YL6900 GC/MS

Quick start manual

 YL6900 GC/MS

MSD Installation procedure

1) YL6500GC and YL6900GC/MSD connection

1. Place a support and YL6900GC/MS to a table.

2. Mount YL6500GC on the support, but you need to consider the transfer line must
be away from YL6500GC left wall.

3. Insert a ceramic chamber to a hole at the left side of GC.

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4. Rotate four rubber legs under the support to adjust the height between Transfer
line and the hole, and then move carefully MSD to left side of GC as close as
possible so that Transfer line is inserted in the ceramic chamber.

2) PC Communication setting
1. Connect an enclosed LAN to rear side of MS and LAN Hub.
2. Connect RS 15 pin cable to GC remote In/Out port and MS.
3. Connect two Power cables to;
A. Main power(220V)
B. Rotary pump
4. Set IP address for PC as below procedure.

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3) Rotary pump installation

1. Power cable: Connect it between Rotary pump and MS Input.

2. Vent line: Connect it to MS vent outlet by a clamp.

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3. Oil Filter: Install an Oil filter by a clamp.

4. Oil port: Open the cap and pour Oil.

5. Oil level sight glass: Fill oil around 70~80% level as indicated.

4) Carrier gas trap installation for GC

-Connect Moisture ->Oxygen ->Hydrocarbon trap in order -> GC Carrier port
-Carrier gas type and purity: 99.999% of He is required.
* Filters are necessary because impurity in carrier gas affects to increase noise level and
longer stabilization.

5) Column installation
1. Inlet side: adjust 2cm from bottom of nut and end of column as below then
tighten the nut to capillary injector.

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2. Mass transfer Line side

-Wipe about 300 mm of column with a cloth moistened with solvent (methanol or
ethanol).

A. Use Column measuring tool in MS-Spare kit as below picture;

i. Place ‘Septum ->Column nut->Ferrule’ to Column measuring tool and

tighten Column nut. (Caution: Ferrule direction)

ii. After inserting Column in Column measuring tool, adjust column length
around 3~4cm from the outlet of tool.
iii. Cut and align the end of column to measuring point as below picture
and remove the tool.

iv. To prevent from contamination, perform clean procedure (A) once again
and then connect column to Mass transfer line.

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MSD Tune procedure

1) Power On
Turn GC power ON (IP is same as general setting.)

2) GC analysis parameter

1. Oven temperature: 40 ℃

2. Carrier gas flow

Access to APC Config window then change flow mode to. GC/MSD mode and type
of carrier gas to Helium, or Hydrogen (under evaluation).
3. Spilt ratio - 1 : 10

4. Inlet temperature: 250 ℃

5. Remote time setting (200 min -> 3000 min) as below access.
System -> Special -> Press Next button -> Remote Access

*Under GC/MSD mode, column flow rate is displayed around 0.9mL/min at oven

temperature 40℃ with 15m, 0.25mm column, He carrier gas. It is for pressure

compensation of vacuum. Column head pressure displays 0.6~0.8psi when actual

column flow rate reaches to 1ml/min.

*Splitless mode
Set Auto Readyrun to off from System -> Special -> Run start. When GC is Ready
status, press Ready Run button and then wait until Ready LED is flickering. After
end of run, split flow rate is not reduced to 0mL/min and flows according to its split
ratio setting.

3) MSD Setting

1. Turn on Yellow switch at rear side of MSD. (Red switch is Service mode purpose.

2. After MSD is on, double click on icon to run YL MS Tune software.

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3. Set IP address to 192.168.55.11 and then press Connect.

4. Turbo pump stabilization for around 10minutes.

(1) Green signal indicates MSD is connected normally.

Red signal indicates Communication failed.
(2) When Fore pressure is higher than 80 mTorr, Red signal displays. When it is
lower than 80 mTorr, Green signal displays.
(3) Ion source and Transfer line temperature is increasing to its setting point and
Yellow signal indicates temperature is raising.

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5. Electric board stabilization for around 5minutes.

6. After stabilization procedure is done, MS ready message appears. Press continue

button to go to next step. (Fore pressure is normally lower than 80mTorr.)

