How to install a capillary column on 5977 Series GC/MSD

Document created by lily Employee on Oct 15, 2020Last modified by carlos_vargas on Nov 3, 2020
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This Information Applies To: 5977A and 5977B 



This procedure is to guide the installation of a capillary column on 5977A/B GC/MS with a standard column nut or self tightening nut.


Steps to follow:

The GC and MS operates at high temperatures. In order to avoid burns, do not touch any parts of GC and MS until you are sure they are cool.

Always wear safety glasses when handling capillary columns. Use care to avoid puncturing your skin with the end of the column.

Always wear clean gloves while handling any parts that go inside the GC or the analyzer chambers.


self tightening column nut for inlet and detectors-Agilent

Column ID          Ferrule PN

0.1-0.25 mm        5181-3323

0.32 mm              5062-3514

0.45-0.53 mm      5062-3512

Figure 2  Self-tightening column nut for inlet/detectorFigure 3  Short graphite/vespel (15%/85%) ferrules
  • Condition the column.
  • Open the front cover and could see the type of ion source for SST, Inert, and Xtr EI, but for high efficiency sources, you just only see the type on the front cover ( see Figure 2)
    check GCMSD ion source type-AgilentGCMS HES ion source type-Agilent
    5977A/B SST EI, Inert EI, Xtr EI, CI5977B High Efficiency Source (HES)
    Figure 2 How to identify GCMS ion source type



1.  Open the analyzer chamber. Be sure you can see the end of the GC/MS interface. You could directly observe the end of the column inside the analyzer chamber for SST and inert EI, but for Xtr, HES EI, and CI source, you need to remove the tip seal assembly (including ceramic tip seal, spring, and tip cap) (see Figure 3). 


5977 inert EI transferline-Agilent

Xtr EI interface-Agilent



GCMS HES source-Agilent

GCMSD CI interface-Agilent

5977A/B SST and inert EI 

5977A Xtr EI   

1- Tip seal   2- Tip cap

5977B Xtr and HES EI 

1- Tip seal   2- Tip cap

5977A/B CI 

1- Tip seal and spring

    Figure 3 Ion source transfer line

3. Slide the column into the GC/MS interface. The tapered end of the ferrule must point towards the nut (see Figure 4). Alternatively use a self tightening nut for MS interface (see Figure 5).



GCMSD interface-Agilent

self tightening column nut-Agilent

Figure 4

1- GCMS interface 2- Ferrule 3- Nut

Figure 5

1-Self tightening nut for inlet, PN G3440-81011

2-Self tightening nut for MS, PN G3440-81013

4. Adjust the column so it extends this specified distance from the end of the transfer line (best to push the column the whole way through, cut the column, then pull back until it’s at a specified length). 

For an SST/Inert/Xtr EI source installation, the column extends 1 to 2 mm.

For a high efficiency source installation, the column extends 4 to 5 mm

For a CI Source Installation, the column extends about 1 mm.

note: Use the flashlight and magnifying loupe if necessary to see the end of the column inside the analyzer chamber. Do not use your finger to feel for the column end.

5. Hand-tighten the nut. Ensure the position of the column does not change as you tighten the nut, and be sure to not over tighten the nut. if you use a self tightening nut, tighten the nut in the clockwise direction, continue to tighten until you feel the ferrule grip the column. and then jump to step 9 to continue the operation (steps 7 and 8 are not needed for self tightening nut).
6. Check the GC oven to be sure that the column does not touch the oven walls.
7. Tighten the nut 1/4 to 1/2 turn.
8. Check the nut’s tightness after one or two heat cycles; tighten additionally as appropriate.

9. Install the tip seal assembly at the end of the GC/MS interface (don't need for 5977A/B with SST and inert EI source). For the CI GC/MS interface and the EI GCMS interface with an Xtr and HES source install the tip seal spring, then align and gently slide the ceramic tip seal, next step for 5977A with Xtr source, slide the tip cap and tighten two screws onto the tip cap. for 5977B with Xtr and HES source, screw the knurled nut onto the end of the interface (see Figure 6).

inert EI isolation tip installation-Agilent



GCMSD CI isolation tip installation-Agilent


5977B HES EI isolation tip installation-Agilent

5977A with Xtr source 

1-Spring  2-Tip seal  3-Tip cap

GC/MS CI source

1-Tip seal and spring

5977B with Xtr and HES source 

1-Knurled nut  2-Spring

Figure 6  GCMS Tip seal assembly

10. Gently check the alignment of the ion source and the interface tip seal for CI GC/MS and EI GC/MS with an Xtr and HES source. When the ion source is aligned correctly, the front analyzer chamber can be closed all the way with no resistance except the spring tension from the interface tip seal.

11. Close the analyzer chamber door.



Learn more on how to effectively operate your GCMS, please refer to the following link:

Agilent 5977 GC/MSD with MassHunter Workstation  e-Learning course on Agilent University 



Keywords: Column installation, 5977A, 5977B, HES, XTR, ion source, self tightening nut