LCxLC Software Users' Guide
New Features and Improvements in Release 2.1
LCxLC Software Release 2.1 (March 2010) has many new features and improvements. See the
LCxLC Software Users' Guide for full documentation.
LCxLC Software R2.1 introduces mesh objects for comprehensive
group analysis. A mesh object is a collection of panels that supports shared edges
and vertices. Chemically similar compounds often form a cluster of peaks. A panel
of a mesh can be drawn to include the peaks of desired compounds and exclude the
peaks of other compounds. The mesh allows a set of panes that can be used for comprehensive
analysis, i.e., covering all of the relevant regions of the chromatogram. LCxLC
Software R2.1 provides a suite of tools that can be used to create complex mesh
objects in a short amount of time.
LCxLC Software R2.1 allows users to define graphic
groups. A graphic group allows reporting of summed blob set features for
a set of graphics. Each graphic group is comprised of a set of graphics with the
same group name that are either areas or included graphics.
LCxLC Software R2.1 has significant improvements for the Computer Language for Identifying
- CLIC supports a set of mathematical functions such as power(), sqrt(), ln() and
- CLIC supports nested functions and expressions.
- Users can specify the peak MS or integrated blob MS with any MS function with "@"
operator (for example "MassRank@peak(1)").
- CLIC supports eight new MS functions, MassRank(), Correlation(), FirstDerivativeCorrelation(),
Euclidean(), AbsoluteValue(), FirstDerivativeAbsoluteValue(), LeastSquares() and
- The Ordinal() function supports multiple m/z arguments.
- LCxLC Software R2.1 allows users to perform customized global qualitative/quantitative
analysis on all blobs with any number of CLICs in Blob Table.
- LCxLC Software R2.1 allows users to perform customized local qualitative/quantitative
analysis on any blob with Analysis CLIC in Blob Properties.
Linear Retention Index
LCxLC Software R2.1 allows users to define one linear retention index
calibration table for each column and automatically computes the linear retention
index for all analytes (blobs and area objects).
New and Improved MS Viewing and Operations
LCxLC Software R2.1 has significant improvements for spectral data analysis.
The MS Viewer now supports:
- Displaying and comparing multiple spectra in one window with three new layouts:
Overlaid, Head-to-Tail, and Difference.
- Displaying spectra from the hit-list returned by library search and pushing library
search hit-lists to blob metadata.
- Improved scrolling over the spectral range and enhanced zooming control.
- Control of the color and visibility for each spectrum.
- Arithmetic operations to add and subtract spectra.
- Scalar operations on spectra for addition, subtraction, multiplication, and division.
- Copying a spectrum to the clipboard as a table or string (full range or selected
range) and copying the MS graph as an image.
LCxLC Software R2.1 introduces a Batch Mode for library search with search performance
up to ten times faster than Interactive Mode.
Blob Analysis Tools
LCxLC Software R2.1 provides several new blob analysis tools and improvements.
LCxLC Software R2.1 has several improvements for
New and Improved Reporting
LCxLC Software R2.1 introduces new user controls for customizing summary reports and other
The Blob Set Table allows user control of
which columns are included and the order in which the included columns are listed.
The Summary Report now supports:
- Saving and reusing multiple Summary Report configurations.
- Reporting in Microsoft Excel file format (.xls).
- User control over the region, size, and orientation of the Image Viewer subreport.
- A simpler mechanism for including a user-selected logo.
- User-supplied comments.
- User control over the inclusion and order of metadata in the Image Attributes subreport.
- Inclusion of an external, user-generated CSV file as a table.
- A setting to include a combined CSV table in a report.
LCxLC Software R2.1 allows users to define a set of rules to filter blob table with Filter Report.
LCxLC Software R2.1 introduces a new interface,
Image Investigator™, which
allows users to analyze multiple chromatograms interactively. Image Investigator
allows users to compare chromatograms, blobs, areas, and blob sets from a set of
chromatograms, and examine the statistical characteristics and trends. In later
releases, Image Investigator will be enhanced with capabilities for clustering,
classification, and fingerprinting. The existing Image Comparison tool, which supports
pairwise chromatographic comparisons, also is included in LCxLC Software R2.1.
Qualitative and Quantitative Analysis
LCxLC Software R2.1 has several improvements for qualitative and quantitative analysis.
- A Reference Peak can be assigned to a
blob to provide additional statistics for quality control, including retention-time
differences, resolutions, and volume ratio.
- The Blob Set Table reports on the residual
set that consists of all blobs not included in any blob set.
- The Area Table reports on the residual area
that consists of all regions not inside any area.
- Users can choose among the total blob volume, area volume, and image volume as the
total response for calculating the percent response for blobs and areas.
- Users can specify the unit of measurement
for calibrated amounts included in reports.
- LCxLC Software R2.1 allows users to define qualifier
and quantifier in Blob Properties.
- LCxLC Software R2.1 allows users to perform internal/external standard calibration with
TIC or quantifier responses.
- LCxLC Software R2.1 reports the summarized amount and amount source for blob sets in Blob
New and Improved Visualization
In LCxLC Software R2.1, the Image Viewer provides several new visualization features.
- Auto Text allows users to select image attributes
(such as source file, sampling rate, modulation period, or user-defined fields)
to be displayed as a text object on the image.
- Users can add a legend with user-defined metadata.
- Users can display an optional colorization legend.
- Users can specify labels for the Column and Column II axes, as well as for the intensity
axis shown in the 3D Viewer.
New and Improved I/O Support
LCxLC Software R2.1 has new and improved I/O facilities.
- Export Image has user controls for the region,
size, and orientation of exported pictures.
- Export Image allows users to export an image
into a one dimensional or two dimensional CSV file.
- Export Image allows users to export the spectra
of selected blobs into a text MS file.
- Additional metadata fields are imported from Agilent Chemstation data files, including
instrument model and sample name.
- Users can add custom metadata fields to the
- LCxLC Software R2.1 can export and import mzXML files.
- LCxLC Software R2.1 allows users to specify an intensity threshold to filter out spectral
peaks during import.
Other New and Improved Operations
LCxLC Software R2.1 has many other improvements, including:
- Included Graphics and Areas have a new Close
flag that can be used to prevent double counting for polygons inside other polygons.
- The Compound Library now supports chemical name and formula searches.
- The Compound Library allows users to export all or selected compounds to and import
compounds from CSV files.
- The Compound Library has a Description field.
- Blob, Area, Graphic objects and Blob Sets have a new Description field that can
be loaded automatically from the Compound Library (if available) with Auto Fill.
- The software is enhanced to support
importation of Sequence Tables with a flexible CSV Importer.
- The software allows Auto Process of linked
runs from a data path specified in Sequence Table.
- The software allows users to create and manage
additional folders in a project.
- The software provides an option to automatically set the color maps of imported
images to use Default, Automatic, Linear, Logarithmic or Exponential value mapping.
- LCxLC Software R2.1 allows users to specify LIMS numbers
- LCxLC Software R2.1 allows users to specify Minimum
Volume Filter for Blob Detection.
- LCxLC Software R2.1 provides standardized and improved mouse behaviors in all modes.
- LCxLC Software R2.1 allows users to lay out multiple selected channel chromatogram windows with Windows
- LC Project R2.1 reports detailed run time for each processing step in Process Runs
and Auto Process.
The people of GC Image welcome your suggestions
of new features, your comments about existing features and documentation, and reports
of any problems. We strive to make LCxLC Software meet the needs of our users in
their many varied applications.
LCxLC Software Users' Guide © 2001–2010
by GC Image, LLC, and the University of Nebraska.