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Additional tools

Scatter plot

Description

Visualization → Scatter plot

This tool shows a scatter plot with data from identified peaks in aligned feature list.

A search for a peak can be done using three options (name, retention time and m/z value).

Scatter plot example

Correlated features \(\Delta\)m/z histogram

Description

Visualization → Correlated features \(\Delta\)m/z histogram

This module plots all m/z deltas between correlated features in a histogram and offers a Gaussian fit.

Parameters

Minimum Pearson correlation

Minimum Pearson correlation of feature shapes.

Limit delta to m/z

Maximum m/z delta is the m/z of the smaller ion (feature list row).

m/z bin width

Binning of m/z values for feature picking

Append to file

Append the correlated features delta m/z to a csv file.

Correlation coefficient histogram

Description

🚧 This module is being updated. Some newer functionality might not be documented.

This module allows to plot all correlations between feature shapes.

Hist

Parameters

m/z bin width

Binning of m/z values for feature picking

Feature intensity plot

Description

🚧 This module has a known bug and is being updated, which might affect its functionality.

Visualization → Feature intensity plot

This plot allows to explore specific features against the raw data.

Intensity plot w/error bars

Intensity plot w/lines

Parameters

Data files

Selects the raw data files from where the peaks were detected

X axis value

X axis display the raw data file name or the parameter defined in the "set sample parameters" window

X axis value

The user can choose from peak's height, area or retention time value to display in this axis.

Peaks

The user can select the peaks to use in this plot.

Kendrick mass plot

Description

Visualization → Kendrick mass plot

In 1963 Kendrick published his idea of a mass scale, the so-called Kendrick mass scale, which is based on defining the mass of CH2 as 14.0000 u.

The Kendrick mass scale is calculated by multiplying the IUPAC mass scale with the factor 14.0000 u/14.01565 u = 0.9988834. This results in the same mass defect for homologous components, the so-called Kendrick mass defect (KMD). The KMD is defined as the \(\Delta\) of a nominal Kendrick mass and its associated Kendrick mass. Using the Kendrick mass scale has the purpose of data reduction.

\[KM(R)=m/z\cdot\frac{round(R)}{R}\]
\[KMD(R)=round(KM(R))-KM(R)\]

where \(KM\) is Kendrick mass, \(KMD\) - Kendrick mass defect, \(R\) - exact mass of selected base unit.

Kendrick example

If you use this module for your analysis or visualization, please cite:

Three‐dimensional Kendrick mass plots as a tool for graphical lipid identification. A. Korf, C. Vosse, R. Schmid, P. O. Helmer, V. Jeck, H. Hayen, Rapid Communications in Mass Spectrometry 32.12 (2018): 981-991.

Expanding the Kendrick Mass Plot Toolbox in MZmine 2 to Enable Rapid Polymer Characterization in Liquid Chromatography−Mass Spectrometry Data Sets A. Korf, T. Fouquet, R. Schmid, H. Hayen, and S. Hagenhoff, Analytical Chemistry 2020 92 (1), 628-633.

Detailed functionality

This module allows to create 4 dimensional Kendrick mass plots. Feature characteristics, such as retention time or feature area, can be plotted as color scale or bubble size.

Charge dependent Kendrick mass plots

Multiply charged ions can cause splits in Kendrick mass plot. Fouquet et al. have shown considering the charge for the calculation of the KM can help to overcome this problem through clustering of features.

\[KM(R,Z)=Z\cdot KM(R)=Z\cdot m/z\cdot \frac{round(R)}{R}\]

where \(Z\) is charge.

Fouquet, Thierry NJ, et al. "On the Kendrick Mass Defect Plots of Multiply Charged Polymer Ions: Splits, Misalignments, and How to Correct Them." Journal of The American Society for Mass Spectrometry 29.8 (2018): 1611-1626.

Resolution enhanced Kendrick mass defect plots

Fouquet and Sato have shown that a fractional base unit (ivisor) can enhance the resolution of Kendrick mass plots.

\[X>1, KM(R,X)=m/z\cdot \frac{round(R/X)}{R/X}\]

where \(X\) is a fractional base unit.

Fouquet, Thierry, and Hiroaki Sato. "Extension of the Kendrick mass defect analysis of homopolymers to low resolution and high mass range mass spectra using fractional base units." Analytical chemistry 89.5 (2017): 2682-2686.

