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.

Mesh Objects

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.

Graphic Group

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.

CLIC

LCxLC Software R2.1 has significant improvements for the Computer Language for Identifying Chemicals (CLIC)™:

• CLIC supports a set of mathematical functions such as power(), sqrt(), ln() and so on.
• 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 FirstDerivativeLeastSquares().
• 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.

• Blob Analysis Tool provides principal component analysis on spectra of blobs.
• Blob Analysis Tool supports a spectral channel as a plot axis.
• Blob Analysis Tool provides a configurable tool tip for mouse-over.
• Blob Analysis Tool provides enhanced mouse behaviors.

Template Matching

LCxLC Software R2.1 has several improvements for template matching:

• LCxLC Software R2.1 provides a comprehensive quality report for template matching.
• LCxLC Software R2.1 allows users to switch between views of the template and the matched peaks and transformed objects.

New and Improved Reporting

LCxLC Software R2.1 introduces new user controls for customizing summary reports and other reports.

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.

Image Investigator™

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 Set Table.

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 Image Attributes.
• 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 for images.
• 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 menu.
• 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.

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LCxLC Software Users' Guide © 2001–2010 by GC Image, LLC, and the University of Nebraska.