This software is available under a dual licensing model:

Non-Commercial Use

For non-commercial use, this software is licensed under the GNU General Public License v3.0 (GPL-3.0). This means you can use, modify, and distribute the software freely, provided that: Any derivative works or modifications you make must also be licensed under GPL-3.0 You provide access to the source code when you distribute the software You clearly display copyright notices and a copy of the license You state any changes made to the program The full text of the GPL-3.0 license is included in the LICENSE-GPL3 file distributed with this software and can also be found at: https://www.gnu.org/licenses/gpl-3.0.html [gnu.org]

Commercial Use

For commercial use, including but not limited to: Integration into proprietary software Use in corporate environments Revenue-generating applications Products or services sold to customers Please contact contact@uominnovationfactory.com to obtain a commercial license. Our commercial licenses provide additional rights for commercialisation and remove the copyleft requirements of GPL-3.0, allowing you to incorporate our software into your proprietary products without the obligation to release your source code.

Third-Party Components

This software utilises third-party libraries which are distributed under their own licenses which can be found in the “3rd Part Licenses” folder in this repo: Tkinter, os, datetime, subprocess, random: Python Software Foundation License Pandas, NumPy: BSD 3-Clause License Matplotlib: Matplotlib License (based on PSF) These third-party licenses are compatible with both our GPL-3.0 and commercial licensing options.

MPM 2 still contains all functionalities and the same processing, merging and filtering logic as version 1. However, version 2 comes with some big improvements, the main ones being listed here: 1. Generate Mobility vs. Mobility at FWHM ion distribution graphs and predict trendlines 2. Academics with access to the ApexRT ion-ID algorithm (currently in development) can choose to use it instead of Apex3D (simply put the executables in the C:\PLGS3.0.3\lib\apex3d folder). 3. Suspicious peptides window – peptides with similar retention times and theoretical masses are highlighted as potential misidentifications 4. Export your final peptide list in the HDExaminer format, which separates single pass (SP) and multipass (MP) peptides into two different lists, as the mobilities will differ (DynamX does not use mobility, hence this is only an issue with HDExaminer). That way users know if a peptide is marked as red due to the mobility being off. 5. Samples can be marked and included/excluded dynamically – sample replicates can be grouped by giving them the same number

1. MassLynx (Waters) to acquire data
2. ProteinLynx Global Server (Waters) for the ion/peptide search algorithm
3. Multi-Pass Merger (Politis Group) to process, merge and filter data
4. DynamX (Waters)or HDExaminer (Trajan) or any other software that allows you to input IM-HDMSe data in the form of .csv excel files for manual mass-spectra assessments

1. A SELECT SERIES cyclic ion-mobility mass spectrometer by Waters
2. A target protein you want to conduct peptide mapping on
3. Any set-up that allows you to get peptides (e.g. a UPLC system with a pepsin column followed by a reverse-phase C18 chromatographic column and a trap; see our publications for details)
4. A Windows 10 or higher computer to process data on