Mascom MC513000 User manual

Operating Manual
GC-APPI Inferface for:
Orbitrap FusionTM TribridTM MS,
and Orbitrap FusionTM LumosTM
TribridTM MS
P/N: MC513000
Revision B

GC-APPI Interface Page 2
GC-APPI-Interface
© 2018 MasCom Technologies GmbH
Original Operating Instructions
The manual describesthe installation and
operation of the GC-APPI-Interface for the
Orbitrap Fusion seriesMS systems.
Revision History:
Revision A: published in December 2018
Revision B: published in May 2019
MasCom Technologies GmbH
Sophie-Germain-Str. 4
D-28201 Bremen
Germany
Tel.: [phone]
[email protected]
Trademarks
Fusion, Tribrid, Lumos, Orbitrap,
Thermo Scientific,Trace, Trace GC Ultra, and
Xcalibur are registered trademarks of Thermo
Fisher Scientific Inc. in the United States.

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Safety Instructions
Please read all ofthese instructions carefully
before starting the installation of theGC-APPI-
Interface and follow all recommendations.
1) Set themass spectrometerto “off”mode.
2) Cool down the heated capillary of the
mass spectrometer
3) When removing theESI sprayer be aware
thatthe heated capillary may still be hot.
4) Caution: don’t squeeze your fingers when
closing the cover of the interface
5) Please use nitrile gloves, or similar ones,
to ensureyour own safety and avoid
contamination.
6) Always unplug the heater cable before
detaching the interface from the mass
spectrometer. Never connect the
interface heatercables when the APPI
interface is not attached tothe mass
spectrometer. There is ahigh risk of over-
heating because the fanis not running.
Caution: hot surface with high risk to get burned!
During operation, the Interface housing may warm
up to 65 deg. C. When the interface is opened, the
heater is automatically turned off but thesource
may still be very hot (upto 330 deg. C, depending
on the operating temperature).
We also recommend watching the GC-APPI-
Interface installation video tofamiliarize yourself
with the procedure. This video has been provided
on a USB stick with theinterface. Alternatively,
you candownload it using the following link:
http://www.mascom-
bremen.de/html/en/downloads/gc-appi-
information

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Important information
Any changes or modification to the GC-APPI
interface, undertaken without our consent, may
endanger the functionality and/or safety, and
will result in the termination of the declaration
of conformity.
Tools required for source switching
Changing from ESI toGC-APPI on the Exactive or
LTQ Orbitrap series instruments only requires a
few tools:
Figure A: Screwdriver for removing the spray cone
and for tighten the plug on the APPI lamp
Figure B: 5/16-wrench for the dopant gas
connection
Figure C: 6 mm Allen screwdriver for locking and
unlocking the interface on the Orbitrap Fusion
systems

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Figure D: Special tool for removing the transfer
tube on Obritrap Fusion only
Tools used for theGC column connection on the
GC injector are described in the GC manual.

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Installation of the GC-APPI Interface
Before installing the GC-APPI-Interface you have
to remove the ESI sprayer. Make sure the mass
spectrometer is set to “Off”, and the heated ion
transfer tubeis set to room temperature (see
Figure 1 and 4).
Caution: Removing the ESI sprayer while the
instrument is on or in standby will load the default
Tune file and eventually start the capillary heating.
Figure 1: Instrument in “Off”mode
Disconnect the waste hose from the bottom of the
TNG source,as well as all gas, syringe, and
electrical connections.
Figure 2: Instrument with ESI sprayer

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Carefully removethe ESIsprayer from the mass
spectrometer interface andput it aside in a safe
place.
Remove the Thermo ion sweep coneas shown in
Figure 3, which is the removable spray shield that
sits just over theion transfer tube. Using a small
flat-head screwdriver, loosen the set screws on
the sides of the spray shield.
Caution: Theion sweep cone may still be hot.
Be sure to cooldown the ion transfer tube.
Figure 3: TNG source with sweep gas cone
Temperature setting is done on the TUNE page
(see Figure 4).
Figure 4: Ion transfer tube temperature setting
35

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The next step (Figure 5 and 6) is for
Orbitrap Fusion Lumos only:
Place the Vespel disk (P/N: MC502620) on the
original ion transfer tube(no need to change it as
on the OrbitrapFusion) with the rounded edge
towards the APPI-Interface (see Figure 6).
Figure 5: Ion source without sweep cone
Figure 6: Ion transfer tube with Vespel disk
The next steps (Figure 5x, 6x and 7x)
are for Orbitrap Fusion only:
After removing the ESI sprayer, you canaccess to
the transfer tube of the mass spectrometer.
Remove the transfer tubewith the special tool

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Figure 5x: Special tool for transfer tube removal
Figure 6x: Standard (A) and GC-APPI (B) transfer
tubes (P/N: MC501730)
(see Figure 5x) or with the 5/16wrench as
described in the operating manual of the mass
spectrometer.
Caution: Exchanging the transfer tubes at high
temperature is difficult and may damage them.
Replace the standard transfer tube (A) with the
GC-APPI transfer tube (B) (P/N: MC501730, see
Figure 6x,), and place the Vespel disk (P/N:
MC502610) on to the transfer tube(Figure 7x).
Make sure the disk is clean andfree of dust.
Figure 7x: GC-APPI transfer tube with Vespel disk
A
B

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All followings steps are for both Fusion type
systems.
Bring the closed GC-APPI Interface in frontof the
Mass Spectrometer and arrange the cable for the
APPI lamp close to its final position. Mount the
interface, open it and lock it (Figure 7a, 7b, 8aand
8b) with a6 mm Allen wrench.
Figure 7a: Locked position of the leftGC-APPI-
Interface connector
Figure 7b: Locked position of the rightGC-APPI-
Interface connector
Figure 8a: Mounting of the GC-APPI-Interface

