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*   JCD Algorithm
Joint Components Detection (JCD) is based on the statistical analysis of all ion profile maxima. Ion profiles (ion chromatograms) with comparable shapes and maxima belonging to a limited time range are considered as a single component. The algorithm extracts individual mass spectral peak abundance profiles to produce a “purified” spectrum or spectral trees and generates the peak shape of a representative component. For best results, use the JCD algorithm, but be aware that it requires significant computer processing resources.
To significantly reduce computation time for large files, apply a threshold filter to the chromatogram before performing JCD. See Thresholding for more information about applying thresholds.
To run the Joint Components Detection algorithm
Click the Components Detection & Spectra Deconvolution button, , and choose JCD.
The Joint Detection Algorithm dialog box opens.
Click Calculate.
Deconvolution page of the Joint Detection Algorithm dialog box
Specifies the mass difference within which the algorithm merges spectral peaks into one m/z value. A low value might result in more components (oscillating ions) and a high value can result in fewer components (merging ions).
Specifies the chromatographic peak width in scans that the algorithm uses to identify a potential component. If a value is too high, the result might be the loss of narrow peaks. If a value is too low, it might split a real component into two different components. Average Peak Width is applied only for scans that are specified in Analyze MS Stages parameter. For example, if Analyze MS Stages is set to Top Stages, then Average Peak width is applied to MS1 scans only.
Applies an automated baseline correction for each ion profile using the Top-Hat algorithm. Use this option only for chromatograms with an elevated baseline.
Performs the smoothing of each ion profile using the Average Peak Width value and the LOESS algorithm. If the Average Peak Width parameter is too large or peaks are shorter than four to five scans, then the smoothing can remove small peaks.
Determines how to adjust the intensity values of spectral peaks with comparable abundances to noise level. You can choose from None, Elimination, or Transition.
Spectral peaks with intensities lower than the specified value are eliminated. Use this method when low abundant peaks are not of interest.
Min. Peak Height: The threshold value applied to each abundance in an ion profile. This value is determined as a percentage of the maximum of the analyzed ion profile. All abundances smaller than this threshold are removed. This option speeds up calculations.
Default. Artificial noise is added to replace random spikes with constant noise for better detection of low abundant components. Abundances with zero value are replaced by artificial noise.
Determines which MS stages are considered in the analysis of ion profiles—that is, which MS stages are used for detecting components. The remaining stages are only used for spectral tree reconstruction. Select one of the following options:
Lower Stages level: Useful if Data Dependent experiment is set so that ions are isolated according to a predefined list of m/z values and top-stage spectra are noisy.
Top Stages (default)
Analyzes only the top stage ions present in the data, where “top” means MS1, or MS/MS if MS1 is not present. The algorithm builds the component tree by joining the corresponding lower stage spectra that meet the following criteria: they occur within the component envelope and the software detected the precursor m/z in the top stage as a component ion (if the deconvoluted MS1 spectrum contains peaks that have been further isolated, the corresponding MS/MS spectra are assigned to the spectral tree). Recommended option for most cases.
Analyzes all ions except those from the top MS stages. The algorithm calculates the spectrum of the top stage from the total ion abundance of the top stage. The resulting spectral trees do not have as much depth as those from the Top Stages option. This option can be useful if the full-scan chromatogram is not well resolved and the lower stages contain enough scans with the same precursor value.
Analyzes all ions regardless of the MS stage. The resulting spectral trees do not have as much depth as those from the Top Stages option. This option is useful in some cases when the FISh algorithm is applied in metabolite ID (see Base Peak Chromatogram).
Determines MS stage where a spectral tree is divided into two or more independent components based on the precursor ion.
Specifies only a part of a chromatogram to be analyzed (time range), which can speed up your work. In this case, the algorithm ignores regions outside of the specified range.
m/z Range
Determines the m/z value range to be analyzed. Ignores other spectral regions. This feature is useful when processing large chromatograms.
Opens the Save JCD Parameters File dialog box where you can save your current parameters to a JCD parameters file (.jcd.par).
Opens the Open JCD Parameters File dialog box where you can choose a JCD parameters file (.jcd.par) to load.
More page of the Joint Detection Algorithm dialog box
Specifies the sensitivity to local minima of ion profiles. Peak ends are detected if the local minimum of analyzed ion profile is greater than this value. Value is determined as a multiple of estimated noise.
Specifies the minimal ion profile peak height to be considered as a potential component. Value is determined as a multiple of the estimated noise.
Specifies the minimal intensity of component peaks. This value is determined as a percentage of intensity of the total ion chromatogram at the position of the component maxima.
Specifies a limit for the time difference of the ion profiles maxima. Too high a value can cause the merging of randomly coeluting components. Too low a value can split a component into more false-positive components. The software merges ion profile peaks within this range into a single component.
Specifies the degree (%) of similarity of ion profile shapes. If two ion shapes meet the specified percentage for the sharpness tolerance, as well as other parameters, the algorithm merges the ions into a single component.
Wide Component Merge Mode
Specifies whether to use a limit for the time difference of the ion profile maxima in a combination of the following parameters: Average Peak Width and Merging Factor. Select this check box (default) to avoid splitting a component into ion peaks that are detected as redundant components in chromatograms with wide peaks. Clear this check box if an incorrect component merge occurs. Recommended for most LC/MS experiments.
Joint Detection Algorithm wizard dialog box
Components Overlapping Sensitivity

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Related Topics:
  RCD Algorithm
  TECD Algorithm
  Direct Infusion Algorithm
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