Combining charge and fractional base unit (Divisor)

If both charge and fractional base unit are changed, the following equation is used:

\[KM(R,Z,X)=Z\cdot KM(RX)=Z\cdot m/z\cdot \frac{round(R/X)}{R/X}\]

Fouquet, Thierry NJ, et al. "On the Kendrick Mass Defect Plots of Multiply Charged Polymer Ions: Splits, Misalignments, and How to Correct Them." Journal of The American Society for Mass Spectrometry 29.8 (2018): 1611-1626.

Fouquet, Thierry, Takaya Satoh, and Hiroaki Sato. "First gut instincts are always right: the resolution required for a mass defect analysis of polymer ions can be as low as oligomeric." Analytical chemistry 90.4 (2018): 2404-2408.

Remainders of Kendrick masses (RKM)

Another option to increase the resolution of Kendrick mass plots is the by Fouquet et al. proposed concept of RKM (remainders of Kendrick masses). [RKM(R)=\Bigg{\frac{KM(R)}{round(R)}\Bigg}]

with \(\{ \}\) being the fractional part function defined as \(x=x-floor(x)\)

Parameters

Kendrick parameters

Feature List

Select one feature or aligned featurel list.

X-axis

Select which metric you want to display on the X-Axis. Possible metrics are m/z, Kendrick Mass, Kendrick Mass Defect, Remainder of Kendrick Mass, Retention Time, Mobility, Intensity, Area, Tailing Factor, and Asymetry Factor.

Repeating unit for X-Axis

Enter a molecular formula which will be used for Kendrick Mass calculation. The field is only acitve if Kendrick, Kendrick Mass Defect, or Remainder of Kendrick Mass is selected.

Y-axis

Select which metric you want to display on the Y-Axis. Possible metrics are m/z, Kendrick Mass, Kendrick Mass Defect, Remainder of Kendrick Mass, Retention Time, Mobility, Intensity, Area, Tailing Factor, and Asymetry Factor.

Repeating unit for Y-Axis

Enter a molecular formula which will be used for Kendrick Mass calculation. The field is only acitve if Kendrick, Kendrick Mass Defect, or Remainder of Kendrick Mass is selected.

Color scale

Select which metric you want to display as a color scale. Possible metrics are m/z, Kendrick Mass, Kendrick Mass Defect, Remainder of Kendrick Mass, Retention Time, Mobility, Intensity, Area, Tailing Factor, and Asymetry Factor.

Repeating unit for color scale

Enter a molecular formula which will be used for Kendrick Mass calculation. The field is only acitve if Kendrick, Kendrick Mass Defect, or Remainder of Kendrick Mass is selected.

Bubble size

Select which metric you want to display as bubble size. Possible metrics are m/z, Kendrick Mass, Kendrick Mass Defect, Remainder of Kendrick Mass, Retention Time, Mobility, Intensity, Area, Tailing Factor, and Asymetry Factor.

Repeating unit for bubble size

Enter a molecular formula which will be used for Kendrick Mass calculation. The field is only acitve if Kendrick, Kendrick Mass Defect, or Remainder of Kendrick Mass is selected.

Van Krevelen diagram

Description

Van Krevelen diagrams are graphical plots developed by Dirk Willem van Krevelen (chemist and professor of fuel technology at the TU Delft) that are used to assess the origin and maturity of kerogen and petroleum.

The diagram cross-plots the hydrogen:carbon (hydrogen index) as a function of the oxygen:carbon (oxygen index) atomic ratios of carbon compounds.

  1. Van Krevelen, D.W. (1950). "Graphical-statistical method for the study of structure and reaction processes of coal", Fuel, 29, 269-84
  2. https://en.wikipedia.org/wiki/Van_Krevelen_diagram

Warning

Since element ratios are plotted only annotated features are considered.

vankrevelenexample

Parameters

vankrevelenparameters

Feature lists

Select feature list to display as Van Krevelen diagram.

Color scale

Select which parameters you want to display as a color scale.

Bubble size

Select which parameters you want to display as bubble size.

kyrasolaris01, kyrasolaris01, omokshyna


Last update: January 9, 2024 13:55:58