7. Check Turbo pump rate is higher than 99.9%, Fore pressure value is between
50~70mTorr and Ion source, Transfer line temperature value.

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4) Column and MSD conditioning

*If you use new or not conditioned column, you must condition it without MSD connection.
After conditioning the column connect it to Transfer line then perform MSD condition.

1. Ion source temperature : 350 ℃

2. Transfer line temperature : 250 ℃

3. Press Set button after enter the setting temperature.

Perform Overnight conditioning with above setting at least 6 hours.
4. After conditioning, set temperature as below.

(Ion source : 200 ℃, Transfer line : 250 ℃)

5. Perform Diagnostics as below after temperature reaches to setting point to check

function of MSD.

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6) Specified range spectrum: Check background noise level to see MSD status.

*Normal background value of TIC is Xe 4~5 .

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7) Air/Water Spectrum

*m/z 18: Water, 28: N2, 32: O2

After turning MSD on, water peak (m/z 18) must be significantly higher than nitrogen peak
(m/z 28) and oxygen peak (m/z 32), and the latter ones must be hardly visible if compared
with it. However, during prolonged continuous operation water is gradually evacuated from
vacuum chamber and water peak becomes smaller than nitrogen peak. For more details,
refer to user manual pg. 35~37.

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8) Calibration gas spectrum (Standard: PFTBA)

* Ensure that mass spectrum of calibration gas contains all its typical peaks: 69, 131, 219,
264, 414 and 502 m/z. The highest peak may be 69 or 219 depending on selected settings.
You need to check above m/z accuracy and W(resolution) value. W is 0.5~0.7 and m/z is
within ±0.1.

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9) Automatic tune
Once 6 hours elapsed after system activation and operating, you can run automatic tune.
Automatic tune is necessary when you install MSD initially or do not use for few days or
Calibration gas spectrum is out of range. (m/z: ±0.1, W: 0.5~0.7)

1. Fast Tune: Suggested every day or no use for 2~3days.

2. Standard: Suggested after cleaning or replacement of MSD components or no use

for more than a week.

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10) MSD Power off

1. Before turn MSD off, set GC Oven temperature cool down with carrier gas on.

2. When Oven temperature is near to 40℃, press Shutdown button as below.

3. When press Shutdown MS button, the following window appears.

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4. When Ion source and Transfer line temperature reaches to lower than 125℃and Turbo

pump rate is 0 %, close YL Tune software and then turn off Yellow switch at rear side of
MSD.

5. Turn off carrier gas and remove MSD front cover. After that, open Vent valve to counter
clock wise. At this time, you need to be aware that near to Vent valve must be clean
because atmospheric air is introduced into MSD.

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YL Clarity Software
1) Instrument setting

1. Install YL Clarity installation file (version 6.1.0.130 or higher), and MSD patch file.
For the patch file, run ‘!regasm.bat’ file in MSD patch folder.

2. Insert a dongle key and enter the user code during installation.

3. Set Instrument type to GC/MS as below:

4. Add YL6500GC and YL6900GC/MS drivers on configuration window.

To search GC and MSD driver, enter ‘6500’ and ‘6900’.

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5. Double click on YL6900 GC/MS driver and set information as below:

*From this window, do not press ‘TEST’ button.
Set IP address to ‘192.168.55.11’ and change MSDetector name and S/N.

6. Set 6500GC driver as same as above procedure.

*From this window, do not press ‘Auto Detect’ button.

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7. Delete not used GC detectors and set Method change option to’ Do Not Send

Method to Instrument’ and type of units from icon.

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8. Set Directory folder where data files are saved.

2) Instrument Control
1. Click on Login button and make and enter name of project.

2. After Login, the following window appears.

a: Device Monitor
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b~d: Setting analysis parameter

e: Single injection setting for Manual injection
f: Sequence setting for Autosampler
g: Data Acquisition window

3. Device Monitor: You can observe current status of GC and GC/MS.

4. Set MSD analysis parameter from MS tab.

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1> Ion source temperature: 200~350C, Transfer line temperature: 250~350C

Transfer line temperature should be higher 20~50 than ion source ion source, but
lower than column maximum temperature.

