---

New Version Available: PepFoot version v1.2 has now been released, with added functionality.

---

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, Loughborough University. Any queries or improvements to the software should be directed there or by submitting an issue on GitHub.

How to Use

• 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 .pfoot files are available for OmpF¹ and USP5² datasets, PXD007207 and PXD004971 respectively.

Installing

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

Windows

To install PepFoot simply run the pepFoot_1_2_1_WinOS.exe installer and follow the wizard. The full PepFoot GUI should then run without problem.

Linux/Python Users

It is recommended to run PepFoot through your local Python3 distribution for security. To install PepFoot simply extract pepFoot_1_2_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.

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 above

Requirements

• Python 3
• PyQt >= 5.11
  • This software requires PyQtWebEngine, this was split into a separate package from 5.12, run pip install PyQtWebEngine if unsure.
• matplotlib
• numpy
• scipy
• pyteomics
• h5py
• requests

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

Change Log

1.2.1

• Fixes bug with startup 'Check for Updates' that caused crashes when offline or on spotty networks.

1.2.0

• Improved UI features:
  • Default mouse action is 'zoom' to prevent unwanted integration/extraction.
  • Refactored spectrum generation to prevent apparent peak splitting.
  • Keyboard shortcuts for copying plots to clipboard. Ctrl+C on main plots.
• Extension of Export to CSV so that extent of modification is included (this has also been added to the Analysis viewer).
• Update checker added. PepFoot will routinely check for a new release on start-up.
• Open Recent projects menu is fully functioning.

1.1.3

• Improved support for Bruker data files.
• Handles 'empty' MSn scans.
• Max number of missed cleavages increased.

1.1.2

• In-software access to msconvert and import of non-.mz5 data files. See the wiki for more details.
• Fixes bug where some user set modifications were not properly stored.
• Note: the last version of PepFoot with a working .dmg installer for MacOS.

1.1.0

• First public release of PepFoot.

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.