394205900a Scion Getting Started PDF

SCION
GC-MS System
Getting Started
Part Number 394205900 Revision A
Table of Contents
1.0
Venting ...................................................................................................... 1
2.0
Installing GC Capillary Column .............................................................. 3
3.0
Evacuating (Pumping down) ................................................................. 10
4.0
AutoTuning ............................................................................................. 12
5.0
Creating an MRM Acquisition Method from Factory Library ............. 13
6.0
Creating an MRM Acquisition Method from User Library .................. 14
7.0
Creating an Acquisition Method Manually ........................................... 16
8.0
Completing the GC Method ................................................................... 17
9.0
Making a Single Injection ...................................................................... 19
10.0 Creating a SampleList Using Templates .............................................. 21

11.0 Creating a Sequence.............................................................................. 23
12.0 Data Processing for Quantitative Analysis .......................................... 25
13.0 Data Processing for Qualitative Analysis ............................................ 35
14.0 Creating a Report ................................................................................... 39
15.0 Ion Source Reference ............................................................................ 40
16.0 Routine Maintenance ............................................................................. 43
17.0 Basic Troubleshooting .......................................................................... 44
18.0 Spare Parts ............................................................................................. 45
SCION GC-MS SYSTEM GETTING STARTED
1.0
Venting
1. Open MS Workstation 8 for SCION.

2. From the System Control Task Pane, click the MS Setup button.
3. Click Manifold; see the following figures.
SCION SQ
SCION TQ

4. Click Vent.
5. Click Cool down (may take up to 5 min).
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
Installing GC Capillary Column
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
Connecting Capillary Column to Injector
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.

5. Inspect the cut to verify it is square and smooth.
1. Capillary column nut

2. Fused silica column
3.
Capillary column ferrule
4.
Properly cut column end
5.
Improperly cut column end
6. Move the nut and ferrule to within 3 cm of column end.

7. Measure the mark point from the end of the column and mark this distance with a felt pen. The use
of the Column Scale tool (part 392575001) improves the ease and accuracy of this measurement.
Using the Split Splitless (SSL) injector, Insertion depth is 3.7 cm.
The ferrule can be contaminated. DO NOT allow the column nut and ferrule to move past the
mark.

8. Partially insert the column into the lower end of the Injector. Thread up the capillary column nut and
ferrule finger-tight.
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.

2.2
Connecting Capillary Column to SCION MS
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.

7. Thread up the capillary column nut and ferrule and fasten until finger-tight. Gently push the column
into the transfer line until the column just emerges through the repeller.
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.

9. Using a 7/16 wrench hold the transfer line union while tightening the column nut using a 5/16"
wrench to tighten the column nut in place. Tighten the column nut only enough to seal the column
and hold it firmly in place. The nut may require retightening after first or second programmed run.
Over tightening will damage the ferrule and seal.
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
Evacuating (Pumping down)
1. Turn on the computer, GC, and MS. The main power switch is on the back of the instrument.
3. Click Manifold; see the following figures.
SCION SQ
SCION TQ
10

4. Click Evacuate.
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.
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
Creating an MRM Acquisition Method from

Factory Library

2. Click the Method Editor button.
3. Click the Method Editor New button
4. Complete the Method Builder wizard by accepting the defaults.

5. From Method Editor, click Acquisition Method.
6. Click the Factory Library button.

7. Select compounds from the factory library. (Ensure compound parameters are edited accordingly.)
8. Click the Save Selected Compounds To Method button.

9. Click OK.
10. Click the Close button.

11. Click the Method Editor Save button
13
6.0
Creating an MRM Acquisition Method from

User Library


6. Click the User Library button and then browse the following directory
(C:\BrukerWS\MSTutorials\TQ):
7. Select compounds from the user library.
8. Click the Save Selected Compounds To Method button.
14

9. Click OK.
10. Click the Close button.

11. Delete the Default Compound. The example method contains 25 compounds, each with two MRMs.
15
7.0
Creating an Acquisition Method Manually


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.)
16
8.0
Completing the GC Method
1. Click Autosampler and then complete the parameters.
2. Click Flow/Pressure and then complete the parameters.
17

3. Click Column Oven and complete the parameters.
18
9.0
Making a Single Injection
1. Prepare sample for injection.

2. Click File menu>Activate Method.
3. Select a method and then click Open.
4. Click Inject menu>Inject Single Sample.
5. Type the instrument parameters and then click OK.
19

6. Type the sample name. (By default, the data file name is the same as the sample name.)
7. Click Inject.
8. Wait for System Control to show a green Ready status.
9. Inject sample into GC.

