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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

SCION GC-MS SYSTEM GETTING STARTED


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.

SCION GC-MS SYSTEM GETTING STARTED

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.

SCION GC-MS SYSTEM GETTING STARTED


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.

SCION GC-MS SYSTEM GETTING STARTED


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.

SCION GC-MS SYSTEM GETTING STARTED


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.

SCION GC-MS SYSTEM GETTING STARTED

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.

SCION GC-MS SYSTEM GETTING STARTED


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.

SCION GC-MS SYSTEM GETTING STARTED


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.

SCION GC-MS SYSTEM GETTING STARTED

3.0

Evacuating (Pumping down)

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

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SCION GC-MS SYSTEM GETTING STARTED


4. Click Evacuate.

5. Click Close.

Message shows in Out box at the bottom of System Control when evacuation is finished.

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SCION GC-MS SYSTEM GETTING STARTED

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.

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SCION GC-MS SYSTEM GETTING STARTED

5.0

Creating an MRM Acquisition Method from


Factory Library

1. Open MS Workstation 8 for SCION.


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

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SCION GC-MS SYSTEM GETTING STARTED

6.0

Creating an MRM Acquisition Method from


User Library

1. Open MS Workstation 8 for SCION.


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 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.

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SCION GC-MS SYSTEM GETTING STARTED


9. Click OK.

10. Click the Close button.


11. Delete the Default Compound. The example method contains 25 compounds, each with two MRMs.

12. Click the Method Editor Save button

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SCION GC-MS SYSTEM GETTING STARTED

7.0

Creating an Acquisition Method Manually

1. Open MS Workstation 8 for SCION.


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. 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.)

7. Click the Method Editor Save button

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SCION GC-MS SYSTEM GETTING STARTED

8.0

Completing the GC Method

1. Click Autosampler and then complete the parameters.

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

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SCION GC-MS SYSTEM GETTING STARTED


3. Click Column Oven and complete the parameters.

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SCION GC-MS SYSTEM GETTING STARTED

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.

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SCION GC-MS SYSTEM GETTING STARTED


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

SCION GC-MS SYSTEM GETTING STARTED

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.

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SCION GC-MS SYSTEM GETTING STARTED


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.

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SCION GC-MS SYSTEM GETTING STARTED

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.

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SCION GC-MS SYSTEM GETTING STARTED


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.

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SCION GC-MS SYSTEM GETTING STARTED

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.

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SCION GC-MS SYSTEM GETTING STARTED


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).

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SCION GC-MS SYSTEM GETTING STARTED


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).

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SCION GC-MS SYSTEM GETTING STARTED


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

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SCION GC-MS SYSTEM GETTING STARTED


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.

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SCION GC-MS SYSTEM GETTING STARTED


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

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SCION GC-MS SYSTEM GETTING STARTED


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.

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SCION GC-MS SYSTEM GETTING STARTED


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.

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SCION GC-MS SYSTEM GETTING STARTED


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.

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SCION GC-MS SYSTEM GETTING STARTED


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.

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SCION GC-MS SYSTEM GETTING STARTED

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.

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SCION GC-MS SYSTEM GETTING STARTED


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.

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SCION GC-MS SYSTEM GETTING STARTED


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.

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SCION GC-MS SYSTEM GETTING STARTED


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.)

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SCION GC-MS SYSTEM GETTING STARTED

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.

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SCION GC-MS SYSTEM GETTING STARTED

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

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SCION GC-MS SYSTEM GETTING STARTED

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

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SCION GC-MS SYSTEM GETTING STARTED

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

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SCION GC-MS SYSTEM GETTING STARTED

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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SCION GC-MS SYSTEM GETTING STARTED

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.

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SCION GC-MS SYSTEM GETTING STARTED

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

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