massXpert2 8.3.1
massXpert2 User Manual
Modelling and simulating mass spectrometric data of linear polymers
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.
- Preface
- 1 Generalities
- 2 Basics in Polymer Chemistry
- 3 XpertDef: Definition of Polymer Chemistries
- 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
- 6 XpertMiner: a Data Miner
- 7 Utilities
- 8 Data Customizations
- A GNU General Public License version 3
- 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 Utilities
- 7.2 Main window of the isotopic cluster generator
- 7.3 Hand-made user configuration of the chemical elements and formula
- 7.4 Typical manual configuration of the isotopic characteristics of the chemical elements
- 7.5 Typical manual configuration of the isotopic characteristics of the chemical elements
- 7.6 Setting-up of the centroid mass peak shaping process
- 7.7 Shaped peaks mass spectral data
- 7.8 Setting-up of the centroid mass peak shaping process
- 8.1 The polymer chemistry definition directory
Copyright 2009-2023 Filippo Rusconi
msXpertSuite - mass spectrometry software suite
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.
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