10. (Optional) Click the view button to monitor the run in the Chro window. This view must be set using
the Advanced Role.
The run is complete when the MS Module Status is Ready.
11. In the Chro window, click the MS Data Review button

chromatogram.
20
to open the data file and view the
10.0
Creating a SampleList Using Templates
1. Open a SampleList template in Microsoft Excel from

C:\BrukerWS\SampleList.
2. Complete the SampleList and save the spreadsheet to a
location.
3. From the Task Pane in MS Workstation System Control,
click the Acquisition button.
4. Click the SampleList button then choose New.
5. Click OK.
6. Type a name for the SampleList and then click Save.
21

7. Click the Import button.
8. Click Browse and select the Excel file to import.

9. Click Browse and select the path to save the SampleList.
10. Click OK.

The SampleList is shown in the SampleList window.
22
11.0
Creating a Sequence
1. From the Task Pane in MS Workstation System Control, click

the Acquisition button.
2. Click the AutoSequence button then choose New.
3. Click OK.
4. Type a name for the SequenceList and then click Save.
23

5. Complete the SequenceList by selecting the appropriate method and SampleList.
6. Click the Begin button.

7. Complete the Instrument parameters window and then click OK.
A message shows you that the sequence will begin.

8. Click OK.
24
12.0
Data Processing for Quantitative Analysis
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

3. Click the Set Default button (from figure in step 1), and then type the calibration concentration
information of the 5 levels and other parameters (using the default ones here).
26

4. Click Calculation Setup and then select External Std on the Calibration Type.
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

7. Click Next to inspect the next compound, until retention time for all compounds are set correctly.
28

8. Select the box next to Select highest transition for the quantifier, make other transitions
qualifiers. Click Start.
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

10. From the File menu, click Save. Now the method contains data handling parameters needed for
processing the data.
30

12.1 Processing and Reporting
1. Click the Data Process button from the Task Pane.
2. From MS Data Process file explorer, go to the directory that contains the raw data files and select
them with the mouse while pressing and holding the Ctrl key.
3. Right-click the data file and point to Recalc List File, and then click Create with Selected Files.
31

4. Type a name for the Recalclist File name, and then click Save.
The resulting RecalcList contains the 6 files of 5 calibration levels and one sample test to be processed.
5. Click the Process Data button
. Data files will be displayed.
32

6. Browse to select the corresponding Method File and the Recalc List File.
7. Click the Process button. The files are processed line by line as shown.
8. Click the View Results button
from the top menu bar to view the processed results.
33

9. Click the Report button from the bottom left, select the report options of your choice.
For example, select Calibration Reports>Curve Report, report will be generated as shown.
34
13.0
Data Processing for Qualitative Analysis
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

3. Click the Build Compound List button.
4. Click on the desired peaks to be added to the spectrum list, or click Build Spectrum List from
Active Chromatogram.
5. Build Spectrum List from Active Chromatogram will generate a spectrum list entry automatically for
every peak in the chromatogram.
36

6. Click Library Search Spectrum List button
to library search all entries.
7. Click Update Library Search Spectrum List button
to accept library search results.
8. Close MS Data Review and open the method in the method editor.

37

9. Click Compound Table, and click Import Compound List button.
10. Select the spectrum list file (.msp extension).
The compounds will appear in the table.

Calibration and analysis standards can now be analyzed and used to optimize compound table
parameter settings (same procedure as in "Data Processing for Quantitative Analysis" on page 25.)
38
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.
4. Click Open to view the report.
39
15.0
Ion Source Reference
SCION EI Source Assembly

Item
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
EI SOURCE BODY, HYBRID

ASSY, ION SOURCE HOLDER
MAGNET BRACKET
LENS 1
LENS 2
APERTURE
LENS INSULATOR
CYLINDER
FILAMENT, EI, RIGHT HAND
FILAMENT, EI, LEFT HAND
MAGNET ARM
MAGNET
RTD ASSY SOURCE, EI
HEATER, SOURCE
CONNECTOR, HEATER & RTD
SOURCE HANDLE
FRONT FLANGE, EI SOURCE
40
SCION CI Source Assembly

The items noted below are different for the CI source assembly. Refer to the figure on page 40 for all
other items.
Item
Part Number
Description
1
2
3
394055001
394043201
394055401
CI SOURCE BODY, HYBRID

APERTURE (CI)
DUMMY FILAMENT HOLDER, LH
41
Repeller Assembly, part number 394040401

Item
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
42
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.
43
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).
17.1 Leak Checking

To determine if the leak is in the MS or the GC, set the scan range from 10 to 50 amu and turn on the
filament and detector. In System Control, click Tools/Plot tic, readbacks, and check TIC and in use.
Increase the carrier gas flow from 1 mL/min to 2 mL/min. If the m/z 28 ion increases or decreases and
the plot in the TIC trace changes then the leak is probably in the GC. Do the injector maintenance and
leak check the GC if the leak persists.
If the m/z 28 ion abundance remains stable, the leak is probably in the MS. Check that the column nut
is tight. If the column nut is secure, set the scan range from 10 to 100 amu and use a Freon type
dusting canister to spray around the various seals: column nut, transfer line O-ring.If these sprays are
not available, use argon CID gas. Systematically spray the argon in short bursts at the seals and look
for an ion at 40 amu. If the location of the leak is still unknown, plug the MS at the transfer line and
repeat the leak check on the MS. If the plugged MS does not leak, connect the GC and leak check the
GC.
17.2 No FC43 (Cal Gas) Signal

