Preserve your SRM transition windows by replacing the same amount of column you remove during maintenance

I’ve been working on a detailed PCB congener analysis using the TSQ-9000 with the AEI. Typically this analysis is done by EPA Method 1668C, which uses high resolution MS. We get some specificity from the selected reaction monitoring, but there are some shortcomings when compared to high resolution data. Where the TSQ-9000 really shines is the sensitivity. We were able to achieve very linear calibrations (avg RF RSD% < 5.5%) for all target compounds using 6 levels (analyzed in triplicate) ranging from 40 ppt to 400 ppb. The 6 point calibration suggested by EPA Method 1668C ranges from 200 ppb (for sensitive instruments) to 2000 ppb.

After 6 weeks of constant running, it was time to perform some maintenance. We needed a new liner and septum, and we needed to trim the column to restore symmetrical peak shapes to the analytes. The SRM method we’re using has well over 500 transitions, many are close together with narrow windows, and the prospect of shifting multiple compounds out of their windows was alarming. Figure 1 shows the pentachlorobiphenyl homologue group. The comprehensive chromatogram would have some congeners from the 3-chloro, 4-chloro, 6-chloro, and 7-chloro homologue groups overlapping, as well as stable isotope labeled internal standards and surrogates.

Figure 1 – The complete pentachlorobiphenyl homologue group. Window defining and WHO toxic congeners are labeled with their ID in blue.


It’s possible to use the speed factor calculated by the EZGC method translator to calculate the new retention times, but it’s a manual process involving measuring a deadtime and calculating a new effective length, translating the method, and manually calculating and updating the new transition windows.

The more prudent course of action seemed to be removing the need to update the transition windows. Replacing the segment of column removed with the same length of the same column should result in virtually no change in elution times, eliminating the need to update the transition table. This is exactly what we saw when we replaced 1 loop of the 0.18 mm x 0.18 µm Rxi-PCB column with a fresh segment of the very same length, using a SilTite µ-Union to make the column connection. The before and after chromatograms for the WHO toxic congeners in the EPA 1668C calibration CCV are figures 2 and 3 respectively.

Figure 2 – Retention times for select toxic and window defining PCB congeners straddling the center third of the chromatogram


Figure 3 – Retention times for the same select toxic and window defining PCB congeners straddling the center third of the chromatogram following the replacement of the head of the analytical column with a fresh segment of Rtx-PCB.

Aaron Lamb from Thermo Fisher and I will be discussing persistent organic pollutant analysis this afternoon using the TSQ-9000. Following us, there will be a discussion on the alternative method of analysis – High resolution MS, specifically the Orbitrap. The webinar is titled ‘Persistent Ongoing Perfection: Optimization of a GC-MS/MS Method for the Analysis of POPs Plus an Alternate Approach Utilizing High-resolution Mass Spectrometry’. Click the link if you are interested. The webinar should be available for on demand viewing within a few days. There are a variety of on demand lectures to pick from on a variety of different analytical techniques.


One Response to “Preserve your SRM transition windows by replacing the same amount of column you remove during maintenance”

  1. Tim Strutt says:

    Have you found this to be better than traditional 2-5m 0.25mm (or 0.18?) retention-gap/guard-columns? I’m a great fan of retention gaps – if the joint doesn’t leak :-)

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