2> When Filament 1 doesn`t work, check Filament 2.

Check Ion gauge if it is installed.

3> Start time: Set ‘Start time’ after elution of solvent peak.

Emission current: 50 ~300, EM gain: 100000~300000

Set Emission current and EM gain as low as possible if intensity is enough.

Scan mode: Enter start mass and end mass value (1~1200 amu)
SIM mode: Enter desired Ion value.

5. Set GC analysis parameter for Injector and Oven.

6. When all parameter reaches to its setting point, press Start button of GC after
injection.

3) Data Processing

1. Integration

When you click on ‘Chromatogram Window’ , the following window appears.

1> Open a data file by this icon , and choose the desired file.

2> The data file created by MSD displays two signals, one is Scan and another
one is SIM. You must select either Scan or SIM which you used the method.

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3> Set ‘Result table signal’ on ‘MS method’ window to Scan or SIM used by the
method.

4> After setting above, perform integration by integration parameters.

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2. Qulification

-There are three types of NIST library search options, Single compound search,
Automatic compound search and Target compound search for Qulification procedure
udner Scan mode. On Chromato gram window, you are able to see three icons

on the top.

*SIM mode is not able to use NIST library search option.

Before searching compound by NIST, set Result table signal to ‘Scan’ on MS

method window, spectrum to ‘Scan specturm’ on Chroamtogram window, and click
on the signal named as Scan.

1> Single compund search

Cllick on icon and place a vertical line to apex of desired peak. NIST library
window shows the result of compound, probability, specturm and match factor.

2> Automatic compound search

The following window appears after clicking on icon.

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(1) Search: To start library search option

(2) Set search options based on application.

(3) Exclude the compounds lower than Min Match factor value.

(4) Set NIST Library source file. Normally, ‘mainlib’ file is necessary for single MS.

(5) After search procedure is done, the highest probability compound is displayed
based on Retention time of peak. Select the compound and press ‘Add all
Selected to Method’ button to copy the compound information to MS method
window.

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3> Target compound search

The following window appears after clicking on icon.

(1) Click on ‘Select Compound’ button.

(2) Enter desired compound name in Search box and then press Ok button.

(3) Min. Match Factor is used for searching compound by match factor.

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(4) Choose desired RT with Match factor and copy the information to MS
method window by clicking on ‘Add Selected to Method’ button.

3. Calibration

1> Calibration curve for SIM file

(1) Open a SIM data file and select ‘Add compound w/o Library spectrum’ MS
menu on Chromatogram window.

(2) Place a vertical line to apex of peak and enter name of compound.

(3) Check compound name and retention time are copied to MS method and
change Spectrum to ‘SIM spectrum’, Quantify on option to ‘SIM’.

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(4) Add the other compounds as above procedure and then click on ‘Create MS
calibration’ button.

(5) Calibration window opens and enter name of calibration file.

(6) Open the Standard file which you add compound information to MS method

for calibration curve from the menu. At this time, Response value is 0.

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(7) Click on Responses from Quant. Signals icon and response values are
copied to the table, and enter Amount value of each compound.

(8) Perform level 2, 3… as same as above procedure to create a calibration

curve, and change calibration level before clicking on icon.

(9) Check calibration curve information for each compound by clicking

compound at the bottom of window.

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(10) Calibraiton curve for Scan file

-In order to create a calibration curve for Scan file, you need to enter name of
STD compounds and retention time by NIST library search or ‘Add compound
w/o Library spectrum’ function into MS method as same as SIM calibration curve.
When compound is entered by NIST Library search, ID and Library source file
information is shown in MS method table as below picture.

*Dodcecane is entered by NIST and Tetradecane is entered by Add compound

w/o Library spectrum.

After enter name of compound and retention time, make a calibration curve as
same as SIM file procedure.

4. Quantitation

1> Open an unknown sample file on chromatogram window.

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2> Qualify name of compound and retention time into MS method window by NIST
library search option (Scan) or Add compound w/o Library spectrum (Scan or
SIM).

3> Move to result table and click on set button to apply a calibration curve.

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4> After applying a calibration curve, result table will show amount of each
compound.

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