- 1 Chromatogram File Explorer (FID)
- 2 Chromatogram Overview (FID)
- 3 Chromatogram File Explorer (MSD)
- 4 Chromatogram Overview (MSD)
- 5 Chromatogram Editor
- 6 Chromatogram Overlay
- 7 Scan (Nominal)
- 8 Peak Targets
- 9 Baseline and Chromatogram
- 10 Selected Ion Chromatogram (Nominal)
- 11 Chromatogram Heatmap
- 12 Peak List
- 13 Processing Info
- 14 Chromatogram Targets
- 15 Edit History
- 16 Excluded Ion Chromatogram (Nominal)
- 17 Scan (Exact)
- 18 Scan (Accurate)
- 19 Mass Spectrum Ions List
- 20 Mass Spectrum Targets
- 21 Peak Mass Spectrum Ions List
- 22 Peak Mass Spectrum
- 23 Peak Values List
- 24 Peak
- 25 Peak With Background
- 26 Selected Ion Chromatogram (Accurate)
- 27 Selected Ion Chromatogram (Exact)
- 28 Selected Ion Chromatogram (Nominal - Combined)
- 29 Selected Peak And Chromatogram
- 30 Mass Spectrum
- 31 Profile Mass Spectrum
- 32 Mass Spectrum File Explorer (MSD)
- 33 Peak Integration Entries
- 34 Peak Quantitation Entries
- 35 Selected Ion And TIC Chromatogram (Nominal)
- 36 MassBank
- 37 SciFinder
- 38 MaSC
- 39 Chromatogram Overlay (Selected Ions)
- 40 Ion Transitions
- 41 Scan (Transition)
Chromatogram File Explorer (FID)
FID files can be selected and loaded from file system. At the moment the only readable vendor-specific FID files are Agilent .CH-files. Apart from this text files holding 2-columns (1st column: Rentention times in min., 2nd column: intensities) can be opened if they are renamed to .xy files. Note, that negative intensity values are not readable at present.
Chromatogram Overview (FID)
Display of a preview of FID/xy chromatograph selected in the File Explorer. Apart from export processing of these files is not implemented yet.
Chromatogram File Explorer (MSD)
MS files can be selected and loaded from file system. The readable vendor-specific formats are listed under Supported File Formats. Note, that in the Community edition only the OpenChrom format .ocb and the open format mzXML are available in the basis software after installation. Access to all other formats listed is granted after their installation via the Marketplace. They are free to use but not open source.
Chromatogram Overview (MSD)
Display of a preview of a chromatograph selected in the File Explorer and recorded in a supported MS data format.
The Chromatogram Editor is the default view for all loaded chromatograms. The results of most processing steps on the active chromatogram are displayed here. Note, that if a retention time window is selected most subsequent processing steps are only applied on this window.
In this view all loaded chromatograms are displayed in overlay. If further chromatograms are loaded or loaded chromatograms are closed the view is updated. Whichever chromatogram is selected in the Chromatogram Editor is the „primary“ chromatogram in the Overlay view. To improve the distinction between the chromatograms it is advised to activate the Legend in the Chromatogram Overlay view. It may be of additional help to use offsets for the overlayed chromatograms: Menu > Window > Preferences > OpenChrom > MSD Preference Page. The colorscale for the graphs can not be edited yet.
This view shows the mass spectrum corresponding to a scan selected in the active chromatogram in the Chromatogram Editor (marked with a "+"). The view is updated on every selection of a new scan. Information on the selected scan, retention time and the intensity of the total ion current (TIC) at the selected scan are displayed above the view along with the type of detector and acquisition mode. In the mass spectrum ions can be selected by clicking on the ion traces. The extracted ion chromatograms will be shown in the Selected Ion Chromatogram view (Selected Ion And TIC Chromatogram).
The Peak Targets view shows the identification results for a selected peak and is updated according to the peak selected in the Peak List view. The identifications may have been edited manually or obtained by mass spectral search of the NIST MS Search software. The number of listed candidates corresponds to the number of desired „best matches“ selected in the preferences of the NIST identifier plug in. Manual peak identification for each peak is edited via the Menu > Chromatogram > Identifier > Manual Identify or the icon. If a chromatogram is stored as an .ocb file all identification results are retained and are excessible after reopening. Note, that manual peak identification results have to be edited for each chromatogram separately. The commercially available plug in PeakIdent allows to create and query user-built mass spectral databases.
Baseline and Chromatogram
The Baseline view displays the active chromatogram in the Chromatogram Editor. If a baseline detector is applied on the chromatogram the result hereof will be displayed. The detected baseline is marked by a red line. Note, that a baseline is only detected for the retention time range displayed in the Chromatogram Editor. A subtraction of the detected background below the baseline can not be subtracted from the chromatogram yet. But the abundance of the calculated background is stated in the text-report.
Selected Ion Chromatogram (Nominal)
This view displays user-selected ion chromatograms extracted from the active chromatogram in the main Chromatogram Editor. The selection of ions can be done interactively using the Scan view (nominal or exact). Optionally the ions can also be selected in the Options flag of the main Chromatogram Editor.
The Heatmap shows a graphical representation of the active chromatogram in the main Chromatogram Editor where the individual intensities contained in a matrix of scans over m/z values are represented as colors. The cursor indicates the m/z, scan and intensity at current location in the map. Note, that values of m/z and scan are displayed by the cursor with 2 decimals due to interpolation between values.
As soon as peaks have been detected by the implemented peak detectors this view displays the list of peak details corresponding with the peaks shown in the active chromatogram in the main Chromatogram Editor.