Upgrade Your Hardware to Vanquish Flex UHPLC Without Disrupting Workflow

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Upgrade Your Hardware to Vanquish Flex UHPLC Without Disrupting Workflow

Team TFS
Team TFS

A reliable Chromatography Data System (CDS) is crucial for efficient and compliant operation in many modern laboratories with strict regulatory requirements. The CDS is a central aspect of your laboratory infrastructure — ensuring critical data is secure, traceable and easily auditable. To guarantee smooth business operations, labs often standardize on one particular CDS across laboratories, sites, and even continents, enhancing data transfer and reducing overall training efforts.


Vanquish Flex UHPLC system.Vanquish Flex UHPLC system.Yet for all the benefits of having a standardized CDS across multiple labs and sites, there is one major downside: the reluctance you may feel to upgrade or change your analytical instrumentation. Even though a new instrument may offer improved reliability, increased throughput, unique detection capabilities, or accelerated return on investment, many labs shy away from making a switch —largely due to concerns over CDS compatibility.


But are those worries warranted? How much does your CDS dictate your ability to upgrade hardware?


Let’s look at one example: Thermo Scientific™ Vanquish™ HPLC and UHPLC systems – an innovative, highly sought after solution with CDS compatibility that may surprise you.


Can Vanquish HPLC and UHPLC systems run with third-party CDS systems?

Yes! In addition to operating under the Thermo Scientific™ Chromeleon™ Chromatography Data System (CDS), all Thermo Scientific Vanquish LC systems—including Vanquish Core, Vanquish Flex and Vanquish Horizon—operate under alternative CDS offerings including Waters™ Empower™ 3 software. It’s all possible by using Thermo Scientific Standard Instrument Integration (SII) software.


How does an SII for Waters Empower 3 integration work?

For seamless connection to Waters Empower enterprise deployments, you simply need Thermo Scientific Standard Instrument Integration (SII) for Waters Empower 3 software to enable instrument control. Data processing, reporting and data storage for Vanquish HPLC and UHPLC systems will remain within Empower software.


While Thermo Scientific Chromeleon™ CDS is the recommended software for control of Thermo Scientific UHPLC, HPLC, GC and IC instruments due to its maximum ease-of-use, reliability and performance, other vendors’ CDS software can also incorporate and operate these instruments with the SII for Empower 3 software plugin.


The SII plugin for Empower software brings elements of Chromeleon CDS to deliver flawless integration of Thermo Scientific liquid chromatography (LC), ion chromatography (IC) and gas chromatography (GC) instrumentation into the Waters Empower 3 CDS infrastructure without loss of functionality. Instrument control, data acquisition and data processing are performed completely under Empower 3 software.


Up to four instruments can be configured per Empower node using the standard SII Instrument Configuration Manager.


What does the SII software plugin for Waters Empower 3 enable you to do?

With the SII integration, you’ve got all the data management functions you need to operate your Vanquish instruments with ease.

  • Control your instruments: SII for Empower software provides a complete set of commands. For users, this means that advanced features, such as preparing the next sample during an ongoing analysis, can be implemented to increase productivity. Monitoring instrument status within Empower can be performed using the Empower Control Panel. Here, an enhanced SII Instrument View is easily accessed to provide further options to control and monitor the instrument and its modules.


  • Set up instrument methods: Setting up an instrument method is simple, intuitive and fast due to the SII for Empower Instrument Method Wizard and Editor, both of which are integrated into the Instrument Method Editor of Empower. The wizard guides the user through all modules, enabling the entry of all necessary information, while the editor allows the review and modification of all aspects of a method.


  • Process your data: Complete data processing takes place inside Empower software, which allows you to use all functionalities as you would normally, for example, overlay of chromatograms or other channels like pressure traces. The Empower user experience does not change for any data processing aspect.


Is the SII software plugin for Empower easy to use?

SII is a very user-friendly environment that seamlessly integrates within the Waters Empower 3 CDS infrastructure. When setting methods or operating the Vanquish platform, SII offers an embedded control panel with a simple visual display, allowing an analyst to begin setting up methods with minimal training. The on-screen graphical display is intuitive and allows users to easily visualize and interpret chromatographic conditions.


How does SII software plugin compare from a product perspective?

Nolan Dean, a staff scientist in the Analytical Development Department at Thermo Fisher Scientific’s Patheon site (Greenville, N.C.), shares his insights.


“Regarding instrumentation, we have very harsh methods here; and those methods that typically have caused a lot of downtime on some of our HPLC systems – we don’t see a lot of that havoc on the Vanquish LC systems,” said Dean. “The overall operation of those systems far exceeds what I’ve seen with other LC systems.”


Dean continued, “The SII interface is easy to control and requires no significant user training beyond a short demonstration. The instrument works within the fully enabled audit trail in Empower and changes are tracked in the instrument audit log which is displayed at the bottom of the SII interface.”


At the Patheon site, the metrology group is directly responsible for supporting the laboratories’ system operation and maintenance. The group is key to the operational uptime of the department, along with robust systems and critically stable connections between instruments and servers, preventing expensive downtime. We connected with the metrology team at Patheon to get their insights on daily operations.


“From an administrator standpoint, the software running on the local LAC/E servers actually is a lot better than we’ve experienced from other vendors,” said one team member. “It’s a lot more detailed and there are options and functions that are a bit more customizable than what we see with the standard Empower interface with other vendors’ liquid chromatography platform.”


How does SII software plugin support a GMP environment?

The SII interface brings a host of valuable GxP-related features developed for Thermo Scientific Chromeleon Chromatography Data System (CDS), which deliver additional compliance capabilities.


“The SII interface contains a live audit trail that tracks instrument status in real time,” explained Dean. “This includes instrument settings, flushing/purging, and when compartments are opened or closed. This audit trail data allows analysts to track system cleaning and equilibration for precise status updates and troubleshooting support.


With SII you can rest assured that all events are captured within the Empower standard audit trail. An added feature of using the SII driver is that if the reviewer requires a more granular view of any event, the SII interface captures a detailed record of these audit trail events.  


Why would I want to upgrade to the Vanquish Flex LC?

This analytical instrument can run both HPLC and UHPLC methods in the same system, reducing system footprint and helping labs optimize valuable bench space. Knowing that it can operate under a variety of CDS offerings (including Waters Empower 3 software) presents a great opportunity to evaluate a new LC hardware supplier based on its highly innovative features. You can learn more and even virtually build your own Vanquish Flex LC here.


In general, upgrading from older HPLC systems to newer technologies provides a number of additional advantages. For example, new technologies enable your lab to modernize older methods and develop newer, faster, and more sensitive methods to improve both data quality and throughput. In line with the recent update to USP General Chapter 621 (also the EP and JP) with regards to method modernization, the Thermo Scientific Vanquish Flex system along with our extensive range of chromatography columns allows you to modernize your methods — allowing seamless and full transfer of your existing method, increasing your productivity and reducing your running costs. Read more on how the Vanquish Flex achieves this here and here.


Want to learn more? Connect with your Thermo Scientific account manager to discuss your specific liquid chromatography needs.

For more information on Vanquish integrations, read these resources:


Stay tuned for more: Watch for our next blog post on making the transition to Vanquish Flex with SII software.