Software to power your SCIEX ecosystem

This is where you enter details about your samples, including the mass spectrometry and liquid chromatography methods and the autosampler values, such as rack position, plate type, vial position and sample injection volume. You can also indicate the processing method to use and where to save the results file in the directory. Building a batch is simple and straightforward, and any existing Analyst software methods can be directly imported into SCIEX OS software.

Other features available in the Batch workspace include auto-calibrate functionality, which enables accurate mass systems to select the right type of calibration solution for your method and the plate layout of the autosampler rack. Previously saved batches can also be reopened, and the Manage tab can be used for adding rows to your batch. When your details are entered, the batch is ready to go and you can hit submit.

After you hit submit in the Batch workspace, you can view the progress of your analysis in the Queue workspace. The acquisition status is displayed, so you can quickly see that your samples are running smoothly. The estimated start time allows you to forecast when the analysis will be complete.

The Queue workspace displays many of the same details from the Batch workspace, such as MS and LC methods. You have the power to start and stop the queue from here, should you wish to make changes to your batch.

Decision rules functionality allows for immediate detection of failures and implementation of corrective action based on criteria that you establish. This non-subjective decision making adapts to changing conditions during analysis.  The decision rules functionality continually checks against customized criteria. With decision rules, you don't have to wait for acquisition, data processing and data review to discover failures and take action.

SCIEX OS software enables you to build separate liquid chromatography methods. The information displayed in the LC Method workspace will depend on the LC configuration you select for your analysis. Here, you can input all the details regarding flow rates, autosampler conditions, column oven temperature controls and potential wavelength data for photodiode array detector (PDA) wavelengths. You can also adjust any other settings you may need, such as executing an auto-purge before analysis.

The Tuning Procedures drop-down menu shows specific options for you instrument. You can use the detector optimization tool to optimize the detector voltage if you notice the sensitivity of the system seems low.

SCIEX OS software enables automated tuning for the SCIEX Triple Quad 7500 system and the X500 series QTOF systems by calibrating all scans across all modes for added confidence that your system is ready to use with fast, easy and simple tuning.

Your instrument will be calibrated correctly with built-in acceptance criteria for a higher first-time success rate, saving you a significant amount of time.

• Faster and easier tuning
• Easy troubleshooting
• Increased calibration confidence

A single calibrant for both positive and negative mode means:

• No calibrant contamination
• No changing solutions
• One 1 optimization procedure

In the MS Method workspace, you can create a standard MRM or MRMHR method, depending on whether you are operating a SCIEX Triple Quad system or an accurate mass instrument. If you are running a SCIEX accurate mass instrument, you might want to create a SWATH acquisition method. Guided method creators are available to assist you in developing new methods for new analytes you want to analyze.

Source parameters (such as source gases, curtain gas and temperature settings) for the Turbo V ion source and the OptiFlow Pro ion source can be configured here.

The Experiment section is for selecting the type of experiment to run, such as TOF MS, MRM and MRMHR. You can select multiple experiments for your analysis, so your system can acquire even more data for you.

Whether it's an infusion, flow injection, on-column or MRM3 approach, the automated compound optimization feature for quantification is simple, flexible and completely automated. There are also options for choosing optimal parameters such as signal-to-noise (S/N) ratio or intensity requirements.

Scheduled MRM (sMRM) helps drive the accuracy and precision of your mass spectrometer. sMRM accounts for any potential retention time (RT) drifts, and all RTs can be updated with a single click. sMRM also has functionality to call out single dwell time instances so you can maximize the abundance of low-intensity ions. In addition, interactive sMRM plots dynamically update with any changes in the sMRM method.

Leveraging the latest acquisition techniques and built on a heritage of proven performance, Biologics Explorer software delivers highly accurate and informative workflows for fully characterizing protein biotherapeutics.

A data visualization tool designed for scientists who wish to visualize their data in terms of sample groupings and apply statistics in order to gain valuable insight into any trends within their mass spectral data. MarkerView is unique in that SCIEX users can explore statistical correlations with direct connections back to the raw data. This allows them to find meaningful relationships much more quickly. Particularly useful for metabolomics, lipidomics, proteomics, food authenticity and water testing.

The navigation tools in the Explorer workspace allow you to quickly move through the samples for an overview of your data. You can view the data in several ways depending on your preference.

• Show tab: allows you to view the total ion chromatogram (TIC), extracted ion chromatogram (XIC) and IDA explorer
• Graph tab: shows different options for displaying your data and allows you to customize the labels in the graph
• Process tab: allows you to apply settings such as baseline smoothing and specify how your data will be processed
• Bio Tool Kit: opens up a section that enables the peptide sequencing

Review by exception

Spend less time digging for answers. Only review data of interest with flag-based labelling and filtering tools.

