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GC-MS System
Getting Started
Table of Contents
1.0
Venting ...................................................................................................... 1
2.0
3.0
4.0
AutoTuning ............................................................................................. 12
5.0
6.0
7.0
8.0
9.0
1.0
Venting
SCION SQ
SCION TQ
Message shows in the Out box at the bottom of System Control when venting is finished.
6. Power off the MS system as needed.
2.0
The SCION GC-MS arrives ready for installation of an analytical column. On first installation, a new
column needs to be conditioned.
Conditioning is performed with the MS end of the column not connected but venting into column oven.
You may need to install and condition a new column after your GC has been in use for some time.
There are potential burn hazards when connecting the column. To help avoid burns, set Injector,
transfer line, source, and column ovens to 50 C and then vent the system.
Prior to installing your column, check that the factory-installed Injector is equipped with the right insert
for your application.
2.1
When a capillary column is used in combination with an Injector, alignment of the column is critical. Use
the following steps to precisely align the capillary column. Unless this procedure is followed, the
injection syringe may damage the top of the column or peak tailing may result.
Capillary columns are installed to the injector with a capillary column nut (PN 394955100) and a single
reversed ferrule made of Graphite/Vespel. Other materials can be used depending on the analytical
technique.
Ferrule ID is based on the diameter of the capillary column. For a 0.25 mm column use a 0.4 mm ID
ferrule.
To ensure a leak-free connection of capillary columns, the ends of the column must be cut squarely and
as smoothly as possible. To achieve this, a proper scoring tool is required. A ceramic scoring wafer
(PN 190015800) is recommended.
1. Cut off sealed section at each end of new column.
2. Uncoil 10 cm at Injector end of column.
3. Slide appropriate column nut and ferrule on each end of column. For a 0.25 mm column use a
0.4 mm ID ferrule. Ferrule points away from the injector.
4. Make a clean cut with the cutting tool 2-4 cm from end of the column.
4.
5.
The ferrule can be contaminated. DO NOT allow the column nut and ferrule to move past the
mark.
9. Gently push the column into the Injector until the mark on the column is aligned with the bottom
edge of the column nut.
10. Tighten the column nut by hand until it is finger-tight. Hold the column and use a 5/16" wrench to
tighten the column nut. Tighten the column nut only enough to seal the column and hold it firmly in
place.
A new graphite-Vespel ferrule needs tightening - to -turn past finger-tight to provide an adequate
seal.
The injector and column should be leak tested using a He leak tester or by carefully monitoring
pressures and flows on the GC.
The nut may require retightening after first or second programmed run. Over tightening will damage the
ferrule and seal.
When this procedure has been completed, conditioning of your new column can begin. It is best if the
column is not connected to the MS during conditioning.
Consult column documentation to condition column prior to first use.
The MS secures the column with a Swagelok nut (PN 2869398870) and a single forward facing
ferrule.
Ferrule ID is based on the diameter of the capillary column. For a 0.25 mm column use a 0.4 mm ID
ferrule. The material used for the ferrule is generally graphite/Vespel, but other materials are available
dependent on application.
Before connecting the column to the SCION MS the system must be cooled and vented. To allow easy
visual of the column position in the source, the source electronics must be opened.
The transfer line must be retracted from the source using the nut, to allow sight of the repeller hole
where the column will come through.
Before connecting column to the MS, connect the column to the injector following the section,
"Connecting Capillary Column to Injector" on page 3.
1. Uncoil 30 cm at MS end of column.
2. Slide appropriate column nut and ferrule on each end of column. For a 0.25 mm column use a 0.4
mm ID ferrule. Note the ferrule direction is different for MS to the injector. Ferrule points towards the
MS column end.
3. Make a clean cut with the cutting tool 2-4 cm from end of the column.
4. Inspect the cut to verify it is square and smooth.
5. Move the nut and ferrule away from the column end. Allow enough length for the column to pass
along the transfer line and emerge inside the source.
6. Partially insert the column into the end of the transfer line.
8. Draw the column back into position until it is visually flush with the front face of the repeller. You
may have to move column back and forth until it is in the correct position.
Note: After tightening the nut, the final position of the column end should be
~0.5-1.0 mm extended out the repeller.
10. Replace transfer line to operating position using the retraction nut. Ensure the repeller fits securely
into the source and fully engages with it.
The source electronics can now be restored to normal operating position in preparation for pump down
and leak testing.
3.0
1. Turn on the computer, GC, and MS. The main power switch is on the back of the instrument.
2. From the System Control Task Pane, click the MS Setup button.
3. Click Manifold; see the following figures.
SCION SQ
SCION TQ
10
5. Click Close.
Message shows in Out box at the bottom of System Control when evacuation is finished.
11
4.0
AutoTuning
It is good practice to AutoTune after venting and to check system leakage before an AutoTune.
1. Ensure the Pressure Pulse is set to OFF under the Constant Flow.
2. From the System Control Task Pane, click the MS Setup button.
3. Open the Role Menu and choose Advanced.
4. From the Status window, click the AutoTune button.
5. Select the option of Q1 and Q3 (for general purpose tuning), click Start.
Message shows at the bottom of the Status window when AutoTune is running. Message shows in the
Out box at the bottom of System Control when AutoTune is finished.
