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Targeted MS based peak tracking in automated method development software

Monday, June 6th

Topic area: LC/MS: Chromatography and Software

Anne Marie Smith, Product Manager, Mass Spectrometry and Chromatography, ACD/Labs

Anne Marie Smith, Richard Lee, Alexey Galin, Andrey Vazhentsev


Chromatographic method development remains a relatively time- and labor-intensive activity. Investment in systematic processes (i.e. Quality by Design processes) has improved the quality and efficiency of method development projects. But such processes still require significant repetitive labor: setting up experiments to cover the design space, processing chromatograms, tracking peaks, and comparing runs to find optimal conditions.

Productivity can be improved by automating these tasks. Method development software can automatically generate lists of experiments to cover a user-defined design space, communicate with chromatography data systems (CDSs) to run those experiments, and perform some automated processing for subsequent review.

Here, we present a new automated workflow in the method development software AutoChrom®, featuring targeted MS based peak tracking for more efficient processing.


A temperature- and gradient- optimization project was created in ACD/AutoChrom. Two peptides and their related impurities angiotensin I and melittin were used as model substances.  Chromatographic conditions: BEH C18 AX column (150 x 2.1 mm, 1.7 µm), 0.1% TFA in water (A eluent) and acetonitrile (B eluent), 30-95%B at 0.4 mL/min, diode array and single quadrupole MS detection.

Nine experiments: 3 temperatures (30, 45, and 60 °C) and 3 gradient times (19, 39, and 58 minutes).

For automated processing, the software was provided with the masses of the target compounds (manually determined from the run with the best separation) and peak picking parameters.

Preliminary data

While automated peak tracking across LC/MS or LC/UV data is a standard feature of AutoChrom on occasion, in previous versions peaks of interest were missed.  Using the automated targeted peak tracking and identification algorithm, all compounds of interest were found.  Furthermore, peaks that were not of interest did not clutter the peak tables, making it easier for users to quickly review data.

Targeted peak tracking improved the automated results for isobaric compounds, which are challenging to monitor across chromatographic traces. However, some manual review was still required to separate coeluted isobaric compounds. The algorithm automatically produced extracted ion chromatograms from the masses in the target list simplifying the review process.

The new method for processing LC/MS data provides a good balance between automation and autonomy. Initial processing is automated, reducing user time spent on tasks like simple integration. But experts can intervene as necessary to correct results based on their expertise. In addition, rather than tracking every peak manually which is a time-consuming process; users can define a list of targets to track across chromatograms, focusing only on compounds of interest. Finally, results can be stored in a method database for future use and customizable reports quickly generated.

The new processing algorithm presents a significant improvement to the post-experimental automation within AutoChrom.

Novel aspect

New targeted peak tracking in method development software improves data processing efficiency and focuses analysis on peaks of interest.

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Vendor-neutral, Browser-based MS Data Processing

Monday, June 6th

Topic area: LC/MS: Chromatography and Software

Richard Lee, Director, Core Technology, ACD/Labs

Anne Marie Smith, Richard Lee, Vitaly Lashin, Sofya Chudova, Nikita Gavrilchik, Rostislav Pol


Analytical data processing is moving to the Internet browser. Browser-based apps are easy to access, and many such apps are cloud-based and available from anywhere. In addition, cloud deployments provide computing power on-demand, cutting costs and time.

In response, several browser-based LC/MS and GC/MS processing tools have emerged. But until now, commercial tools have not been vendor-neutral.

With most scientific labs owning chromatography and MS instruments from multiple vendors, software complexity increases. Each vendor outputs data in its own format and provides its own processing tools. Scientists must learn and switch between multiple processing interfaces.

Here, we present a simplified software landscape: Spectrus JS, a vendor-neutral browser-based tool for processing MS data. Now, scientists can handle all their data in one interface.


LC/MS and GC/MS data in multiple major instrument vendor formats was imported into Spectrus JS. Peaks were detected and integrated, and chemical structures were assigned. The processed data was saved, and an auto-generated report was created from the results.

Preliminary data

Spectrus JS successfully handled peak detection and integration. It also recorded all actions in an audit trail, allowing processing steps to be traced for data integrity. The software worked with major vendor formats and all major browsers (Chrome, Safari, Firefox, Edge, and Opera).

NMR, chromatography, and hyphenated chromatography-MS data could also be analyzed in Spectrus JS, further reducing software learning requirements for scientists who use NMR, chromatography, and MS.

Spectrus JS was designed for both cloud and on-premise deployment. Cloud deployments employ clustering technology to address scalability and load demand. This flexibility allows organizations to choose the model that fits their size, use patterns, and security requirements.

MS-related innovation

A vendor-neutral browser-based tool allows scientists to process any MS data from one interface, decreasing the data-handling barrier for MS labs.

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