Skip to content

Additional tools

Chromatogram plot

Description

Visualization → Chromatogram plot

There is a possibility to display chromatographic peaks outside of raw data overview. This standalone two-dimensional plot visualizes TIC/XIC data. All the chromatograms are displayed in the same plot.

The x-axis corresponds to retention time and the y-axis is the intensity level of the signal.

Chromatogram example

Parameters

Raw data files

List of raw data files to display in the TIC visualizer.

MS level

Scan level (MS1,MS2,... ,MSn) to display in the plot.

Plot type

TIC or base peak

Retention time

Retention time (x-axis) range.

m/z range

Range of m/z values. If this range does not include the entire scan m/z range, the resulting visualizer is XIC type.

Selected peaks

List of chromatographic peaks to display in the TIC visualizer. This option is available only if a peak list related to the selected raw data file exists in the current project.

MS spectrum

Visualization → MS spectrum

Displays all the ions from a selected scan. Can be used to explore mass spectrum outside of raw data overview. Only one raw file can be chosen.

It shows a plot of two dimensions, where X axis corresponds to m/z value and Y axis is the intensity of the ion signal.

Parameters

Scan number

Choose the scan to visualize

2D visualizer

Visualization → 2D plot

This tool displays a plot of two dimensions, where X axis corresponds to retention time and Y axis is the m/z value. This visualization of spots in the plot corresponds with the intensity of the data in that region.

2D plot

User can define features from the feature list to be displayed on the plot.

Parameters

Type of data

This plot can use either resampled data as input (faster), or raw data (slower).

Scans

Here user can set up the level (MS1,MS2,... ,MSn), polarity, retention time, and the other parameters of the scans to be used.

m/z

Defines range of m/z values.

3D visualizer

Description

Visualization → 3D plot

This tool presents a three dimensional plot where X axis represents the retention time, Y axis the m/z value and Z axis the intensity of the signal. This plot is the collection of all the information from the raw data in a graphical representation.

3D plot example

Parameters

Scans

Here user can set up the level (MS1,MS2,... ,MSn), polarity, retention time, and the other parameters of the scans to be used.

m/z range

Range of m/z values.

Features

Features that will be taken as an input.

Retention time resolution

Number of data points on retention time axis.

m/z resolution

Number of data points on m/z axis.

Scan histogram

Description

Visualization → Scan histogram

This module creates m/z distribution histograms of all m/z values in mass lists across specified scans. The binning width, in which the m/z values are counted, can be changed dynamically. The number of scans that contain a specific m/z value (bin) are plotted.

Scan histogram dialog

https://youtu.be/31hwc74vUjA

Parameters

Scans

Here user can set up the level (MS1,MS2,... ,MSn), polarity, retention time, and the other parameters of the scans to be used.

m/z

Limit the range of the histogram (can improve performance).

Signal intensity range

Optional parameter

Allows to limit signal intensities (can improve performance).

Mass defect

Optional parameter

Filters for mass defects in the signals.

Type

Type of the histogram to be created. Available options:

  • m/z,
  • Intensity,
  • Intensity (noise recalibrated),
  • Mass defect.

Bin width

The binning width to count m/z value occurence in scans.

Use mobility scans

If the input data has ion mobility dimension, this data can be used instead of the data from the summed frames.

Scan inject time analysis

MS(n) spectra tree

omokshyna


Last update: November 24, 2022 21:13:07