mineXpert2 8.1.1
mineXpert2 User Manual
Visualization, exploration and analysis of MSn mass spectrometric data
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) and of the Plasma desktop
To all the readers who helped me with this manual.
- Preface
- 1 Generalities
- 1.1 Citing the mineXpert2 software.
- 1.2 General concepts and terminologies
- 1.3 Acquiring Mass Data Along Time: To Profile or Not To Profile?
- 1.4 Mass Data Visualisation: To Combine or Not To Combine?
- 1.5 Examples of Various Mass Spectral Data Integrations
- 1.6 Installation of the software
- 1.7 Building the software from source
- 2 The program's graphical user interface
- 3 Mass Data Integrations Featured by mineXpert2
- 4 Mass Spectral Deconvolutions
- 5 Isotopic cluster calculations
- 6 The processing flow in a data exploration session
- 7 Recording data exploration discoveries
- A GNU General Public License version 3
- 1 Addresses to report feedback to
- 2.1 General View of the Graphical User Interface
- 2.2 The open MS run data sets
- 2.3 The table view-based scrutiny of one MS run data set
- 2.4 Mass spectral data set filtering using combined criteria
- 2.5 Resizing the plot widgets with the splitter
- 2.6 The total ion current (TIC) chromatogram window
- 2.7 The mass spectrum window
- 2.8 The drift spectrum window
- 2.9 The int = f(rt, m/z) color map window
- 2.10 The int = f(dt, m/z) color map window
- 2.11 The int = f(rt, dt) color map window
- 2.12 Description of the various widgets that make a composite plot widget
- 2.13 Single TIC intensity value for any mass spectral data feature
- 2.14 Trace plot widget main menu
- 2.15 Color map plot widget main menu
- 2.16 Color map plot widget main menu
- 2.17 Zooming-in operation
- 3.1 Setting the MSn fragmentation parameters
- 3.2 Shortcut to the fragmentation MS level setting
- 3.3 Unusable combination spectrum without binning
- 3.4 The m/z integration parameters window
- 3.5 Effects of binning settings on the combination mass spectrum (low m/z region)
- 3.6 Effects of binning settings on the combination mass spectrum (middle m/z region)
- 3.7 Effects of binning settings on the combination mass spectrum (high m/z region)
- 3.8 Removing 0-intensity data points
- 3.9 Smoothing traces with the Savitzky-Golay filter
- 3.10 Integrating mass data from a TIC chromatogram to a mass spectrum
- 3.11 Integrating mass data from a mass spectrum to a single TIC intensity value
- 3.12 Integrations from a color map plot using a skewed selection rectangle (first step)
- 3.13 Integrations from a color map plot using a skewed selection rectangle (last step)
- 3.14 Integrations from a color map plot using a skewed selection rectangle (first step)
- 3.15 Example of signal-to-noise ratio enhancement
- 3.16 Example of chained integrations, color map where data exploration may start
- 3.17 Multiple chained integrations
- 4.1 Mass spectrum plot widget-specific deconvolution menu
- 4.2 Charge state-based mass deconvolution
- 4.3 Isotopic cluster-based mass deconvolution
- 4.4 Calculation of the resolving power
- 5.1 Calculation of the isotopic cluster of an analyte
- 5.2 Isotopic cluster calculation dialog window
- 5.3 Hand-made user configuration of the chemical elements and formula
- 5.4 Typical manual configuration of the isotopic characteristics of the chemical elements
- 5.5 Results from the isotopic cluster calculation
- 5.6 Setting-up of the centroid mass peak shaping process
- 5.7 Shaped peaks mass spectral data
- 5.8 Creation of a shim MS run data set
- 5.9 Selection of a MS run data set
- 5.10 Spectrum created using the peak shaping feature
- 6.1 The processing flow dialog window
- 7.1 Setting-up of the recording of the data exploration discoveries
Copyright 2009-2020 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, a program to model polymer chemistries, perform a wide array of (bio-)chemical reactions and simulate the corresponding mass spectrometric data;
mineXpert2, the successor of mineXpert, a program to visualize and mine MSn 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.
The flying frog picture is courtesy http://www.papuaweb.org. The specific license as of 20190104 is: Please acknowledge the use of Papuaweb resources in your publications. To do this include the complete item URL (for example "http://www.papuaweb.org/gb/ref/hinton-1974/63.html") or a general reference to "http://www.papuaweb.org" in your citation/bibliography. This will improve recognition of these resources by Google Scholar and similar search engines.