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Installing the CI Source Option / GCT

This procedure describes how to add CI functionality to the GCT mass spectrometer.

Parts required
Table 1: Parts required

Part Number Description Qty

205000397 GCT CI Upgrade Kit 1

Table 2: Upgrade kit 205000397 components

Part Number Description Qty

M960057DC3 Kit of Parts CI Option 1

6070130 Ferrules Swagelok 1/16SS100-SET 1

6070202 1/16” X 1/16” Union SS-100-6 1

6070826 Nut Swagelok 1/16” SS-102-1 1

6346003 Tube Peek 1/16” x 0.010” 1

M960178BD1 Bulkhead 1/16” 1

M960298BD1 Line Capillary (CI) 1

S100999DC1 Leak Check Kit (CI) 1

715001433 GCT - CI Source Upgrade Installation Document 1

Table 3: Kit of parts CI option M960057DC3 components

Part Number Description Qty

M960234AD1 Labels (valves) ISS 01 1

M960079BC1 Inner Source Assembly (CI) Cooled 1

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Table 4: Leak check kit S100999DC1 components

Part Number Description Qty

6062813 Plug Valve 1/8” Stainless Steel 1

6070905 Plug 1/8” Stainless Steel 1

6071000 Tube Cap 1/8” Stainless Steel 1

Tools/materials required
• 2.5-mm Allen wrench
• ½-inch open-end wrench
• 2 x 5/16-inch open-end wrenches
• 2 x 7/16-inch open-end wrenches
• 7-mm open-end wrench
• Large adjustable wrench
• Tube-cutter for 1/8-inch stainless steel tubing (required for adding 1/8-inch plug valve)

Procedure
The procedure to add CI functionality to GCT instruments consists of nine sections:
1. Benchmark sensitivity test
2. Installing the CI upgrade kit (if necessary)
3. Connecting to the CI gas flow-metering valve
4. Installing the CI gas cylinder and plug valve
5. Leak checking the system
6. Installing the GC interface
7. Installing the CI source
8. Performing specifications
9. Training the customer

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Benchmark sensitivity test

NOTE: Test the instrument before performing the upgrade. Do not perform the upgrade
until the benchmark tests have been completed.

NOTE: After the upgrade has been performed, repeat the benchmark tests to make
sure that the levels achieved are the same.

NOTE: The instrument must achieve an acceptable level of performance before

performing the upgrade. Any work to achieve this is not included in the cost of
the upgrade. Do not perform any corrective work on the instrument without
authorization from the Service Manager.

1. Perform a sensitivity benchmark test using octafluoronapthalene in EI positive ion,

Full Scan Mode.

NOTE: The measured signal-to-noise ratio for hexachlorobenzene, obtained from the
mass chromatogram of 283.8102 Da must be >10:1 peak-to-peak.

a. Measure the signal/noise ratio obtained from an injection of 1 pg of hexachlorobenzene

(m/z 283.8102) whilst acquiring full spectra over a mass range up to m/z 800.
b. Run the acquisition in EI+ TOF MS mode with the following parameters:
• Scan time 0.9 sec
• Inter scan delay 0.1 sec
• Mass range 0 to 800 Da
• Data format Centroid
c. Use an absolute window of 0.015 Da in MassLynx Tools.
d. Use a combine window of 0.050 Da in the Spectrum window.
2. Record the results in Table 5.
3. Make hard copies of the data and print out the Tune page settings for future reference.

Table 5: Sensitivity test results

Test Pre-Upgrade Post-Upgrade Comment

Sensitivity

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Installing the CI upgrade kit (if necessary)

1. Check whether your instrument requires the upgrade.

NOTE: The upgrade is NOT required if a stainless steel capillary is already installed
into the outer source (Figure 1). Continue with the ‘Installing the CI gas cylinder
and plug valve’ section of the procedure.

NOTE: The upgrade MUST be performed if a blank nut is in place of the stainless steel
capillary on the outer source.

