TraceFinder Software

Simplifying high-throughput screening and quantitation

Driven by a powerful and intuitive set of acquisition and data processing tools, Thermo Scientific TraceFinder software provides rapid access to your results and increases output across the entire laboratory. Drive your productivity with built-in intelligence provided through TraceFinder software acquisition and data processing. Smart sample flagging, flexible data review, and custom report generation remove the bottlenecks associated with data review and simplify sample analysis at each step of the process. TraceFinder software enables control of multi-channel LC, single quadrupole, triple quadrupole and high-resolution LC-MS systems, as well as IC and GC systems. This control helps streamline and standardize operating procedures, minimizing training requirements and simplifying lab operations.

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Key benefits of TraceFinder software

Maximize productivity Minimize risk Drive workflow flexibility Improve quality

The ability to customize, whether that is for an assay requirement or a user preference, enables faster and more reliable method building and data review.

The customizable user interface allows analysts to display only the desired data parameters and outputs, while storing those that are not required.

Automated data review tools, for identifying components or samples that require additional investigation, are essential for confidence in data quality.

With custom flagging, table sorting and filtering, and customizable reports, results can be prioritized with visual cues that allow data review to be focused where it's needed most.

With acquisition control and data processing for LC, GC, IC, triple quadrupole, and HRAM systems, workflows can be standardized across a single software package.

Using a single software solution across the laboratory allows for consolidated training and greater operational flexibility through streamlined processes.

Screening assays benefit from the inclusion and incorporation of high-quality spectral libraries.

Full integration with the industry leading mzVault high resolution MS2 spectral library, as well as the ability to use custom libraries, delivers superior searching and confirmation capabilities and best-in-class quality.


Strategies for making small-molecule unknowns known

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Learn more about the quantitative and screening capabilities of TraceFinder software

Quantitative workflow requirements often vary based on the application and operating environment. Providing the flexibility to meet a wide range of application and workflow requirements while providing a simplified user interface is at the core of TraceFinder software.

Quantitation is simplified across IC, LC and GC-MS systems for both large and small target lists through:

  • Template-driven workflows
  • Compound databases for method building
  • In-depth data visualization capabilities
  • A customizable user interface
  • Automated custom reporting

TraceFinder software provides a wide range of features and capabilities, but not all features are required for all experiments. Using the application-wide customizable user interface, the workspaces and data display can be configured to visualize as few or as many of the application features as necessary for the analyst and experiment type. Utilizing a fit-for-purpose display increases productivity during system setup, training and SOP development, and assay data review because quantitation isn’t about tedious method development, it’s about being able to make decisions based upon your results.

A display of data that has been simplified to show just the required information
Although there is the need for certain data processing and reviewing functionalities, not all are required. Being able to fully customize the user display to reduce complexity simplifies the review of data, as is shown above where the original display (top) has been simplified to provide review of the information required for this particular assay (bottom); streamlining data review and user training.

Quantitation using a high-resolution accurate mass (HRAM) approach can provide additional benefits and capabilities that increase data quality and confidence in results. To help amplify the potential benefits of a HRAM quantitation approach, TraceFinder software is fully integrated with Thermo Scientific mzVault, the industry’s largest and most highly curated HRAM spectral library based upon the content within Thermo Scientific mzCloud.

In addition to isotopic pattern matching, mass accuracy evaluation, and fragment confirmation, MS2 spectral library matching can be performed against any mzVault library within a given quantitative assay. Coupled with customizable flags and flexible data table layouts, these additional evaluation criteria can be easily displayed and reported providing enhanced levels of confidence to any high-resolution quantitative experiment.

The list of monitored compounds required for targeted screening assays is always increasing, meaning building and maintaining accurate target lists and reviewing all generated results can sometimes create a challenge. With comprehensive and streamlined method setup and data review tools, TraceFinder software meets the challenges of even the most demanding screening assays.

Large lists of target compounds can be easily and accurately managed with the use of TraceFinder customizable compound databases. Target compounds can be added, removed, or edited within the database and subsequently included in a new or existing processing method. Compound databases are designed to include all the information necessary to accurately identify your target compounds and can be created by manual entry or through the automated import of instrument inclusion lists and csv/text files. For example, these files might come directly from Thermo Scientific Compound Discoverer software.

Search features can be easily included or excluded
Targeted screening methods in TraceFinder software focus around three main search features: retention time, fragment ions, and isotopic pattern. Each search feature can be easily included or excluded within the processing method and optimized with user-defined criteria to provide the right level of search requirements for any assay.

Increasing confidence in the screening assay results helps to simplify data review and increases productivity. In addition to retention time, fragment ions, and isotopic pattern searching, spectral library searching for high-resolution accurate mass data delivers an unmatched level of confidence to the targeted screening workflow.

Library searching in TraceFinder software is fully integrated with both mzVault (based upon the extensive content from mzCloud) and NIST libraries to provide a powerful and customizable set of search criteria. Library matching specifications can be optimized based on both precursor m/z and MS2 match scoring, with both forward and reverse searching strategies.

