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MassXpert3 User Manual
MassXpert3 User Manual
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###### MassXpert3 10.4.3

# MassXpert3 User Manual

## Modelling and simulating mass spectrometric data of linear polymers

Author: Filippo Rusconi
Publication Date: April 14, 2026 , Version: 10.4.3

# Dedication

To María Cecilia

To all the admirable people acting in the “Free Software Movement” for a better and more ethical computing world

To all involved in the development of the K Desktop Environment (KDE)

To all the readers who helped me with this manual.

1 Addresses to report feedback to
2.1 Peptidic bond formation by condensation.
2.2 End capping chemistry of the protein polymer.
2.3 Phosphodiester bond formation by esterification.
2.4 End capping chemistry of the nucleic acid polymer.
2.5 Osidic bond formation by condensation.
2.6 End capping chemistry of the polysaccharidic polymer.
2.7 Protein cleavage by water and cyanogen bromide
2.8 Protein fragmentation patterns most widely encountered.
2.9 Peptide product ion mass calculation for the different ion series
2.10 DNA fragmentation patterns most widely encountered.
2.11 Nucleic acids product ion mass calculation for the different ion series
3.1 select one polymer chemistry definition file.
3.2 Polymer chemistry definition window.
3.3 Isotopes definitions
3.4 Monomer definition
3.5 Monomer mass differences
3.6 Modification definition
3.7 Cross-linker definition
3.8 Cleavage specification definition
3.9 Fragmentation rule definition
3.10 Fragmentation definition with generic specification
3.11 Fragmentation definition with specific rules
4.1 Selection of a sample polymer sequence
4.2 Selection of the polymer chemistry definition
4.3 The XpertEdit main window
4.4 Multi-character code sequence editing in XpertEdit
4.5 Bad code character in XpertEdit sequence editor
4.6 Finding a sequence motif in the polymer sequence
4.7 Clipboard-imported sequence error-checking
4.8 Clipboard-imported sequence purification
4.9 Modification of a monomer in a polymer sequence
4.10 Rendering of a monomer modification in a polymer sequence
4.11 Modification of the left end of a polymer sequence
4.12 Cross-linking of monomers
4.13 Polymer sequence cleavage window
4.14 Oligomer fragmentation window
4.15 Starting a fragmentation that accounts the cross-links
4.16 Complicated cross-linking situation
4.17 Searching masses in a polymer sequence
4.18 Oligomer data filtering
4.19 Calculation of ranges of m/z ratios
4.20 Determination of the compositions
4.21 Different pKa values for a number of amino-acids' chemical groups
4.22 Acido-basic computations: net charges
5.1 Selecting a polymer chemistry definition for use with XpertCalc
5.2 Interface of the XpertCalc module
5.3 Interface of the chemical pad
5.4 The XpertCalc recorder window
6.1 mzLab window
6.2 m﻿/﻿z list's empty input m﻿/﻿z list dialog window.
6.3 m﻿/﻿z list's data-filled input m﻿/﻿z list dialog window
6.4 m﻿/﻿z list's (m﻿/﻿z) textual data-filled input m﻿/﻿z list dialog window.
6.5 m﻿/﻿z list's (m﻿/﻿z,z) textual data-filled input m﻿/﻿z list dialog window.
6.6 Match operation between two m﻿/﻿z lists, output list dialog window.
7.1 The scripting console window
7.2 Mass spectrum as generated using the script displayed in MineXpert
8.1 Simulation of the isotopic cluster for a protein
8.2 Isotopic clusters main menu
8.3 Isotopic cluster generator window
8.4 User-modified standard element table
8.5 Isotopic exported from the isotopic data table view'
8.6 Hand-made user isotopic configuration of an elemental composition
8.7 Typical manual configuration of the isotopic characteristics of the chemical elements
8.8 The user manual configuration might be exported to a text file and loaded back
8.9 Results from the isotopic cluster calculation
8.10 Setting-up of the centroid mass peak shaping process
8.11 Shaped peaks mass spectral data
8.12 Isotopic cluster automatically displayed in MineXpert
8.13 Combination of mass spectra obtained for different isotopic cluster calculations
8.14 Reusing the isotopic cluster shaper dialog window
8.15 Ensuring that the bins are “ phased ” in the various isotopic cluster mass spectra
8.16 Avoiding the combination artifact due to having “ unphased bins ”
9.1 Utilities
9.2 Setting-up of the centroid mass peak shaping process
9.3 Dynamic communications configuration between MassXpert and MineXpert
10.1 The polymer chemistry definition directory

2.1 Quick comparison of three biopolymers with examples of monomers

Copyright 2009-2025 Filippo Rusconi

MsXpertSuite - mass spectrometry software suite

http://www.msxpertsuite.org/

This book is part of the MsXpertSuite project.

The MsXpertSuite project is the successor of the MassXpert project. This project now includes various independent modules:

- MassXpert, program to model polymer chemistries and simulate mass spectrometric data;

- MineXpert, program to visualize and mine mass spectral data (mass spectrum, drift spectrum, XIC chromatograms) starting from the TIC chromatogram.

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org .

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