Stainless steel
capillary

Figure 1 - Top view of the instrument

Perform the CI upgrade as follows.

1. Switch the instrument to standby and vent the source by selecting Isolate Source from the
vacuum menu on the Tune page.
2. Remove the instrument covers.
3. Remove the column and GC interface or probe lock (if fitted), to access the inner and outer
sources.
4. Remove the source lid assembly and locate the CI blank.
5. Use the 7-mm wrench to remove the M5 nut and washer on the outside of the CI blank and
retain for step 7.
NOTE: If necessary, hold the blank bolt from the inside face of the source lid using a
½ inch open-end wrench.
6. Remove the blank bolt and retain the O-ring.
7. Insert the 1/16 inch bulkhead (M960178BD1) and O-ring from the inside face of the source lid
and secure in place with the M5 nut and washer retained from step 5 (Figure 2).

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Figure 2 - CI bulkhead connection on the source lid

8. Pass the long length of the CI capillary (M960298BD1) through the 1/16 inch nut (6070826),
ferrule set (6070130) and the 1/16 inch bulkhead from the inside face of the source lid as
shown in Figures 2 and 3.

Figure 3 - Inside face of the source lid

9. Insert the end of the CI capillary into the brass block on the outer source, next to the
reference capillary line (Figure 3).
NOTE: The CI capillary is an improved design and should already be bent into shape.
10. Finger-tighten plus 1¾ turns the 1/16 inch nut to secure the CI capillary.

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11. Refit the source lid assembly onto the housing.

12. Fit the GC interface blank flange and the EI inner source.

Connecting to the CI gas flow-metering valve

NOTE: If no CI gas flow-metering valve is fitted, the CI valve assembly kit

(M960051DC1) must be ordered and fitted before continuing with this procedure.

NOTE: Contact Global Services Support (+44 (0)161 435 4490) for assistance when
installing the CI valve assembly kit.

1. Use the 2.5-mm Allen wrench to remove the three cap head screws securing the flow valve
bracket to the front of the instrument.

Figure 4 - Flow valve bracket

NOTE: The valve fittings are either 1/16 inch Swagelok or 1/16 inch Valco.

Figure 5 - CI gas flow-metering valve

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2. Connect the PEEK tube capillary (6346003) to the rear of the flow valve (Figure 6) and tighten
the nut and ferrule using the 7/16 inch wrench.

NOTE: The flow valve side port should already be connected to the CI gas steel
capillary coming from the bottom of the instrument.

Figure 6 - Flow valve connections

3. Feed the PEEK tube capillary underneath the reference reservoir and connect to the
CI capillary fitted to the outer source, using the 1/16 inch union (6070202). See Figure 7.
4. Use the two 5/16 inch wrenches to tighten the 1/16 inch union.

1/16 inch
union

Figure 7 - Connected capillary tubes

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5. Ensure the EI inner and outer sources and the GC interface blank flange are fitted securely.
6. Loosen the black knob on top of the reference reservoir.
7. Pump down the source.
8. Enter the following temperature settings:
• Source temperature 180 °C
• Reference reservoir 20 °C
• Reference re-entrant 150 °C

NOTE: After 30 minutes pumping, the source pressure should be in the region of
1.0 E-6 on the Tune page.

NOTE: If 1.0 E-6 source pressure is not reached there may be a gross leak. Before
proceeding, vent the source and check all the connections made in the
procedure.

Installing the CI gas cylinder and plug valve

The CI gas cylinder must be as close to the instrument as possible. It is the customer’s
responsibility to ensure that it is safely located and that the cylinder and regulator are leak tight.
The regulator must be capable of regulating down to 12 psi. There must be a plug valve attached
in the CI gas line, within 1 m of the back of the instrument, for the purge test detailed below and
to protect the diaphragm of the regulator when purging.
The customer must supply all reducers necessary, as required in the Site Preparation Guide
(715000574).

