GC IMAGE - GC Image LCxLC Edition - User Guide 2024R3

New Features and Improvements in Version 2024

GC Image LCxLC Edition 2024 has many new features and improvements. See the GC Image LCxLC Edition User Guide for full documentation.

What's New in Version 2024 Release 3 (December 2024)

New 64-bit Support for Importing Thermo Raw Data Files

Version 2024R3 now supports the 64-bit Thermo Scientific MSFileReader (including the latest version 3.1SP4) for importing Thermo .raw files. This upgrade enables the importing of larger .raw data files and improves overall import reliability.

Faster Rolling Ball Baseline Correction

The rolling ball baseline detection algorithm now has substantially faster performance, particularly when using small ball radius values.

Improved CLIC Functionality and Performance

Version 2024R3 significantly improves CLIC capabilities and performance, including:

• Increased CLIC Column Support: The Blob Table now supports up to 20 CLIC columns, doubling the previous limit of 10.
• Improved CLIC Performance: Faster CLIC column recomputation leads to faster operations for editing blobs, undoing actions, and initiating review.
• New CLIC Functions:
  • ISNAN( arg1 ): Checks if the argument is not a number.
  • STRCONCAT( string1, string2, ... ): Concatenates the specified strings.
• Enhanced Isotopic Functions:
  • The ISOTOPEMATCHES, ISOTOPESIMILARITY, and MATCHEDMASS CLIC functions now support using configured mass binning settings.
  • The ISOTOPEMATCHES and ISOTOPESIMILARITY CLIC functions are now significantly faster.

Comprehensive Library Search Review Mode HRMS/Adv-MS Only

Version 2024R3 introduces a dedicated Library Search Review mode designed for efficient evaluation of library search hit list assignments and more confident compound identification for all blobs. This mode incorporates:

• Hit Evaluation Constraints: Leverage predefined Blob Table columns to assess hit quality based on factors like retention index, base peak, molecular weight ions, and isotopic similarity.
• Color-Coded Scoring: Visually identify compounds with uncertain (yellow) or likely incorrect (red) identifications through color-coded values.
• Alternative Hit Selection: Easily explore and select alternative identifications in hit lists from the interface.

Spectral Group Review Mode with Targeted Ion Chromatograms HRMS/Adv-MS Only

Version 2024R3 introduces a new Spectral Group Review mode that facilitates rapid exploration and visualization of targeted ion chromatograms (SICs) defined by a variety of input sources.

• Flexible Range Selection: Analyze data based on the full spectral range, common hydrocarbon groups, or custom spectral ranges imported from CSV or XML files.
• Interactive Range Exploration: The Review Spectral Ranges table enables interactive selecting and viewing of SICs and supports options for adjusting spectral ranges based on tolerance, adducts, etc..

New Configurations and Enhancements for Review Mode

Version 2024R3 introduces several improvements to Review Mode, including:

• New 1D View Settings: Control visibility of blobs or areas in 1D View with Always Show Blobs and Always Show Areas options.
• Improved Initialization:
  • Review now automatically selects the first blob if no selection exists.
  • Review now automatically displays the selected spectrum from the hit list.
• The 1D View now displays a more descriptive title for the SIC data series.
• Duplicating an existing configuration now creates a configuration with a unique display name.
• The features table of a review configuration is now more readable with a wider feature column and improved resizing behavior.

Improved Support for Multi-Sample Alignment Workflow

Version 2024R3 now includes an Enhanced with Library Search option for the Auto Feature workflow, which provides a convenient way to enable library searching on feature areas in order to assign potential identification for each feature in the feature template.

What's New in Version 2024 Release 2 (September 2024)

New Enhancements and Improved Usability for 1D View

Version 2024R2 includes significant improvements to the 1D View:

• Blob Selection: When the Show Blobs option is enabled, blobs can now be selected directly from the 1D View graphs. Hovering the mouse over a blob will highlight the blob, and show the blob ID in the tooltip.
• Layout and Navigation: The graph layout now ensures a minimum graph height while expanding to fit the specified view count. A scroll bar has been added to replace the page buttons, allowing for smoother navigation through multiple graphs.
• Series and Groups: The 1D View series list has been improved for better organization. A new Groups table provides a clear overview of graph groups, allowing users to select rows to highlight and scroll the corresponding graph into view. Additionally, selecting a row from the Series table will now highlight the series in bold within the graphs.
• Unit Labels: Location-based series and group names now include units, providing more context. In addition, the graphs' x-axis labels display units.
• Visual Enhancements: The 1D View graphs have been visually improved with the use of anti-aliasing and better y-axis label positioning. These enhancements also benefit the MS Viewer.