An example showing color-coded indicators, library matching flags and configurable data displays in TraceFinder software
Identifying relevant results is essential in any screening assay; with color-coded indicators, library matching flags, and configurable data displays, TraceFinder software makes data review fast and efficient. Additionally, built-in filtering tools such as matrix blank subtraction, retention window limits, and the option to display only the target compounds found in the sample, means less time needs to be spent reviewing large data sets, allowing more time for other value-added activities.

Though targeted screening workflows in TraceFinder software are powerful and easy to use, some screening assays require additional quantitative components; targeted screening workflows can be built directly into general quantitative methods, providing ultimate assay versatility.

When targeted screening is combined with quantitation, library matching and calibration curves can be reviewed together in the customizable layout, with color-coded visualizations to aid data review. Custom flags for library matching and quantitative results can be displayed based on analyst preference and assay requirements, streamlining the data review process and enhancing efficiency.

An illustration of the plots available to show relevant data for your samples
The display capabilities allow you to review data based upon what you need to see, with multiple plots available to show relevant data for individual samples or multiple compounds within a sample or across samples. Utilize multiple monitors and pop out windows to view your data, from peak integrations, calibration curves, spectral isotope matches, fragment confirmations as well as a wide range of available tabulated data; all configurable based upon your users, assays and data needs.
An easy-to-view list of compounds to be screened and quantitated in an assay
Target compounds are easily selected from any available TraceFinder compound database, creating an easy-to-view list for all compounds to be screened and quantitated in the assay. Target compounds can be added, removed, or edited all within the processing method.

Additionally, processing methods can be built directly from data files using the intelligent TraceFinder Method Forge tool. Method Forge automatically enables large numbers of target peaks to be identified within a data file and built into the TraceFinder software processing method with minimal editing and modification from the analyst.

While defining the target components and processing parameters for any targeted screening assay is an important first step, adjusting these parameters when necessary is just as critical. TraceFinder software provides a wide array of tools for adjusting integration parameters, confirming peak ratios, and other critical parameters on a peak-by-peak basis or globally across the method. Additionally, one of the most important identifying criteria in any screening assay is the expected chromatographic retention time for each target compound; as chromatographic columns age, or as gradients are adjusted, fast and easy updating of target retentions times is essential.

Tools within TraceFinder that adjust target retention time
TraceFinder software has several tools for adjusting target retention time including a global adjustment by time, percentage, linking to a reference file or auto-adjustment by linking to reference compounds within the sample.

The ability to identify features of interest in a single sample or across a large set of samples requires a wide-ranging set of tools. TraceFinder software for unknown screening has combined best in-class library search capabilities with a comprehensive set of data visualization tools to provide a reliable, straightforward workflow for unknown component detection.

Confidence in unknown component identification is increased through tools such as:

  • Heat mapping
  • Cross-sample peak lists
  • Cross-sample peak overlays
  • Group averages
  • Isotope matching

Unknown screening in TraceFinder software provides the highest flexibility for any environment; component detection can be utilized for individual sample analysis or across a large sample set and can be added to any subsequent targeted screening or quantitation method providing maximum productivity in any workflow.

Visualization tools within TraceFinder help interrogate large data sets
TraceFinder software provides multiple options to easily visualize and interrogate large datasets, such as using heat maps for group analysis, user defined retention time alignment, and simultaneous library searching for mzVault and NIST. This comprehensive set of tools helps to facilitate identification and simplifies the decision-making process.

The ability to easily and accurately report assay results is as essential as the data acquisition itself and is often a laboratory bottleneck. Although there are standard reporting templates, customized report generation is an integrated component within TraceFinder software saving time and resources, minimizing the potential for error, and maximizing throughput.

View of a custom report built in the TraceFinder software
With intuitive and predefined options for inserting chromatograms and building data tables, custom reports can be easily built to meet a wide range of reporting requirements. A broad selection of pre-built reports is available and ready for immediate use or can be used to provide a starting template for further report customization.
Additional reporting features include custom logic statements, data filters and custom calculations
Report generation provides an additional tool for assay evaluation that can built into the overall data review process. Using additional reporting features such as custom logic statements, data filters, and custom calculations, the custom reporting capability can be utilized to provide a high-level overview of assay results and to identify samples that require additional interrogation with the data review workspace. Custom reports can be generated automatically or on-demand for batch analysis providing flexibility throughout the data review process.

TraceFinder software not only has the ability to control multiple inlets (IC, LC, GC and multi-channel LC) and types of instrumentation (single quadrupole, triple quadrupole and high-resolution MS), it also allows bi-directional flow of methods and results from LIS/LIMS (Laboratory Information System/Laboratory Information Management System) to further enhance your productivity.

A diagram showing the relationship of LIS/LIMS to B Link and TraceFinder software

B-link®, a universal instrument connector, enables TraceFinder software to connect any LIS, LIMS or middleware, allowing the transfer of requests, information, and results. These requests can be in real time or in batch mode, without any user-action required within B-link once an initial simple system integration has been performed.


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