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Figure 8b: Mounting of the GC-APPI-Interface
Next, attach the transfer line tothe APPI-source.
Remove the APPI lamp for better access to the
transfer line connection.Place the connector in
front of the transfer line (Figure 10) and after
inserting the GC column place the graphite ferrule
with the conical side towards the transfer line.
Figure 9: Transfer line connection to APPI source
Figure 10: Transfer line with connector
Figure 11: Transfer line with connector and ferrule

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Attach the transfer line with connector and ferrule
to the APPI sourceand only slightly tighten the
connector (see Figure 12).
Figure 12: Transfer line connection to APPI source
Adjust the GC columnbefore finally tighten the
connector. It just has to protrude out of the inner
source (see Figure 13a and b) by about 0.5 to 1
mm (check with a flashlight).
Figure 13a: GC column inside APPI source
Figure 13b: GC column inside APPI source,
zoom-in

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Finally tighten the transfer line connector and
press the transfer line against the connector
before fixing itwith the clamp (see Figure 15).
Figure 14: Transfer line in its final position
Now insert the APPI lamp intothe lamp holder
and tighten the two screws to fix the lamp inits
final position.
Figure 15: Transfer line fixing with clamp
Figure 16: Positioning ofthe APPI lamp

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Figure 17: Fixing APPI lamp inits final position
When the lamp is inserted and fixed, connect the
cable to the lamp and fix the plug with the screws.
Figure 18: Connecting the APPI lamp cable.
Figure 19: Fixing APPI cable.
Close the cover of the interface and make sure the
protection shieldcompletely covers the transfer
line.

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Figure 20: Closed APPI interface with dopant gas
line connected
In case you want touse an optional dopant gas,
remove the blind plug and connect the dopant gas
line as seen inFigure 20. If you do not wantto use
any dopantgas, please check if the blind plug is
properly tighten.
When everything isattached to the mass
spectrometer,you can plug in the power line of
the GC-APPI interface either into theTrace 1310
GC or Trace GC Ultra.
When the power line is connected and the cover is
closed, check if the fan is running (air stream
underneath the interface).
Figure 21: APPI sourceheater connection on Trace
1310GC
Caution: do not connect theheater cable without
the interface attached to the mass spectrometer!
Please note:when connecting the heater cable for
the first time, it will only be recognized by the GC
if the cover is closed.

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Operation of the GC-APPI Interface
Setting up the Instrument Configuration for
Thermo GC Systems
Close all Xcalibur programs andopen the
Instrument Configuration. Make sure the GC
devices are installed and select the ThermoFocus,
Trace 2000,Trace Ultra or Trace 1310 GC from
the list of GC devices.
Figure 22: Xcalibur Instrument Configuration
If you are using an autosampler, please select it
from the list too. Check that the communication
of theGC (and autosampler) is correct and close
the Instrument Configuration panel.
Setting up the Instrument Configuration for
APPI Source usage
In the Instrument Configuration select the
Orbitrap Fusion and click on configure (see Figure
23).

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Figure 23: Xcalibur Instrument Configuration with
Orbitrap Fusionselected
Change the Default Source Type to ‘Dedicated
APCI’and click on ‘Apply’. Leave this page with
‘OK’(see Figure 24).
Figure 24: Xcalibur Instrument Configuration for
Orbitrap Fusion
Close the Instrument Configuration, start Xcalibur
and wait for all instruments toinitialize and to
become “Ready for download”.

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Tune the MS
Turn on the MS and tune the mass spectrometer
in APPI mode. Make sure the APPI lamp switchis
in on position (blue LED is on,see Figure 25).
Figure 25: APPI sourcewith lamp switch
If the APPI lampis off, the noise level will be very
high (see Figure 26).
Figure 26: MS tune spectrum when APPI lamp is
off
When using a dopant gas you cantune the MS
using the dopantgas’molecular ion (i.e. m/z 92
for toluene). Without a dopant gas the easiest
way to tune the MS is to select a GC column-bleed
ion like m/z 207 or similar.
Once the tuning is optimized, save theTune file
(an example canbe seen in Figure 27).

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Figure 27: Example of MS tuning in APPI mode
Setup the Instrument Method
The following is validwhen using theThermo
Scientific Trace 1310 GC. For any other GC, we
refer toits dedicated manual.
Figure 28: Instrument Method Setup
Open the Instrument Methodeditor from the
Xcalibur Home page. In the editor,you will see the
different instruments.
Select the Trace 1310 GC and setup the desired GC
method. On the Aux Temperatures tab you have
to enter the temperature of the transfer line and
the temperature of the APPI source (listed as Aux.
Heater 2, seeFigure 29). Both temperatures

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should notdiffer a lot from each other. Typical
temperatures are between 225and 300 deg. C.
Please note:
The maximum temperature of the APPI sourceis
330deg. C.
For details of theGC setup and/or programming,
we refer to the GC Manual.
Figure 29: Aux Temperature for Trace 1310 GC in
Instrument MethodSetup
Switch to the MS to select or setup the
appropriate MS method with the corresponding
MS Tune file. If an autosampler is in use, also
setup the correctautosampler method. Save the
Instrument Method and setup a sequence file.
Setup the Sequence File
From the Xcalibur Home page, select the
Sequence editor to setup one or moresample
measurements. For details, we refer to the
standard MS operation manual.
Running a GC sample
When all instrument devicesin Xcalibur are
“Ready for download”,you can start the sample or
sequence measurement from the sequence setup.