Import Image now imports the known method parameters from JEOL AccuTOF GCx profile or centroid data files acquired by the JEOL MsAxel program. The imported method parameters can be accessed through Image Attributes - Miscellaneous tab or Summary Report - Image Attributes report.
Processing > Extract Ion Peaks as Area Objects now asks a user to delete existing areas before detection. If the user chooses not to delete them, the program will delete an existing ion peak area automatically if an exact duplicate is detected.
Compatibility: Older versions do not check for duplication. Therefore, two identical ion peak areas may be present if ion peaks were extracted twice.
Processing > Extract Ion Peaks as Area Objects now supports Gaussian or Savitzky-Golay smoothing for both Column I and II.
Processing > Extract Ion Peaks as Area Objects now allows a user to specify one or more mass ranges (e.g. "41, 52.5-56.5") using the new Mass Range filter.
Compatibility: The software automatically converts the remembered Min and Max Mass settings specified in old versions to the new Mass Range filter. For example, Min Mass 40 and Max Mass 500 are converted to "40-500,500". The converted mass range represents an effective range from mass 40 to mass 500.5 (exclusive) if the rounding parameter is 0.5 in MS Data Binning settings. The original effective range is from mass 50 to mass 500 (inclusive).
Processing > Extract Ion Peaks to Areas has a new Perform Library Search for Extracted Ion Areas option. If the option is selected, library search will be performed using the deconvolved spectra of extracted ion peak areas automatically.
Processing > Extract Ion Peaks as Area Objects stores additional attributes as custom attributes of the extracted ion peak areas. The following ion peak attributes are reported: Peak 1, Peak 2, RT1, RT2, Peak Width, Peak Value, and Qualifier Count. They can be added to Blob Table - Area tab through CLIC columns using CLIC function CUSTOMATTRIBUTE("Attribute Name").
Processing > Extract Ion Peaks as Area Objects now records the Ion Peak Detection parameters in Journal.
After Start Review, a blob or an area can be selected in Image View directly to review its information. The selection action updates all views including 1D View, SIC, Spectrum View, and Blob/Area Table selection automatically.
Review now updates all views to display information of the currently selected blob or area upon start.
Configure> Settings> Library Search now includes replib from NIST Library in addition to mainlib by default in order to improve the accuracy of the search results for common compounds.
Blob Table now has columns for accessing the top three hit list entries returned by Library Search including:
Additional hit list entries can be added as CLIC columns, for example, "Hit_Name[5]" or "Hit_Match_Factor[5]".
The following three new CLIC functions are added to support matching Reference MS with other spectra.
Investigator now report %RSD (RSD in percents) in addition to absolute values as one of the built-in computed statistics.
Investigator now has a new Analysis menu. The menu replaces the configuration button for selecting computed statistics and provides several preset configurations of commonly used statistics including:
Also, the selected statistic settings are now remembered between sessions.
Investigator now computes class mean and standard deviation as long as there is no missing value for the specific class, which further allows reporting differences and FDRs between two classes that both do not have missing values. In addition, missing values are ignored when overall mean and standard deviation are computed.
Compatibility: v2.8r2 or older versions do not report overall statistics if there is a missing value. Now overall statistics are always reported as long as there is a valid value.
File > Import Agilent 2D-LC might duplicate cuts when importing 2DLC data acquired in comprehensive mode with peak-based cutting if the Combine Comprehensive Cuts option is selected.
Workaround: Import Agilent 2D-LC without selecting the Combine Comprehensive Cuts option will import data correctly, but will not combine cuts.
File > Import an Agilent ChemStation MS file acquired with a mass range beyond 1638 resulted in negative m/zs.
Configure > Settings > Blob Detection > setting the CLIC Filter to an expression that has a scientific notation with negative exponent (e.g. 1e-1) caused an uncaught exception when detecting blobs.
Workaround: Remove negative exponent from CLIC Filter.
Edit > CLIC Expression did not list the ExactMass() function when a non-MS image is open. Manually entering the function did not work because the function was not computed.
A template peak with qCLIC that utilizes chemical formula, such as, ABS(MASSRANK(1)-EXACTMASS("C6H2"))<0.05 did not match any blob even if there is a blob that satisfies the constraint.
Version 2.8r2 did not show the transformed location of graphic objects (e.g. polygons and rectangles) after matching template as previous versions if the Interactive Match or Transform Template UI is not open.
Workaround: Open Template > Interactive Match and Transform after matching template.
During Processing > Search Library, if the searching process is canceled in the middle, the program might throw a null pointer exception. Also, view a spectrum > Library Search > cancel in the middle of process, and then an inaccurate error message of "No match is found in the library!" was shown.
After Review > Start Review > select a blob, the Search Library > Apply Hit list menu was disabled in the drop-down of Library Search of Review MS View.
Workaround: Switch to MS mode > click on the same blob to open the regular MS View > Library Search > Apply Hit List. There is no workaround for searching library with Reference MS that is only loaded during review.
Investigator > Attributes > PCA Chart > set some PCA setting. Then, File > Assign Classes, the specified PCA settings were lost.
Investigator > File > Open an analysis that contains areas, but no blobs. Select Attributes > View Areas > PCA Chart, and run PCA. Then switching between View Blobs and View Areas might cause an uncaught exception.
Investigator > Summary > Filter by Compound Name did not support a simple wild card search as expected. Same problem existed in:
Investigator - Configure buttons at the top-right corner of data tables for selecting computed statistics have been replaced by Analysis > Custom Settings... menu.
Configure > Settings > Search Library > Auto Locate and Browse buttons now only apply the NIST library path change upon Apply or OK. In v2.8r2 or older versions, the change is applied immediately even if canceled later.