CycloBranch
Dereplication

Dereplication in MS Data

CycloBranch supports the dereplication of compounds in single mass spectra (MALDI-MS). The mode "Compare Peaklist(s) with Database - MS or MSI data" must be selected (see Mode). The detectable ion types are listed in Ion Types in Theoretical Spectra. An output report example is shown in the following picture.

msdataoutputreport.png
Single mass spectrum was searched against an in-house database of siderophores - output report.

The detail window is opened by a double-click on a row in the output report if a linear peptide was identified. The Enter key can also be used if the row is selected. See also Linear Peptide Detail Window and Toolbar for Linear Peptides. The differences for MS data are following:

  • Only the windows on the left side are available.
  • The red peaks in the graphical visualization of a mass spectrum were assigned to compounds in a database.

The following details are listed in the table of peaks:

  • Ion Type - a name of a theoretical peak including information about its charge (if Generate Full Isotope Patterns is disabled)
  • Pattern Type - a name of a theoretical isotope pattern including information about its charge (if Generate Full Isotope Patterns is enabled)
  • Theoretical m/z - a theoretical mass-to-charge ratio of the peak
  • Theoretical intensity [%] - theoretical intensity of the peak (if Generate Full Isotope Patterns is enabled)
  • Experimental m/z - a mass-to-charge ratio of a matched peak
  • Relative Intensity [%] - a relative intensity of a matched peak
  • Absolute Intensity - an absolute intensity of a matched peak
  • Error [ppm] - a ppm error
  • Score - the angle distance calculated between theoretical and experimental isotopic patterns (if Generate Full Isotope Patterns is enabled)
  • FDR - false discovery rate of a matched isotopic pattern (if Generate Full Isotope Patterns is enabled)
  • Summary Formula - a summary formula of a neutral molecule
  • Name - a name of a compound
  • Reference - a link into a database if available (ChemSpider, PubChem or Norine)

Note that theoretical peaks which were not assigned to experimental peaks are not reported in the table.

msdatadetailwindow.png
Single mass spectrum was searched against the in-house database of siderophores - detail window.



Dereplication in LC-MS data

CycloBranch supports also the dereplication of compounds in LC-MS data. The mode "Compare Peaklist(s) with Database - MS or MSI data" must be selected (see Mode). The data files containing spectra from multiple LC-MS scans are processed automatically. In this case, each row in the output report corresponds to one scan.

lcmsdataoutputreport.png
Batch processed LC-MS data - output report.

The compounds detected in the scans are summarized in the Summary Table of Matched Peaks. The "ID" in the summary table of matched peaks refers to the "Spectrum ID" in the output report, and it is the scan number. See the Summary Table of Matched Peaks in the following image and the corresponding chromatogram (see also Chromatogram).

batch-lc-ms-1-ferri-ferrioxamineB.png
List of peaks assigned to ferri-ferrioxamine B in the batch-processed LC-MS run.


eic.png
Extracted ion chromatogram (EIC) of ferri-ferrioxamine B.



Dereplication in MSI Data

CycloBranch supports the dereplication of compounds in imaging mass spectra (MSI). The mode "Compare Peaklist(s) with Database - MS or MSI data" must be selected (see Mode). An imzML file must be used as the input file in the settings dialog. A row in the output report corresponds to single mass spectrum with the coordinates [X,Y].

msidataoutputreport.png
A mass spectrometry imaging dataset was searched against the in-house database of siderophores - output report.

If MSI data are analyzed the Summary Table of Matched Peaks includes compounds detected in all single mass spectra. The CrossVis tool visualizes the localization of compounds in an optical image.

msi-summarytable.png
Summary table of matched peaks - desferri-ferrioxamine B was filtered by its theoretical m/z ratio.


desferri-ferrioxamineB-msi.png
CrossVis - detail of a region containing desferri-ferrioxamine B.



Databases of Compounds

The databases of sequences/compounds can be created/edited using Sequence/Compound Database Editor. The same database can be used in both MS and MS/MS mode. However, the column "Sequence" must be defined in MS/MS mode. See List of Available Sequence/Compound Databases.