Spectral deconvolution

This method finds analytes by combining similar peaks into clusters and using their intensities to construct fragmentation mass spectra. The following steps are performed:

  1. All EIC peaks are clustered based on proximity of their retention times. The user can specify minimum distance between clusters, minimum number of peaks forming a cluster, and minimum cluster intensity. If preview is selected, the top right plot displays the result of the clustering with dots corresponding to EIC peaks and colors corresponding to different clusters.
  2. In each cluster, EIC peaks are filtered based on their sharpness and on their elution profiles. All EIC peaks with shaprness below minimum shaprness are filtered out. If Find shared peaks is selected, than shared peaks are filtered out as well. he user can specify minimum edge-to-height ratio and minimum delta-to-height ratio that are used in determining shared peaks.
  3. EIC peaks that have passed the filtering step, are clustered based on their elution profiles. The user can specify shape-similarity tolerance: small tolerance corresponds to large number of clusters, while large tolerance corresponds to a small number of clusters. If preview is selected, the result of the clustering is shown on the bottom-right plot.
  4. Each cluster corresponds to one analyte. Among all EIC peaks in the cluster, a model peak is chosen to represent the elution profile of the analyte. If Choise of Model Peak based on Sharpness is selected, then the EIC peak with the highest sharpness in the cluster is selected to be a model peak. If Choice of Model Peak based on Intensity is selected, then the EIC peak of the highest intensity is selected to be a model peak. If Choice of Model Peak based on M/z value is selected, then the EIC peak with the highest m/z value in the cluster is selected to be a model peak.
  5. In order to build fragmentation spectra for analytes, each EIC peak is decomposed into a linear combination of the model peaks with the weighting coefficients obtained by solving an optimization problem. These coefficients and m/z value of the EIC peak contribute to the fragmentation spectra of the corresponding analytes.

Method definitions

EIC Peak

Sharpness
In order to find sharpness, the medians of the slopes of the lines connecting the peak apex to its other data points are calculated on each side of the peak apex. The sharpness is defined as the average of the two medians.
Shared peak
EIC peak is considered to be shared (i.e. produced by two co-eluting analytes) if at least one of the following conditions is satisfied:

Method parameters

Min cluster distance (min)
Minimum distance between any two retention-time clusters
Min cluster size
Minimum number of peaks in a cluster
Min cluster intensity
Minimum intensity of the highest peak in a cluster
Find shared peaks
If selected, shared peaks are determined and do not participate in the second clustering
Min edge-to-height ratio
Minimum value of a boundary intensity divided by the apex intensity of EIC peak that is considered to be shared
Min delta-to-height ratio
Minimum value of the absolute difference of the boundary intensities divided by the apex intensity of EIC peak that is considered to be shared
Min sharpness
Minimum sharpness of EIC peak that can participate in the second clustering
Shape-similarity tolerance (0..90)
Tolerance is used in the second clustering based on the similarity of peaks' elution profiles: small tolerance corresponds to large number of clusters; large tolerance corresponds to a small number of clusters
Choice of Model Peak based on
In each cluster, a model peak is chosen. If Sharpness is used, then EIC peak with the highest sharpness in the cluster is chosen to be a model peak. Is Intensity is used, then EIC peak of the highest intensity in the cluster is chosen to be a model peak. If M/z value is used, then EIC peak with the highest m/z value in the cluster is chosen to be a model peak.
Exclude m/z-values
Optionally, the user can specify a list of deprecated m/z values such that EIC peaks with those m/z value could not be chosen as model peaks. It is possible to specify single m/z values as well as ranges of m/z values. For example: 1-50, 73, 100