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mineXpert2 9.3.2

mineXpert2 User Manual

Visualization, exploration and analysis of MSn mass spectrometric data

Author: Filippo Rusconi
Publication Date: February 26, 2024 , Version: 9.3.2


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) and of the Plasma desktop

To all the readers who helped me with this manual.

Software feature offerings and intended audience
Feedback from the users
Project History
Program and Documentation Availability and License
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
2.1 Opening Mass Spectrometry Data Files
2.2 The Window Layout
2.3 The Main Program Window Menu
2.4 The Loaded MS Run Data Sets
2.5 Mass Spectral Data Listing in a Table View
2.6 The Main Data-Plotting Windows
2.7 General Structure of the Plot Widgets
2.8 General Operation of the Plot Widgets
3 Mass Data Integrations Featured by mineXpert2
3.1 General Behaviour of Plot Widgets
3.2 Various mass spectral data integrations
3.3 Integrations Originating in Color Map Plots
3.4 Noise Reduction in Color Map Plots
3.5 Low Intensity Signal Removal in Traces
3.6 Chained Integrations
4 Mass Spectral Deconvolutions
4.1 Deconvolution based on charge state
4.2 Deconvolution based on isotopic cluster peaks
4.3 Reading the resolving power based on mass spectral data
5 Isotopic cluster calculations
5.1 Calculating Isotopic Clusters with IsoSpec
5.2 Shaping mass peak centroids into well-profiled peaks
6 The processing flow in a data exploration session
6.1 The processing flow records all the steps in a data exploration session
7 Recording data exploration discoveries
A GNU General Public License version 3
List of Figures
1 Addresses to report feedback to
2.1 Probing the specific timsTOF MS runs
2.2 General View of the Graphical User Interface
2.3 The open MS run data sets
2.4 The table view-based scrutiny of one MS run data set
2.5 Mass spectral data set filtering using combined criteria
2.6 Resizing the plot widgets with the splitter
2.7 The total ion current (TIC) chromatogram window
2.8 The mass spectrum window
2.9 The drift spectrum window
2.10 The int = f(rt, m/z) color map window
2.11 The int = f(dt, m/z) color map window
2.12 The int = f(rt, dt) color map window
2.13 Description of the various widgets that make a composite plot widget
2.14 Single TIC intensity value for any mass spectral data feature
2.15 Trace plot widget main menu
2.16 Color map plot widget main menu
2.17 Color map plot widget main menu
2.18 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 Effects of the bin size on the color map involving one m/z dimension
3.9 Removing 0-intensity data points
3.10 Smoothing traces with the Savitzky-Golay filter
3.11 Integrating mass data from a TIC chromatogram to a mass spectrum
3.12 Integrating mass data from a mass spectrum to a single TIC intensity value
3.13 Integrations from a color map plot using a skewed selection rectangle (first step)
3.14 Integrations from a color map plot using a skewed selection rectangle (last step)
3.15 Integrations from a color map plot using a skewed selection rectangle (first step)
3.16 Example of signal-to-noise ratio enhancement
3.17 Example of low intensity signal removal (starting trace)
3.18 Example of low intensity signal removal (configuration)
3.19 Example of low intensity signal removal (creation of a new trace)
3.20 Example of low intensity signal removal (display of the new trace)
3.21 Example of chained integrations, color map where data exploration may start
3.22 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 2009-2023 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, 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.

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