CycloBranch
Annotated Features Overview

Annotated Features Overview

The table is opened using the command "Tools -> Annotated Features Overview" from the Main Window. Use F1 to open this help.

Annotated Features Overview

Toolbar

Export to CSV (CTRL + E)

Export the table into a .csv (comma-separated values) file.

Export to Database (CTRL + D)

Export matched formulas to a Sequences/Compounds Database - the feature is available only if Compound Search - MS, LC-MS, MSI mode was used.

Close (Esc)

Close window.

Search PubChem... (CTRL + P)

Search molecular formulas of compounds in PubChem. Available only in Compound Search - MS, LC-MS, MSI mode.

Example - names of compounds identified by CycloBranch were searched in PubChem.

HTML Documentation (F1)

Show HTML documentation.

View

Select a value type which is reported for every compound and every dataset.

  • Maximum Relative Intensity - maximum relative intensity of a given compound in the respective LC-MS data file.
  • Maximum Absolute Intensity - maximum absolute intensity of a given compound in the respective LC-MS data file.
  • Peak Area (Chromatogram) - All Isotopes - peak area under the extracted ion chromatogram of a given compound
    (the extracted ion chromatogram is constructed from the sum of absolute intensities of all isotopes of a given compound in every spectrum).
  • Concentration - All Isotopes - concentration of a given compound calculated using the respective peak area
    (the extracted ion chromatogram is constructed from the sum of absolute intensities of all isotopes of a given compound in every spectrum).
  • Peak Area (Chromatogram) - Highest Peak - peak area under the extracted ion chromatogram of a given compound
    (the extracted ion chromatogram is constructed from the highest intensity peak of a given compound in every spectrum).
  • Concentration - Highest Peak - concentration of a given compound calculated using the respective peak area
    (the extracted ion chromatogram is constructed from the highest intensity peak of a given compound in every spectrum).
  • Retention Time

Peak Shape

Select a function which is used to estimate shape of a chromatographic peak in profile mode from peaks in line mode.

  • Gaussian - common Gaussian function
  • ex-Gaussian (tailing) - exponentially modified Gaussian function with tailing
  • ex-Gaussian (fronting) - exponentially modified Gaussian function with fronting

Standard

All compounds detected in at least one LC-MS datafile are listed.

Calibration Curve

The equation is used if View is set to "Concentration - All Isotopes" and "Concentration - Highest Peak". Enter the input parameters a and b for the equation y = a * x + b, where x is concentration and y is peak area. If Standard is selected, the peak area of a given compound is automatically divided by peak area of standard.

Buttons:

  • "Set" - set the parameters a and b, and recalculate the table.
  • "Define" - define samples, calibration curve and recalculate the table.
  • "View" - view the calibration curve and statistics.

Define Samples and Calibration Curve

Define parameters of calibration curve.

The parameters a and b of a calibration curve can be estimated from an input set of LC-MS data files. Check the filenames which should be used to estimate the parameters of curve. In our example, a mixture of PvdD and PvdE was spiked into the respective samples in concentrations 1-500 ng/mL. The samples were collected in triplicates. The values of concentration were entered into respective fields. If a value is used more than once, the results were averaged. The areas of chromatographic peaks of selected ions (i.e., PvdD and PvdE) were summed. The resulting area was divided by the area of selected internal standard (i.e., FoxE).

If the slope (parameter a) is the only parameter which should be estimated, select the equation y = a*x. If the slope (parameter a) and y-intercept (parameter b) should be estimated, select the equation y=a*x + b. The extracted ion chromatogram of a given compound can be created by two different approaches - using 'Highest Peak (e.g., 12C)' (the extracted ion chromatogram is constructed from the highest intensity peak of a given compound in every spectrum) or 'All Isotopes (e.g., sum of 12C + 13C + 13C2 + ...)' (the extracted ion chromatogram is constructed from the sum of absolute intensities of all isotopes of a given compound in every spectrum). When calculating the area of chromatographic peaks, the peak shape can be estimated using Gaussian function, exponentially modified Gaussian function with tailing, and exponentially modified Gaussian function with fronting.

Define groups of samples.

If data files with unknown samples are analyzed, choose the value 'Sample' in 'Data Type'. Annotate technical replicates with the same Group number. The results are then automatically averaged. If calibration data files are selected at the same time, the parameters of calibration curve can be estimated automatically. Optionally, choose 'Enter parameters manually' in 'Equation' field and type the parameters 'a' and 'b' manually.

View Calibration Curve and Statistics

View calibration curve and statistics.


View groups of samples.

Export to CSV (CTRL + E)

Export the table into a .csv (comma-separated values) file.

Export Image (CTRL + G)

Export the image into a PDF, PS (Windows only), PNG or SVG file. PS files in Linux can be generated outside of the application, e.g., using the pdf2ps tool.

Close (Esc)

Close window.

Zoom In (CTRL +)

Zoom in.

Zoom Out (CTRL -)

Zoom out.

Zoom Reset (CTRL + R)

Reset zoom.

Hide Labels (CTRL + L)

Hide/show labels of calibration points, limit of detection and limit of quantification.

HTML Documentation (F1)

Show HTML documentation.

Concentration

  • First field - a minimum value of concentration to be shown on x-axis.
  • Second field - a maximum value of concentration to be shown on x-axis.
  • "Set" button (or Enter key if the field is focused) - apply the changes.
  • "Reset" button - reset the range of concentration.

Columns

The following columns are reported:

  • Name - compound name
  • Ion Type - detected ion type
  • Formula (M) - molecular formula (M) of the compound
  • Theoretical m/z - theoretical mass-to-charge ratio of the highest intensity peak
  • PubChem Results - number of results with the same formula which were found in PubChem
  • Num. of Datasets - number of datasets in which the respective ion of the compound was detected

The other columns correspond to analyzed datasets. If a user clicks on an item, the corresponding extracted ion chromatogram is shown in Chromatogram window. If a user clicks on the item and CTRL is pressed, the detail of a mass spectrum is opened where the peak with the highest absolute intensity was found. If a user clicks on an item in the columns Formula (M) and PubChem Results, the formula is searched in PubChem and the results are opened in a web-browser. If a user clicks on the column Name, a reference is opened in a web-browser if it was defined in Sequence/Compound Database Editor. If any reference was not defined, the compound name is searched on PubChem.