shutterstock_374801338Remember the first time you used an expensive piece of lab equipment? Terrifying, right?

I was an undergrad and my graduate student mentor had just set up for an experiment, loaded her samples on a sample tray and closed the instrument door. She turned to me and told me to take the joy stick, position the arm, load the samples in the mass spec and start a run – cue the cold sweat.

I had been working in the lab for several months learning about the basics of mass spectrometry (MS); trying to understand how it all worked all on paper, how a sample could be turned into ions and sent into this black box and somehow this process would generate informative data on the computer. But I had never touched the instrument. That mass spectrometer was worth more than my college education in the U.S. and I was not going to be the person that broke it. With sweaty hands I took over the controls, and I can tell you that I successfully ran my first run without breaking the instrument.

Fast forward to graduate school where I started in a new lab using liquid chromatography (LC)-MS and, again, I had that same terrified feeling of ‘this mass spec is worth more than my stipend – I cannot break this.’ And again my fears turned out to be unsubstantiated.  I did not break the LC or MS.

After I got over my fear, broke a few things (cracking two sapphire LC pistons in one day had to be the worst, or that time I sonicated a nickel tube lens in nitric acid… we won’t go there) and had to fix the LC-MS, I gained my confidence.

It’s funny to reflect back on how nervous I was to use MS instruments – I perceived MS instruments as delicate, complicated and expensive. I never was worried about breaking the other lab equipment (i.e. UV-Vis, florescence detector, pH meter) since they just seemed sturdier and easier to use  (maybe because they let us use them in undergraduate lab so I figured they had to be pretty robust to let a bunch of kids use them).

As an LC-MS veteran I can tell you my perception was wrong. True or False?

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  1. MS instruments are delicate – False
    Modern MS systems, like the new Thermo Scientific™ ISQ™ EC single quadrupole mass spectrometer, are robust and built to be reliable workhorses that can be used for routine applications.
  2. MS is hard to understand and difficult to use, even for chromatographers – False

Of course with learning any new technique like MS, there’s the beginning phase of ‘I have no clue what’s going on,’ but the good news is there are great resources like the mass spectrometry learning center that can help you understand the theory and background of MS.
Even better news? The ISQ EC was built with ease-of-use in mind with built-in tools that guide users through method set up and sequence runs. Follow the intuitive software wizard that guides you through and a few clicks – you’re ready to go!


  1. MS always requires me to learn new software – False
    The new ISQ EC is fully implemented with native control and data processing into the Thermo Fisher Scientific Chromeleon 7.2 chromatography data system. With the Autospray™ intelligent source settings, even novices can successfully setup methods with minimum familiarity to MS and electrospray interface design and settings. Processing the data is then just an extension of the same and identical tools used for other conventional chromatography detectors, like UV-Vis or fluorescence detection. In that context, the new ISQ EC single quadrupole MS is helping novices and experts alike to become more productive using MS in very short time without compromising on data quality, data integrity and, if applicable, compliance.

It took a while to learn and build my confidence in LC-MS, but the benefits outweigh the challenges of learning a new technique. The new ISQ EC single quadrupole MS is a new system that allows all chromatographers the chance to use MS for their assays.
Why use the ISQ EC single quadrupole MS?

  • Exceptionally low mass detection capabilities (as low as 10 mass-to-charge ratio with the ISQ EC).
    This makes the instrument the best performing single quadrupole MS also for small molecule LC-MS and ion-chromatography-MS. With its powerful electrospray interface, it often does not require adding organic modifier to improve response and nebulization. This means that formerly difficult environmental assays can be simplified.
  • Detect multiple analytes within a single run with segmented time/dedicated data windows. The ISQ EC lets user choose Full Scan or Single Ion Monitoring (SIM) mode to either scan a mass range for all detectable analytes or focus on a specific compound.
  • Powerful specificity based on mass-to-charge ratio giving you the ability to have a second layer/dimension of identification beyond retention time with an LC separation. Why is this important? If you have tricky separation and just cannot resolve two peaks chromatographically, you would be able to separate these two compounds based on their mass-to-charge ratio with MS. This gives you the ability to separate co-eluting peaks by mass-to-charge. False positives or negatives can be easily eliminated using the power of mass confirmation.
  • Multi-analyte capabilities. They work for a wide range of analytes with various chemical properties. As long as you can ionize it, you have a shot to measure it.
  • Run at scan rates suitable for HPLC and fast UHPLC applications while delivering picogram detection limits.
  • Full integration into the Thermo Scientific™ Chromeleon™ 7.2 chromatography data system (CDS) and the Thermo Scientific™ AutoSpray™ smart method set-up make LC-MS operation and data analysis straightforward and intuitive (read about these intuitive parameters in this blog post.

The ISQ EC is:

  • Robust – Maximum uptime allows you to get more work down with a reliable system. The new source design provides high levels of instrument robustness, even with challenging matrices. The user can change gas flows to design assays that will be robust and sensitive.
  • Easy-to-maintain – easy access parts to make it easier for the user. Clean the transfer capillary/source without needing to vent the system. This translates into more uptime since you don’t need to wait for your MS to pump down.
  • Easy-to-use – the ISQ EC was built to make MS available to chromatographers and users. It’ll take no time to get comfortable with MS with built-in tools to guide new users and help optimize source parameter–which effects how well your LC eluent is ionized) with an AutoSpray feature. This lets users use slider bars based on 3 chemical properties, making it intuitive for new users to adjust/optimize source parameters. After a little bit of playing around you’ll quickly figure it out.

Mass spectrometry is an important tool for LC as it allows verification of the analyte by mass confirmation. LC-MS is helpful for applications like drug synthesis   where drug impurities must be monitored. Using a single quadrupole MS like the ISQ EC, you can run a Full Scan over a wide mass range, quickly determine the yield of the reaction and check for impurities related to the proposed drug candidate in the same analysis.

In the routine space, such as quality control  , UV-based detection is still the standard, but MS detection is gaining acceptance because of its clear advantages. Besides its lower detection limit, it also allows immediate analyte identification based on its respective mass and straightforward peak purity analysis based on its mass spectrum.

With all the benefits that MS offers, don’t be afraid to test it out. The ISQ EC was designed to be robust and easy to run with the sensitivity and performance you need for your most challenging analyses. And with all the built-in tools to help you get running faster, I’m sure you’ll get the hang of MS in no time!