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MS TIP No. 12 - Elimination of Memory Peaks and GC Background Noise

Tip Mass Spec Tips is a collection of tips relating to the operation and service of mass spectrometers. Some of these Tips have been reported in our newsletter, "The Mass Spec Source." If you have a question relating to the operation or service of mass spectrometers or would like to add your comments to the below tip and would like to have it included in this forum, please contact us. Input to this database of MS Tips is needed from our readers to complete this section.

Author: John J. Manura

Affiliation: Scientific Instrument Services

S.I.S. has recently completed an investigation into the causes of memory peaks and background noise in the total ion chromatograms from a Hewlett Packard 5890 Series II gas Chromatograph. A technical bulletin describing the entire study is available from Scientific Instrument Services. A short description of this study is summarized below. To obtain a free copy of the extended article call our order desk at (908) 788-5550 and ask for a copy of Technical Bulletin No. 3 entitled Elimination of Memory Peaks from Thermal Desorption.

Background noise is the constant signal apparent above a zero level baseline in the gas chromatograph chart. The sensitivity of a GC analysis is judged by the signal to noise ratio. If the background noise increases, this in turn reduces the sensitivity of the analysis. As a result background noise level should be kept to a minimum. The major source of GC chromatogram background noise is from the GC injection port and its various components. GC septa have long been recognized as an important source of GC background noise. As a result manufacturers have developed and now offer a wide variety of Low bleed septa to reduce this source of background noise. The manufacturers of these septa have developed elaborate cleaning and conditioning procedures to minimize septa bleed.

In addition the manufacturers of many gas chromatographs have designed the GC injection port to minimize septa bleed. Many manufacturers use septum purge lines to purge the carrier gas near the septum area to avoid its migration into the injection port and GC column. In the H.P. 5890 Series II GC, the temperature gradient from the middle to the top of the injection port can be as much as 100 degrees. When the user sets the injection port temperature to 250 degrees C, this is in fact the temperature of the injection port in the center region. The temperature of the injection port in the septum area is about 80 degrees less. This lower temperature minimizes the direct heat exposure to the septum and therefore reduces septa bleed. However this cooler septa can be a source of sample condensation or other contamination on the underside of the septa. In addition when liquid samples are injected into the GC injection port and rapidly expand to the gas phase, contamination of gas inlet and outlet lines can occur in these cooler regions. This again can be a problem in instruments such as the H.P. GC in which the carrier gas is not preheated before it enters the GC injection port. Any of this contamination in the septum area and gas inlet lines will slowly bleed into the GC injection port and column and contribute to the background noise. Contaminated injection port liners and degraded liquid phases at the front of the GC capillary column can also contribute to this noise.

In conventional GC methods, liquid samples are injected into the GC injection port via a syringe injection, after which the samples are immediately chromatographed through the column. In order to determine the sources of background noise originating from the GC injection port, the Short Path Thermal Desorption System and GC Cryo-Trap were attached to the GC injection port. This permits the purging of volatiles originating from the GC injection port over a period of 5 to 10 minutes and the subsequent trapping of the volatiles at the front of the GC column. The cryo-trap is then heated to release the volatiles from the front of the GC column. The chromatograph charts display distinct GC peaks for each of the contaminants which were then identified by the mass spectrometer. As a result we were able to identify the types of contaminants and then perform several studies to determine the source of contamination and GC background noise. This was followed up with the development of methods to clean the injection port and techniques to minimize future contamination.

In studying a variety of septa as a source of background noise, we have found that the Supelco Thermogreen septa are the lowest bleed septa on the market. Only three minor peaks in the chromatogram originate from the septa and were determined to be due to the siloxanes used in the silicone polymer. The mass spec peaks at M/e 207, 281, 267 and 355 common in the background signals in many GC/MS systems are due to these siloxanes which can originate from both the GC septa as well as from the silicone liquid phases used in many GC columns.

A new GLT low dead volume injection port liner was developed for use with our thermal desorption system to maximize sensitivity and reduce GC injection port contamination. This new injection port liner has a narrow I.D. (0.75 mm) to permit good thermal conductivity to the syringe needle. This enhances the detection of higher boiling compounds due to the syringe needle staying hotter. This injection port liner proved useful for thermal desorption and GC headspace injection techniques where an expansion volume is not needed. Normal GC injection port liners for liquid injection have inside diameters of 2 to 4 millimeters as compared to the 0.75 mm I.D. of this new injection port liner. Therefore this new GLT liner may not prove practical for larger liquid sample injections where an expansion volume is required. The GLT liner permits greater heat transfer to the septum area of the injection port. This raises the temperature of the injection port at the septa about 50 degrees higher than it normally occurs in the H.P. injection port. By raising the temperature near the septa this will minimize sample condensation on the underside of the GC septa. The overall result is less sample condensation and contamination in the injection port and therefore lower background noise levels.

A method was developed to provide for a thorough cleaning of the GC injection port as well as the areas in which samples, solvents and degradation products might condense. This new technique involves flushing the GC injection port with high volumes of hot carrier gas and purging this gas out the septum purge and split vent lines. The hot carrier gas is generated in the Short Path Thermal Desorption System which can preheat the carrier gas at temperatures up to 350 degrees C. This technique has proven to be very effective in cleaning the injection port and septum area of the gas chromatograph. In a typical study in which a gas chromatograph was used for liquid injections, the GC background was reduced by more than 99% by cleaning with this method.

Figure 1

Figure 1 - Chromatogram background before and after cleaning and conditioning GC injection port.

The complete injection port cleaning method is outlined in the Technical Bulletin # 3.

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