12
5.0
13
6.0
6. Click the User Library button and then browse the following directory
(C:\BrukerWS\MSTutorials\TQ):
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15
7.0
6. For each compound, type the Name, Precursor and Product ions, Collision energy, and set the Q1
Resolution and Q3 Resolution to Standard (default); specify the Quantifier, Qualifier, and Qualifier
ion ratio in %. (These entries can be left blank and assigned later from processing of a selected data
file.)
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8.0
17
18
9.0
19
7. Click Inject.
8. Wait for System Control to show a green Ready status.
20
10.0
5. Click OK.
6. Type a name for the SampleList and then click Save.
21
22
11.0
Creating a Sequence
3. Click OK.
4. Type a name for the SequenceList and then click Save.
23
24
12.0
Note: The example files used in this section are located in C:\BrukerWS\MSTutorials\TQ
1. Click Compound Table in the MS Data Handling section then click the Select Data File button.
2. Browse to select a data file (normally a mid to high concentration file, in which all compounds can
be detected), and then click Open File.
25
26
5. Click Compound Table in MS Data Handling and then click the Update Ion Ratios (from figure in
step 1).
6. Click a line in the Quan Ion column in the Compound Table shown in step 1, inspect the MRM
chromatogram to see if the retention time tag (flag) is sitting on top of the peak, if not, drag the flag
onto the top of the peak to assign the retention time (shown in the next figure).
27
28
9. Click Close after updating from the processing of the selected data file.
Note: If the Quantifier and Qualifier ions are not assigned in the Acquisition Method, the
updating will automatically assign the Quantifier (the most intense MRM), Qualifier(s) and
their ratios. However, if Quantifier and Qualifier ions have been assigned previously in the
Acquisition Method, only the ion ratios will be updated, but not the assignment.
29
30
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The resulting RecalcList contains the 6 files of 5 calibration levels and one sample test to be processed.
32
33
For example, select Calibration Reports>Curve Report, report will be generated as shown.
34
13.0
1. Acquire a mid to high level calibration standard with a full scan acquisition method.
2. Go to the method editor, click on Compound Table, and then select the data file.
35
5. Build Spectrum List from Active Chromatogram will generate a spectrum list entry automatically for
every peak in the chromatogram.
36
8. Close MS Data Review and open the method in the method editor.
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14.0
Creating a Report
1. From the System Control Task Pane, click the Report button.
2. Click the MS Report button.
3. Select the data file to create the report.
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15.0
Part Number
Description
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
9300008800
394055501
394032001
394043401
394031401
394031701
394043501
394043101
394052501
394054001
394031801
394032701
394033501
394032801
394053001
394040301
394031501
40
Part Number
Description
1
2
3
394055001
394043201
394055401
41
Part Number
Description
1
2
3
4
5
6
394040801
394040901
394040701
394040501
394040601
394061401
NUT, REPELLER, EI
PIN CONNECTOR REPELLER, EI
CAP, EI, REPELLER
REPELLER, EI
MOUNT, REPELLER, EI
CI REPELLER, HYBRID, SOLID
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16.0
Routine Maintenance
Your application may require different intervals than the following, depending upon sample load, matrix,
and QC requirements. For instructions, see the appropriate manual.
Daily or Weekly
Check/refill autosampler solvent wash vial (daily).
Check autosampler syringe (daily); replace as needed.
Check for leaks using air/water report (daily).
Check for tightness of column nut on transfer line and injector (daily).
Replace injector septum (50-200 injections).
Replace insert and O-ring.
Clip column (8-30 cm, depending upon matrix).
Check gas filters, carrier gas supply, and other gases.
Monthly
AutoTune if needed.
Clean the source if needed
Run Electronics Diagnostics.
2 to 3 Months
Replace column if necessary.
Check the color of the oil in the foreline pump, if it is dark or muddy; change the oil and the oil
mist cartridge more frequently.
Yearly
Change foreline pump oil and oil mist filter cartridge.
Variable
Replace detector when EDR maximum voltage reaches 2000V.
Refill calibration gas bulb when empty.
Calibrate CI/CID pressures when gas is changed or pressure does not reach set point.
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17.0
Basic Troubleshooting
Run Diagnostics when hardware failures occur. Refer to the hardware manual for more information.
Check that the column is positioned correctly in the ion source. Check air and water in the spectrum
(scanning from 10 to 50 amu).
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18.0
Spare Parts
Part Number
Description
Injector Type
2869458001
PTV/SSL
CR298777
PTV
392534201
PTV
390842300
PTV/SSL
190015800
PTV/SSL
7200008400
PTV/SSL
CR298713
9 mm Septa
SSL
RT210462145
SSL
394955100
PTV/SSL
8850103100
PTV/SSL
190010906
PTV
BR-F0301
394052501
Filament EI RH
394054001
Filament EI LH
CR213200
394083101
Exhaust Filter, AF 8
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Bruker Corporation
3500 West Warren Avenue
Fremont, CA 94538
Phone +1 (510) 683-4300
Fax +1 (510) 687-1217