Enhanced Ion Chromatogram Extraction with Peptide Sequence

Version 2024R2 introduces enhanced capabilities for MS range selection, allowing users to specify peptide sequences for selected ion chromatogram (SIC) extraction.

• Peptide Sequence Input: View SIC now accepts peptide sequences represented by one-letter symbols for amino acids. The MS Viewer also accepts peptide sequences.
• Delta Mass Consideration: A Delta Mass field is available for specifying the mass change from peptide modifications.
• Adduct Selection: The MS range editor now remembers recently used Adduct selections, making it easier and more efficient to choose adducts for the following analysis.
• MS Range Table Enhancements: The MS range tables of the MS Cube and Multiple SIC View tables have been updated to show Expression and Tolerance columns.

Enhanced Review Mode for Examining Ion Peak Areas

Version 2024R2 includes several enhancements to the Review Mode for evaluating ion peak areas:

• Ion Peak Width Metadata: Ion Peak detection now reports additional peak width properties including front-half, back-half, and FWHM. These new properties provide more insights into ion peak shapes.
• 1D View Enhancements in Review Mode:
  • Area Display: Visualize ion peak areas and review detection in the 1D View with the new Show Area display toggle.
  • Area Selection: Select drawn areas directly in the 1D View for easier interaction.
  • Selection Ions: Choose the number of Qualifier and Quantifier ions to display individually in the 1D View to examine prominent and apexing ions with the new Review Configuration options.
  • Apex Normalization: Compare individual ions apexing together more effectively with the new Apex Normalization option, which normalizes all plots to the selected blob or area's apex location.
• Tile Selected Windows Enhancements:
  • Freeform: Fit windows to a custom grid based on their current positions with the new Freeform option.
  • Revert: Quickly restore the previous layout with the Revert button.

Improved Alignment Control and Performance for Multi-Sample Analysis

Version 2024R2 introduces several enhancements to multi-sample analysis:

• A peak template can be specified to provide reliable peaks for the Auto Generate Feature Template process. This allows for direct control over which chromatogram peaks are used in the alignment process, such as a set of internal standard peaks. This new option significantly reduces the processing time compared to the automated creation of reliable peaks.
• The performance of spectrum parsing and spectral matching calculations is substantially improved. This translates to quicker execution of the Compound Finder, with the processing time decreased by as much as 20%.

What's New in Version 2024 Release 1 (March 2024)

Improved Reliability and Performance for Importing Shimadzu Data Files

Version 2024R1 introduces significant improvements to the reliability and performance of importing Shimadzu GCD, QGD, and LCD files. The readers for Shimadzu files have been optimized to eliminate random failures and significantly improve speed and efficiency.

Enhanced Quantification with Group-Based Response Factors

Version 2024R1 includes a suite of new features designed to streamline and enhance the quantification workflow using group-based response factors.

• Improved Calibration and Response Factor Options:
  • New Calibration Table from Response Factor Table: Easily generate a calibration table from existing response factors with the new New Calibration Table from Response Factor Table menu under Quantification.
  • Support Fit Intercept to 0: Gain greater control over calibration ranges by forcing a calibration curve to pass through the origin (0,0) with the new Set Intercept to 0 option.
  • Flexible calibrant assignment for Unknowns: Choose None, Default, Group Neighbor, or Nearest Neighbor for uncalibrated compounds.
  • Default Response Factor for Unknowns: Apply a pre-defined Default Response Factor to uncalibrated compounds.
  • Target Group Assignment for Calibrants: Enhance the accuracy of your group-based calibration by assigning specific target groups to individual calibrants using the new Target Group option.
• Improved Reporting and Visualization:
  • Interactive Calibration Report: Review the calibration quality with an interactive report directly accessible from the Calibration Table.
  • Response Factor Column in Calibration Report: View response factors alongside other crucial calibration parameters, if appropriate.
  • ISTD Column Visibility: ISTD columns are now only displayed for ISTD calibrations, simplifying reports.
  • Increased Decimal Places for Amount and Response: Improved visualization of small values in the Calibration Table with 4 decimal places displayed for amount and response values.

