JCD (Joint Component Detection) 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. We recommend using the JCD algorithm, but this requires significant computer processing resources.

To start automated component detection and the spectra deconvolution procedure using the JCD algorithm:

1. Click on the Components Detection and Spectra Deconvolution button and choose the JCD pop-up menu item

2. When the parameters setup dialog window appears, change the settings if required, and then click the Calculate button

The JCD algorithm dialog window contains various parameters that can be optimized for specific types of analysis:

Mass Merge Power: Specifies the mass difference within which the algorithm merges spectral peaks into one m/z value. A low value may result in more components (oscillating ions) and a high value can result in fewer components (merging ions).

Average Peak Width: Specifies the chromatographic peak width in scans that the algorithm uses to identify a potential component. If a value is too high, this can result in the loss of narrow peaks. If a value is too low, it may split a real component into two different components.

Baseline Correction: If checked, an automated baseline correction for each ion profile will be applied using the Top-Hat algorithm. This option should only be used for chromatograms with an elevated baseline .

Smoothing: If checked, the smoothing of each ion profile will be performed using the Average Peak Width value and the Loess algorithm

Noise Modification: Determines how to adjust the intensity values of spectral peaks that abundances are comparable to noise level. The following methods can be chosen from:

• None: Spectral peak intensities will not be altered

• Elimination: Spectral peaks with intensities lower than the specified value will be eliminated. Use this method if low abundant peaks are not of interest.

• Transition (default): Artificial noise will be added to replace random spikes with constant noise for better detection of low abundant components.

Analyze MS Stages: Determines which MS stages will be considered in the analysis of ion profiles that mean which MS stages will be used for detecting components. The remaining stages will only be used for spectral tree reconstruction. The choices are as follows:

• Top Stages (default): Analyzes only the top stage ions present in the data, where “top” means MS1, or MS2 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 MS2 spectra are assigned to the spectral tree)

• Lower Stages: 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.

• All Stages: 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.

The Top Stages level is recommended in most cases. The Lower Stages level can be useful if a Data Dependent experiment is set in a way such that ions are isolated according to a predefined list of m/z values and top-stage spectra are noisy. The All Stages level is useful for the preliminary analysis of complex data.

Eliminate non model ion stages: If checked, the product ion spectrum along with subsequent stages will be deleted if its precursor ion is not a model ion (usually the most intense) in the top stage.

Retention Time Range: Allows you to specify 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: Allows you to specify only a part of a chromatogram to be analyzed (m/z range), which can speed up your work. In this case, the algorithm ignores regions outside of the specified range.

Baseline Threshold: Specifies the peak baseline as a percentage of base peak height.

Merging Factor: 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. See also the Wide Component Merge Mode.

Sharpness Tolerance: 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 a limit for the time difference of the ion profile maxima will be used 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.