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License Release Downloads Python

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:

PepFoot is currently maintained by Jedd Bellamy-Carter, University of Birmingham. Any queries or improvements to the software should be directed there or by submitting an issue on GitHub.

How to Use

Installing

Download the appropriate file from Releases and follow the instructions below.

Windows

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.

MacOSX

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. Note: the latest .dmg version of PepFoot is v1.1.2 compiled on El Capitan, if you require the most up-to-date version for MacOS then please use the python package as described below

Linux/Python Users

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.

Requirements

NGL viewer is provided by the minified file ngl.js that is included in this directory.

Project Schema

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

References

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.