinting, however it may be expanded to encompass more in future releases. PepFoot is released under the LGPL-3.0 license
If you use this software please cite the following article:
- Bellamy-Carter, J; Oldham, N. J. PepFoot: a software package for semi-automated processing of protein footprinting data. J. Proteome Res. 2019, 18, 2925−2930. doi: 10.1021/acs.jproteome.9b00238
PepFoot is currently maintained by Jedd Bellamy-Carter, University of Nottingham. Any queries or improvements to the software should be directed there or by submitting an issue on GitHub.
- A User Guide is provided with the latest release of PepFoot.
- Additional instructions may be found in this repository's wiki
- A Video showing basic PepFoot usage is available.
- Example
.pfootfiles are available for OmpF1 and USP52 datasets, PXD007207 and PXD004971 respectively.
Download the appropriate file from Releases and follow the instructions below.
To install PepFoot simply run the pepFoot_1_1_WinOS.exe installer and follow the wizard. The full PepFoot GUI should then run without problem.
To install PepFoot simply mount the pepFoot_1_1_MacOSX.dmg file and drag pepFoot.app into your Applications. The full PepFoot GUI can then be accessed from this app.
It is recommended to run PepFoot through your local Python3 distribution for security. To install PepFoot simply extract pepFoot_1_1_Python.zip and run python setup.py install --user. This will add the command pepfoot to your local Python distribution as well as handle the package dependencies described below. Launching pepfoot from a terminal will launch the full PepFoot GUI.
Linux users can add pepFoot.desktop to your local applications directory and place a copy of pepFoot.png in your local icons directory. This .desktop file can now be used to launch the full PepFoot GUI.
- Python 3
- PyQt >= 5.11
- This software require
WebEngine, this was split into a separate package from 5.12, usePyQt5==5.11.2if unsure.
- This software require
- matplotlib
- numpy
- scipy
- pyteomics
- h5py
NGL viewer is provided by the minified file ngl.js that is included in this directory.
PepFoot .pfoot files are a human-readable JSON file. The keys correspond to the following schema:
| Key | Description |
|---|---|
| name | Project name |
| creation date | Creation datetime of project |
| data files | List of data files [filepath1, filepath2, ...] |
| sequence | Sequence of protein |
| length range | Peptide length range parameters |
| charge range | Charge state range parameters |
| enzyme | Enzyme used for cleavage |
| missed cleave | Number of missed cleavages |
| fixed mods | List of fixed modifications applied to protein |
| differential mod | Differential modification applied to peptides |
| peptides | 1xN array of peptide ids e.g. 1-15 |
| m/z array | 2xN array of m/z ranges for analysis [[unmod m/z, ...],[mod m/z, ...]] |
| charge array | 1xN array of peptide charges |
| rt array | 2xN array of rt ranges for analysis [[unmod rt, ...],[mod rt, ...]] |
| areas | 2xNxM array of area values from analysis [[unmod area, ...],[mod area, ...], ...] |
| fractional mod | NxM array of fractional modification values from analysis |
| treatment | Nested list with indices for data files grouped by treatment [[#, ...],[#, ...]] |
| pdb file | PDB file associated with project |
1: Manzi, L.; Barrow, A. S.; Hopper, J. T.; Kaminska, R.; Kleanthous, C.; Robinson, C. V.; Moses, J. E.; Oldham, N. J. Carbene Footprinting Reveals Binding Interfaces of a Multimeric Membrane-Spanning Protein. Angew. Chemie - Int. Ed. 2017, 56, 14873–14877.
2: Manzi, L.; Barrow, A. S.; Scott, D.; Layfield, R.; Wright, T. G.; Moses, J. E.; Oldham, N. J. Carbene footprinting accurately maps binding sites in protein-ligand and protein-protein interactions. Nat. Commun. 2016, 7, 1–9.