Run the electronics diagnostics to check for an electrical problem.
The most common reasons for loss of signal:
Dirty lenses Clean the source.
Worn out detector. Increase the detector voltage to see if the signal is recovered. Run the EDR
calibration.
17.3 Loss of Signal on Sample Runs

Run AutoTune and then rerun the sample. Compare the AutoTune to a report generated when the
instrument was operating properly. If the reports are comparable, the problem is probably the GC. The
GC injector may need maintenance or the column head may need to be cut. If the AutoTune results
look poor in comparison to the previous run, the source may need cleaning. If the signal is lost rapidly
after cleaning the source, check the system for leaks.
44
18.0
Spare Parts
Part Number
Description
Injector Type
2869458001
0.4 mm Graphite / Vespel Ferrules
PTV/SSL
CR298777
BTO Septa 11.5 mm, 50/pk
PTV
392534201
Ferrule, Insert, Graphite
PTV
390842300
Injector Nut Wrench
PTV/SSL
190015800
Ceramic Scoring Wafer
PTV/SSL
7200008400
Septa Extraction Tool
PTV/SSL
CR298713
9 mm Septa
SSL
RT210462145
Inlet Sleeve, Siltek, 4 mm w/Frit, 5/pk
SSL
394955100
Capillary Injector Nut
PTV/SSL
8850103100
Viton O-rings, 25/pk
PTV/SSL
190010906
Inlet Sleeve, SPI, 0.5 mm, 5/pk
PTV
BR-F0301
Bruker Triple Filter
394052501
Filament EI RH
394054001
Filament EI LH
CR213200
1/8 Poly/Graph FER PK/10
394083101
Exhaust Filter, AF 8
45
Visit www.scionhasarrived.com for the latest SCION information.
Bruker Corporation
3500 West Warren Avenue
Fremont, CA 94538
Phone +1 (510) 683-4300
Fax +1 (510) 687-1217

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SCION

Part Number 394205900 Revision A

Installing GC Capillary Column .............................................................. 3

Evacuating (Pumping down) ................................................................. 10

Creating an MRM Acquisition Method from Factory Library ............. 13

Creating an MRM Acquisition Method from User Library .................. 14

Creating an Acquisition Method Manually ........................................... 16

Completing the GC Method ................................................................... 17

Making a Single Injection ...................................................................... 19

10.0 Creating a SampleList Using Templates .............................................. 21

SCION GC-MS SYSTEM GETTING STARTED

1. Open MS Workstation 8 for SCION.

SCION GC-MS SYSTEM GETTING STARTED

5. Click Cool down (may take up to 5 min).

SCION GC-MS SYSTEM GETTING STARTED

Installing GC Capillary Column

Connecting Capillary Column to Injector

SCION GC-MS SYSTEM GETTING STARTED

1. Capillary column nut

Capillary column ferrule

Properly cut column end

Improperly cut column end

6. Move the nut and ferrule to within 3 cm of column end.

SCION GC-MS SYSTEM GETTING STARTED

SCION GC-MS SYSTEM GETTING STARTED

Connecting Capillary Column to SCION MS

SCION GC-MS SYSTEM GETTING STARTED

SCION GC-MS SYSTEM GETTING STARTED

SCION GC-MS SYSTEM GETTING STARTED

SCION GC-MS SYSTEM GETTING STARTED

Evacuating (Pumping down)

SCION GC-MS SYSTEM GETTING STARTED

SCION GC-MS SYSTEM GETTING STARTED

SCION GC-MS SYSTEM GETTING STARTED

Creating an MRM Acquisition Method from

1. Open MS Workstation 8 for SCION.

4. Complete the Method Builder wizard by accepting the defaults.

6. Click the Factory Library button.

8. Click the Save Selected Compounds To Method button.

10. Click the Close button.

SCION GC-MS SYSTEM GETTING STARTED

Creating an MRM Acquisition Method from

1. Open MS Workstation 8 for SCION.

4. Complete the Method Builder wizard by accepting the defaults.

7. Select compounds from the user library.

8. Click the Save Selected Compounds To Method button.

SCION GC-MS SYSTEM GETTING STARTED

10. Click the Close button.

12. Click the Method Editor Save button

SCION GC-MS SYSTEM GETTING STARTED

Creating an Acquisition Method Manually

1. Open MS Workstation 8 for SCION.

4. Complete the Method Builder wizard by accepting the defaults.

7. Click the Method Editor Save button

SCION GC-MS SYSTEM GETTING STARTED

Completing the GC Method

1. Click Autosampler and then complete the parameters.

2. Click Flow/Pressure and then complete the parameters.

SCION GC-MS SYSTEM GETTING STARTED

SCION GC-MS SYSTEM GETTING STARTED

Making a Single Injection

1. Prepare sample for injection.

3. Select a method and then click Open.