The software has a new Convert Profile Data to Centroid option for importing Thermo raw data files (.raw). When the option is selected, profile spectra are centroided before being imported. The centroids are calculated as the weighted average of masses with intensities at 50% of the profile peak height. There are two additional settings:
Compatibility: For Thermo raw data files, v2021r2 or older versions invoke a legacy centroiding API of the Thermo MSFileReader library at import when certain MS Data Binning settings were specified in the runtime configuration. This legacy API may result in mass values off by 0.01 compared with profile spectra. With this release,
The software now supports importing MS channels from the Agilent OpenLab raw data file format (*.dx). This support requires that OpenLab CDS version 2.6 or later is installed on the same computer.
The software now automatically sets the modulation period when importing Agilent ChemStation and MassHunter data files that are acquired with an Agilent flow modulation system.
The software now supports calculating concentration from amount with Multiplier and Dilution Factor. New Concentration and Relative Concentration attributes can be added to the Blob Table and included in reports, similarly to the existing Amount attributes.
The software now allows specifying amount unit, concentration unit, multiplier, and dilution factor for the Apply Amount Table method command. The units and factors are stored in methods and can be changed during run time.
Compatibility: For an existing method saved by v2021r2 or older, amount units and factors are not specified in the method and cannot be changed during run time. To specify units and factors, edit the method with the latest release and save.
The Vials > Amount Table in Project now supports importing a multi-column CSV file. The import interface allows users to specify which column contains compound names and which columns contain amounts for which vials. In addition, the import interface has an option to parse Multiplier and Dilution factors for specified vial columns from the rows with "Multiplier" or "Dilution Factor" as compound name.
Inactive Project Vials may now be deleted. A Vial may now have one of three status states:
While importing or editing a Sequence Table, new Vials may be created. After concluding edits to the Sequence Table, some of these Vials may be Inactive. These newly created but Inactive Vials are now automatically deleted after exiting edit mode on the Sequence Table.
Vials, Amount Tables, and Sequence Table now have an in-place editing mode triggered by the Edit button or double clicking on tables. After entering edit mode and making edits, clicking Apply will save the edits, while clicking Cancel will discard the edits.
Also, the interfaces for editing have been reworked in several ways to improve functionality and consistency. This includes the following changes:
In the Investigator program, the feature template creation step of Auto Feature has improved speed.
Additionally, in the Image program, Processing > Extract Areas from Blobs has similarly improved speed.
Investigator automatically adds the Spectrum attribute when loading images with spectral data instead of requiring the user to create a CLIC expression beforehand. The software always loads peak spectrums for the auto loaded Spectrum attribute with mass values up to 8 decimal places and intensities up to 6 decimal places.
Compatibility: If a CLIC column is already specified as a Spectrum attribute, the software will use that CLIC expression to load spectra, as in v2021r2 or older versions.
Compound Finder automatically derives the Base Peak attribute from images with a Spectrum attribute instead of requiring the user to create a CLIC expression beforehand.
Compatibility: If a CLIC column is already specified as a Base Peak attribute, the software will use that CLIC expression in Compound Finder, as in v2021r2 or older versions.
Importing a filtered data channel instead of Full MS from a VUV .db file would throw an exception if a shorter run time was specified.
File > Export Profile to Centroid would throw an exception when exporting from profile data with size greater than 4GB.
The following import options were not remembered on Project's Auto Processing dialog (Run > Auto Processing):
When performing quantification, the warning message was unclear for when multiple blobs exist for a selected compound name. The message has been updated to make the warning clear as well as state the resulting behavior.
The Extract Areas from Blobs menu item was not correctly enabled or disabled after Undo, Run Script, and Run Method actions.
Workaround: If the Extract Areas from Blobs menu item has been incorrectly disabled, saving and reopening the image will fix the menu item.
When plotting values with an extremely small range in 1D view, the program would hang.
Affected Versions: This bug only affected version 2021r2.
When vertically resizing the 1D view window, the Y axis range will re-adjust. In some cases, it was not possible to restore it to its original range by further resizing.
If the image has a CSV calibration table file, creating a method using Method > New Method from Current Image did not save the following Calibration Table settings with the method:
Workaround: Manually adjust the Calibration Table after running the method, or save the .gccm calibration table file and manually apply.
An unclear exception was thrown when running a method with a Subtract Spectrum from Image step on a non-MS image.
When running a method with an Apply Amount Table step, success was reported but no change was made to the amount table if there was already an existing table. Additionally, the command would have no effect if the Amount Table dialog was ever viewed, even when no table was present.
Workaround: If an amount table is present, clear the amount table. Save and reopen the Image software before running the method with the Apply Amount Table step.
Creating a method using Method > New Method from Current Image would not add an Apply Amount Table command properly if the image's Amount Table was set by copying from a file or manually entered.
Certain letters or symbols such as Greek letters or foreign characters would not be exported and then imported correctly for the Amount Table of a project vial.
The Import Images dialog (Project > Images > Import) had a typo (".cgi") in the filename description.
The Project > Vials > Amount Table would sometimes flicker question mark symbols in every cell after committing changes from Edit Table.
The Edit Record button at Project > Vials > Amount Table was always disabled instead of enabling when a row was selected.
Workaround: Double click on a row to edit a single row or click Edit Table to edit the entire table.
Saving a project-linked image to a custom folder within the project (such as one created in the Others node of the project tree) would unlink the amount unit of the image's amount table.
If an existing project with Amount Units defined was open, creating a new project would carry over the units from the open project instead of resetting them.
The Scatter Chart would throw an uncaught exception when attempting to plot data points with infinite values on the Y axis.
The Spectra plots in the Compounds tab had an m/z range defined by the first spectrum rather than an m/z range spanning all considered spectra.
If a previously saved analysis had a Spectrum CLIC column with no entries (due to loading non-MS data), loading MS images to the analysis and saving would result in an exception.
Loading an existing analysis would change the remembered Attribute settings on the Load Images dialog to use the attributes from that analysis instead of those last used when loading images.
If a linked amount table file is not accessible, v2021r2 or older versions remove the path to the linked amount table when the Refresh button is clicked in Quantification > Amount Table. Now, the amount table is emptied, but the path is kept. To remove the path, the Clear button should be used.
In v2021r2 or older versions, the default amount unit (Configure > Settings > Blob Statistics > Calibration Amount Unit > Always use default unit) was automatically applied to and saved with image or project files when no other unit was specified. Now, the default unit is shown in tables, reports, and UI when no other unit is specified, but is not saved to the image or project file.
The legacy XML type is removed from the file chooser for exporting the amount table from a project vial. Now, the CSV type is the default amount table file format that is actively supported. An existing XML amount table file still can be imported manually.
Various labels and UI elements have been changed from "composition" to "amount" when referencing the amount table or compound amounts.
The Report Viewer now defaults to selecting the HTML format as the default when saving. The other file formats can be selected with the file format drop down.