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GC Troubleshooting Guide to Broad Peaks and Loss of MS Sensitivity

The Problem

A GC-MS method was being used to analyze a Minnesota A pesticide test mix.  Normally the method produced very sharp peaks across the whole chromatogram. 

No deliberate changes had been made to the method; however, the chromatogram began to exhibit broadened peaks with the later eluting analytes being affected to a greater extent (Figure 1). 

The peak broadening has also resulted in a loss of MS sensitivity.  It was noted that there were no real shifts in retention times.

Column: 5% Phenyl PDMS.  30 m x 0.32 mm x 0.55 μm
Temperature: 40 °C, 2 min.
40-300 °C, 10 °C/min., 8 min.
Carrier: He at 2 mL/min.
Inlet: Splitless (Splitless 4 mm liner)
Splitless time 2.0 min. at 50 mL/min.
250 °C
Detector: MSD
Source - 230 °C
Quad - 150 °C
Sample: Minnesota Mix A Pesticide test mix in acetone

This page is part of our series of 6 free Chromatography Troubleshooting Guides.


Changes in Selectivity, Retention
and Resolution »

Cycling Baselines and Pressure Fluctuations »

Solving HPLC Peak Splitting Problems »


Broad Peaks and Loss of MS Sensitivity »

Broad, Double/Split, Fronting Peaks »

Peak Area Reproducibility and Reduction
of Sensitivity »

Split Peaks

Figure 1: GC-MS chromatogram showing peak broadening of later peaks and a loss of MS sensitivity.


The CHROMacademy GC Troubleshooter

In this case we have both a chromatographic (broad peaks) and instrument symptom (loss of MS sensitivity), both of these can be entered simultaneously in to the CHROMacademy GC Troubleshooter in order to produce a much more precise list of possible causes based on the combination of symptoms (Figure 2).

If you are unsure of what problems you are seeing in your chromatogram there are also helpful rollovers which illustrate each symptom.

Figure 2: Input of both chromatographic (top) and instrument (bottom) symptoms into the CHROMacademy GC Troubleshooter.


There you have it, in three simple steps the troubleshooter has produced 32 possible causes for the symptoms we have entered (Figure 3).

Figure 3: CHROMacademy GC Troubleshooter results page, including causes of broadened peaks and a loss of MS sensitivity,
solutions to each individual cause, and further resources for resolving the problem.


32 does seem like an awful lot of things to have to check, this could be time consuming.  Troubleshooting often is time consuming; however, the CHROMacademy troubleshooter can be used to accelerate the process. 

Although there are 32 possible causes of our problem, each cause is given a star rating, based on a unique algorithm, which indicates the number of symptoms which are matched and how commonly that problem occurs i.e. how likely that suggested cause is for the combination of symptoms we have selected.


The Solution

From the results screen, it can be seen that the most common cause of our problem is ‘column stationary phase loss too great to produce required efficiency/resolution’, however, this only matches one of our symptoms (peak broadening) and while it is a very common cause of peak broadening common sense tells us that with only one symptom matched and also a very sudden change in chromatography, this may not be the answer we are looking for.

There is only one cause in this list that matches both of our symptoms; number 8 ‘MS: Source or interface (transfer line) not hot enough’. Therefore, we decided that this was an ideal point to start troubleshooting. It was found that the transfer line seemed cool relative to its normal temperature.

This was further investigated and it transpired that whilst the instrument was reading out the correct temperature, in fact the transfer line was not being heated. After an engineer fix to the heating element, the chromatography was repeated and the chromatogram in Figure 4 was obtained.

Figure 4: Good chromatogram obtained following repair of a faulty MS transfer line.


The transfer line, source, and quadrupole analyzer are maintained at successively higher temperatures to prevent compounds from condensing on their surfaces. The transfer line heating also helps to keep the sample rapidly moving towards the source, which is especially important for higher boiling, less volatile, later eluting analytes.

Some systems also use the heat of the transfer line to conductively heat the source, which remains 100–150 °C below the transfer line temperature. The loss of sensitivity and low efficiency of higher boiling compounds fit well with the observed chromatographic symptoms and the immediate return of performance after fixing the transfer line heater confirms this was indeed the problem.

Whilst most systems will have a transfer line heating set-point specification, the heater and thermocouple may fail simultaneously or there may be no read back device fitted. Other systems may allow analysis to proceed even though the transfer line heater has not reached the desired set point temperature.

Of course if we had simply worked down the list taking each cause in turn we would also have quickly reached the solution to our problem and this is a perfectly acceptable way to use the troubleshooter.


Have you ever had a problem with the following symptoms?

Solvent peak tailing


Chair shaped peaks

Use the CHROMacademy GC Troubleshooter to see what could be causing the problem and how to resolve it.

GC troubleshooting


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