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massXpert 5.8.0

massXpert User Manual

Modelling and simulation of mass spectrometric data of linear polymers

Author: Filippo Rusconi
Publication Date: January 31, 2019 , Version: 5.8.0

Dedication

To Marìa 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.

Preface
Software feature offerings and intended audience
Feedback from the users
Project History
Program and Documentation Availability and License
1 Generalities
1.1 On Chemical Formulæ and Chemical Reactions
1.2 The massXpert Framework Data Format
1.3 Chemical Entity Naming Policy
2 Basics in Polymer Chemistry
2.1 Polymers? Where? Everywhere!
2.2 Various Biopolymer Structures
2.3 To Sum Up
2.4 Polymer Chain Disrupting Chemistry
3 XpertDef: Definition of Polymer Chemistries
3.1 The atoms
3.2 The polymer chemical entities
3.3 Saving the definition
4 XpertEdit: a Powerful Editor and Simulation Center
4.1 XpertEdit Invocation
4.2 XpertEdit Operation: In Medias Res
4.3 The Editor Window Menu
4.4 Editing Polymer Sequences
4.5 Finding sequence motifs
4.6 Importing Sequences
4.7 Multi-region Selections
4.8 Polymer Sequence Modification
4.9 Monomer Cross-linking
4.10 Sequence Cleavage
4.11 Oligomer Fragmentation
4.12 Mass Searching
4.13 Oligomer Data Filtering
4.14 m/z Ratio Calculations
4.15 Monomeric And Elemental Composition
4.16 pKa, pH, pI and Charges
4.17 General Options
5 XpertCalc: a Powerful Mass Calculator
5.1 XpertCalc Invocation
5.2 An Easy Operation
5.3 The Programmable Calculator
5.4 The Log Book Recorder
5.5 The m/z Ratio Calculator
5.6 The Isotopic Peaks Calculator
6 XpertMiner: a Data Miner
6.1 XpertMiner Invocation
6.2 mzLab: Mining m/z Ratios
6.3 Creating a New Input m/z List
6.4 Working on One Input m/z List
6.5 Working on Two Input m/z Lists
7 Data Customizations
A GNU General Public License version 3
List of Figures
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 DNA fragmentation patterns most widely encountered.
3.1 select one polymer chemistry definition file.
3.2 Polymer chemistry definition window.
3.3 Atom definition
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 Spectrum simulation for cleavage-obtained oligomers
4.15 Simulated spectrum for cleavage-obtained oligomers
4.16 Oligomer fragmentation window
4.17 Starting a fragmentation that accounts the cross-links
4.18 Complicated cross-linking situation
4.19 Searching masses in a polymer sequence
4.20 Oligomer data filtering
4.21 Calculation of ranges of m/z ratios
4.22 Determination of the compositions
4.23 Different pKa values for a number of amino-acids' chemical groups
4.24 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
5.5 The isotopic pattern calculator
5.6 An isotopic pattern calculator output example
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 polymer chemistry definition directory

Copyright 2009,...,2019 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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