Enhanced Side-by-Side Chromatogram Comparison

Version 2024R1 has new and improved functionality for Compare Images Side-by-Side, making user analysis workflow more efficient and intuitive:

• Enhanced Navigation: Auto-pan functionality upon selecting a blob in the Compare Images tables eliminates the need for manual scrolling, allowing the user to focus on specific regions of interest in both chromatograms easily.
• Customizable Blob Attributes: Customizing blob attributes based on current blob table configuration allows the user to tailor the displayed information to the user's specific needs and highlight the information most relevant to the investigation.
• Multitasking: The enhanced Compare Images tool now allows the user to open multiple instances, each operating independently. This enables the user to interact with other tools freely, while comparing the open image with multiple images side-by-side and performing additional analyses concurrently.

Improved Multi-Sample Alignment Workflow

Version 2024R1 has several improvements to the Auto Feature workflow, designed to streamline the process and enhance efficiency:

• Automatic ISTD Selection: The Auto Feature process now automatically identifies and sets the internal standard (ISTD) present in all samples within the feature template. This ensures that the subsequent analyses are based on reliable and consistent reference peaks derived from the same ISTD compound across all samples.
• Improved Error Handling and Logging: During the Auto Feature validation step, any invalid run paths will now be logged for easier troubleshooting. This helps identify potential issues with data inconsistencies and facilitates addressing them promptly.
• Persistent Configuration for Streamlined Analysis: The Use Configuration option will now persist across sessions. This eliminates the need to manually re-select the option each time for a multi-sample alignment task.

Simplified Multi-Sample Comparison with New Compound Finder Algorithm and Enhanced Spectra View

Version 2024R1 includes two new improvements that will enhance the workflow for analyzing and comparing compounds across multiple sample classes:

• New Compound Finder Algorithm: The enhanced Compound Finder 2024r1 algorithm improves the identification of both common and unique compounds. It analyzes representative spectra of defined classes, focusing on those consistently present within the majority of samples belonging to the same class. These representative spectra are then compared with spectra from other classes. This refined approach leads to more accurate identification of common compounds across multiple samples and unique compounds specific to individual samples.
• Enhanced Spectra View: The Spectra View now provides a clearer and more informative presentation of class data, including:
  • Class names in title - Quickly identify the associated class for each spectrum.
  • Class groups - Easily visualize spectra grouped by their assigned class.
  • Alternating color scheme - Improved visual distinction between different classes in the spectra plot.

Improved Window Management

Version 2024R1 introduces several enhancements to the window management system, making it easier to organize the workspace, including:

• Enhanced Window Layout: The Tile Selected Windows menu now manages all open windows, allowing the user to easily arrange them in various tile layouts.
• Enhanced Window Switching: Access any open window directly from the Windows menu, eliminating the need to look for them on the screen.
• New Close All SIC Windows Menu: Close all SIC windows with a single click.
• Auto Window Repositioning: Off-screen windows will automatically come back into view when selected. Also, the main Image window will be placed into view if it is off-screen. This improvement makes it easier to switch between single and dual monitor setups.
• Clearer Layout Icons: New icons for Tile Vertically and Tile Horizontally menus provide a more intuitive understanding of the available layout options.

Other New Improvements

Version 2024R1 has other improved operations, including:

• Simplified MS Range Editing:
  • Up to 10 recently used MS ranges and formulas for opening SIC views and selecting ranges will be remembered. This helps save time and effort when revisiting frequently used analyses.
  • A list of common hydrocarbon general formulas is now conveniently listed within the MS Range edit UI. This eliminates the need for manual entry and reduces the risk of errors.
  • The MS Range edit UI pane is now more compact and collapsible in MS View.
• Enhanced Blob Set Table: For analyses involving sets of sets (e.g., constellations, graphic groups, residuals), Blob Set Table has a new ordering and color scheme. This improved visualization makes it easier to identify and differentiate between different levels of group hierarchy.

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GC Image™ LCxLC Edition User Guide © 2001–2024 by GC Image, LLC, and the University of Nebraska.