Leak checking the system

WARNING: This test is designed to detect gross leaks within the instrument's CI
system and prevent the release of gases at levels where they may become
hazardous.

WARNING: It does not prove that the system is "leak tight" and may not detect leaks
that will affect performance. It will not detect leaks in the customer’s CI
gas delivery system (bottles, regulators, wall tubing), which is their
responsibility.

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1. Ensure the GC interface blank flange is fitted.

2. Ensure that the EI source has been pumping for at least 30 minutes with the source
temperature at 180 °C.
3. Make a note of the pressure in the source region.
4. Check that the CI gas line is blanked off at the back of the instrument, or that there is a closed
gas tight valve in this line within 1 m of the back of the instrument (1/8 inch plug valve 6062813).
5. If necessary, use the 1/8 inch tube-cutter to cut the CI gas line and fit the 1/8 inch plug valve.

CAUTION: Do not overtighten the black CI flow needle valve.

6. Ensure that the black CI flow needle valve on the front of the instrument is closed.
7. Open the Vacuum Monitor in the Tune page and ensure that the Backing Pressure is offscale
(below 1.0 E-2 mbar).
8. Switch to CI mode and select CI Purge on the Inlet tab of the Tune page

NOTE: You will hear valves click on the back of the instrument. The backing pressure
will normally rise and come down to about 2 or 3 E-4 within 30 seconds. The CI
purge will time out after 45 to 70 seconds. When this happens, it is normal to
hear a clicking noise and see the backing pressure rise briefly before falling again.

9. Deselect the CI Purge and then re-select it to initiate another CI purge.

NOTE: The backing pressure should come down to 1.0 E-2 mbar within 30 seconds.

10. Keep purging the CI gas line until it times out again.
11. Deselect the CI Purge and wait five minutes.
12. Select CI Purge again.

NOTE: The pressure should not exceed 2.0 E-2 mbar or not change at all. This
indicates a leak tight external CI gas system. When the purge is de-selected,
it is normal for the backing pressure to rise and fall again.

NOTE: If a leak is detected during this test, use the Swagelok 1/8 inch blanks (male
and female included in the kit), to isolate areas of the internal and external CI
gas plumbing and identify the source of the leak.

NOTE: It is recommended that all minor leaks are checked and eliminated in EI mode,
using an easily ionized gas with a known mass (such as argon at m/z 40, or
some spray dusters) around all O-rings, seals and ferrules.

NOTE: For further assistance contact Global Service Support on +44 (0)161 435 4490.

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Installing the GC interface

1. Vent the source.
2. Remove the GC interface blank flange and attach the GC interface.
3. Re-pump down the source.
4. Check and eliminate any leaks in EI mode, using an easily ionized gas with a known mass.

Installing the CI source

1. Remove the inner source probe from the instrument.
2. Attach the CI inner source to the source probe, so that the filament enters the instrument
facing upwards.

Performance specifications

GC-CI sensitivity, positive ion

The measured signal-to-noise ratio obtained from an injection of 100 pg of benzophenone
(m/z 183.081) onto a capillary column while acquiring full spectra over a mass range up to
m/z 800 is > 150:1.
Signal-to-noise ratio

GC-CI sensitivity, negative ion

The measured signal-to-noise ratio obtained from an injection of 1 pg of octafluoronapthalene
(m/z 271.9872) onto a capillary column while acquiring full spectra over a mass range up to
m/z 800 is > 100:1.
Signal-to-noise ratio

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Training the customer

CI overview (if applicable)
Tuning in CI positive
Tuning in CI negative
Cleaning the CI inner source

Upgrade confirmation

I confirm on behalf of that the above upgrade procedure

(Company Name) has been satisfactorily completed.

Signed Date

I certify that the instrument upgrade above has been successfully completed.

Engineer Date

INSTALLING THE CI SOURCE OPTION / GCT