1. Peak Integration

Increase performance with the powerful AutoPeak integration algorithm for more reliable integration across samples, batches and analytes. This will allow you to achieve reliable peak integration with ease, even with low-level peaks and complex matrices. No manual intervention is needed to re-integrate peaks, remove interferences or adjust retention time.

• The AutoPeak integration algorithm is a second-generation peak modeling integration algorithm that improves data quality and ease of use
• Improved peak finding based on 3 Gaussian peak model
• All chromatograms in the batch are evaluated to determine which sample is the best peak model for each transition
• More consistent peak integration between samples, batches and analytes

2.  Workspace layouts

In a high-throughput lab environment that requires consistency and the continued delivery of high-quality data, you need a layout for your analysis that is familiar and enables you to interpret data faster. Custom workspaces can now be saved.

• Saves time by reducing clicks to customize the workspace
• Consistent data review reduces variation in data interpretation
• Browse to user-specified location
• Column settings, filtering, graphs and docking/undocking are saved as part of a layout
• Can set a default project layout

3. Automatic outlier removal

Simplify calibration curve review.

• Automatically removes outliers outside of the criteria, saving time and manual review for multiple analyte panels
• Remove tedious and error-prone manual review steps
• Optimize your linear regression fit and highlight any points that fail to meet user-specified rules faster, even when quantifying large sample sets

4. Calculated columns and flagging rules

• Users can create custom calculated columns for use in the results table
• Flag samples that fail user-specified criteria for that calculated column’s results
• Create customized flagging rules to optimize data review of samples that fall outside criteria
• Combine more than one flagging rule to create a simplified flagging in the results table for easy data review
• Ability to query non-numeric values
• Ability to query confidence flags
• Improved formula validation

Support of “IF” statements

SCIEX OS software has the ability to support “IF” statements for your analysis queries. There is functionality to execute calculations within the “IF” statement. “IF” statements can be built into the flagging rules when the outcome is a numeric value. Some of the data analysis you wish to conduct may be complex, therefore there is no limitation on the formula size of your query. Nested “IF” statements are also supported, and they can be packaged into a .frml file format and shared.

Driven by MS and MS/MS data analysis coupled with extensive libraries, Molecule Profiler software delivers highly accurate and flexible workflows for determining impurities and biotransformations for a wide variety of therapeutic molecules.

Molecule Profiler is fully integrated as part of SCIEX OS, and has the same look and feel. Easily multitask with other functions in SCIEX OS. And, there is no need to move data around.

The Configuration workspace displays active devices, allowing you to activate or deactivate the hardware in your workflow.

The Configuration workspace also provides the ability to add devices you may need or edit the configuration of your instruments. Within the workspace, you can adjust settings for queue management, such as maximum idle time allowed before the system goes into standby and the maximum number of samples allowed. There are also rule settings that advise users on what to do when a sample is missing, for example. If you are operating one of the X500 series QTOF instruments, you can specify calibration settings and what the system should do if there is a calibration failure.

• Project tab: specify the project folders or root directories on your laboratory's network that will store your acquired data'
• User Management tab: assign user roles, such as administrator, method developer, analyst and reviewer'
• Roles tab: assign permissions for each role'
• Security tab: set the security parameters, such as screen lock times, auto logoff times and logon failure parameters'
• Licenses tab: view the current licenses that are available, and install additional licenses or add-ons if needed'
• LIMS tab: connect to a laboratory information management system (LIMS) server by entering its URL (note that this connection is not necessary for a Watson LIMS, which is compatible with SCIEX OS software for direct data transfer)'
• With the most recent version of SCIEX OS software, users can now check to see if their software is up to date'

From compliant routine analyses to flexible research workflows, the intuitive Audit Trail workspace ensures full traceability and accountability. It includes built-in data integrity features that allow you to tailor each functionality specifically to your lab's compliance and data security requirements.

• Fully compliant with GxP and 21 CFR Part 11
• Configurable security settings
• Electronic signatures and audit trails
• Customizable security management
• End-to-end audit trail

SCIEX integrated compliance services include integrated analytical instrument qualification and software validation packages that cover your complete SCIEX system workflow.

The Library workspace is used to import a library that you would like to use as part of your workflow. Libraries provide additional confirmation and assurances for confirm your data acquisitions. You can import a LibraryView software package or your own custom library.

During this process, you can select which compounds you would like to include in your processing. You may want to include every compound in the SCIEX All-in-One HR-MS/MS library, for instance, or just extract the compounds that are crucial to your experiment.

The Event Log workspace shows you useful diagnostic information and events happening within SCIEX OS software. Within this workspace, you can archive a log at your specific intervals. You can also open previously archived event logs here, so you can dig into any of the information that may be of use.

• Filter events depending on what you want to investigate
• Segment the log based on the device or workspace
• Customize the view to find just the events you want to interrogate