Varian 210-MS User manual

Varian, Inc.
2700 Mitchell Drive
Walnut Creek, CA 94598-1675/USA
03-954143-55:Rev. 1 1 of 33
210-MS and 220-MS GC/MS
Ion Trap Mass Spectrometer
Installation Procedure

Contents
Overview....................................................................................................................................4
Typical Installations .................................................................................................................4
Setting Up..................................................................................................................................5
Checking the Installation Site .....................................................................................................................................5
Unpacking...................................................................................................................................................................5
Connecting Components ............................................................................................................................................5
Setting Up the GC.....................................................................................................................8
Filling the Cal Gas Vial ...............................................................................................................................................8
Plumbing and Purging ................................................................................................................................................8
Installing the Column in the GC..................................................................................................................................9
Installing the Column in the MS..................................................................................................................................9
Setting Up the Foreline Pump .................................................................................................9
DS-42 Pump ...............................................................................................................................................................9
Powering Up the MS...............................................................................................................11
Baking Out the GC/MS .............................................................................................................................................11
Preliminary Tuning.................................................................................................................12
Monitoring the System..............................................................................................................................................12
Adjusting the RF Ramp ............................................................................................................................................13
Adjusting Cal Gas .....................................................................................................................................................15
Auto Tuning ............................................................................................................................16
Auto Tuning ..............................................................................................................................................................16
Testing Specifications............................................................................................................17
Specification Table ...................................................................................................................................................17
EI Methodology.........................................................................................................................................................17
Acquiring OFN ..........................................................................................................................................................18
Reviewing the Data...................................................................................................................................................18
Calculating the Signal to Noise Ratio .......................................................................................................................20
Library Searching......................................................................................................................................................22
CI Methodology.........................................................................................................................................................25
Installing Liquid CI ....................................................................................................................................................25
Adjusting Liquid CI Reagent Flow ............................................................................................................................26
Methodology .............................................................................................................................................................27
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Acquiring BZP...........................................................................................................................................................27
Calculating the Signal-to-Noise Ratio.......................................................................................................................28
Familiarizing the User Representative..................................................................................29
Creating a Sample List .............................................................................................................................................29
Activating and Running a Sample List......................................................................................................................29
Reviewing Results ....................................................................................................................................................30
Basic Source Maintenance.......................................................................................................................................30
Checklist for Familiarizing the User Representative.................................................................................................31
Appendix 2: Spare Parts........................................................................................................32
Kits, Assemblies, Boards, and Cables ...............................................................................................................32
Trap Components ..............................................................................................................................................32
Pumps ................................................................................................................................................................33
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Overview
Before scheduling the installation, call the customer to determine if they have met
the site requirements listed in the Pre-Installation Instructions.The critical site
requirements are bench space and load, power, temperature, humidity, carrier
gas purity (helium), and CI gas purity (methane).
Use these procedures to set up the 210-MS and the 220-MS GC/MS Ion Trap
(210/220-MS GC/MS), meet product specifications, and familiarize the customer
with the system. Also, test and demonstrate the CI ionization mode if it was
purchased.
Under normal circumstances, the installation of the 210/220-MS GC/MS Ion Trap
with EI requires 2 days on site.
Typical Installations
NOTE: Unless specified, these instructions are for both the 431-GC and the
450-GC
1. System unpacking, setup and checking 2 hours
2. Power up, pump down, demo 4 hours
3. Verification of GC/MS System Operation 2 hours
4. EI checkout and demo 1 hours
5. Additional customer familiarization 4 hours
Option Installation
1. Autosampler installation, check out, familiarization 1.5 hours
2. CI ionization mode demo, familiarization 0.5 hour
3. MS/MS demo 0.5 hour
Enter installation results into the Installation Tracking Database.
NOTE: Test samples are not shipped overseas with the system. Before going on
site to do an installation, ensure that you have all the necessary samples, or that
they have been shipped to the customer from a local Varian office. Installation
engineers outside of the USA should confirm the availability of test samples from
their home office as much as two weeks in advance. For US shipments the
samples are shipped with the system.
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Setting Up
Checking the Installation Site
Determine if the installation site meets the requirements listed in the
Pre-installation Instructions.
Unpacking
The MS, foreline pump, and gas chromatograph are heavy. To prevent
personal injury, use appropriate moving and lifting techniques.
While unpacking the system, check thoroughly for missing parts and shipping
damage. Use caution when unpacking the MS; do not use the transfer line as a
handle.
Using the transfer line to lifting the instrument can result in damage to the
analyzer.
Before setting up and starting the GC/MS, ensure that all parts and kits were
delivered and are complete. Review with the customer the contents of the
accessory kits and their functions.
Report all shipping damage or missing parts to the Customer Service department
(Phone: [phone], Fax: [phone], email: [email protected]),
Varian, 2700 Mitchell Drive, Walnut Creek, CA, 94598.
Note any shipping damage or missing items on the installation checklist and in
the Installation Tracking Database.
Connecting Components
1. Set the GC, MS, and PC on the bench.
2. Check that the instruments are wired for the installation site voltages.
3. Keep the GC and MS separate at least 46 cm (18 in.) to allow easy access to
both instruments.
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4. Remove the turbo pump shipping restraint from the MS.
5. Remove the shipping restraints from the GC including the metal dowel at the
rear of the GC.
6. Instruct the customer to keep the removed restraints, in case the system
needs to be transported.
7. Connect the foreline hose to the foreline pump. Connect the power cord of
the foreline pump to the LINE VOLTAGE PUMP ONLY connector at the rear
of the MS. To minimize vibrations, put the foreline pump on the floor not on
the bench.
8. Connect the power cords of the MS, the GC, and the PC into the appropriate
outlets.
9. Connect the GC to the MS as follows:
•431-GC: Connect the sync cable to the back of the GC at J2 sync
analog out and to the back of the MS at J43 Remote Option.
•450-GC: Connect the sync cable under the GC top cover at J401
sync analog out and to the back of the MS at J43 Remote Option.
J2 Sync/Analog Out
J2 Sync/Analog Out on back of 431-GC
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J401 Analog Out
J401 connection on top of 450-GC
J43 Remote Option
J43 Remote Option on back of 210/220-GC/MS
10. Connect the USB cable to the rear of the MS at J42 USB and to a USB port
on the PC.
11. Connect a crossover Ethernet cable to the GC and to the PC. Be sure to
connect the Ethernet cable using the side connector of the Tee and NOT the
terminators
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Setting Up the GC
Filling the Cal Gas Vial
1. Remove the empty Cal Gas vial from behind the MS front door by loosening
the two mounting screws and twisting the vial while pulling down.
Do not overfill the Cal Gas vial installed in the MS. Overfilling can result in
FC-43 contamination that interferes with Cal Gas adjustments.
NOTE: The Cal Gas part number, FC-43 392035300, is shipped in a separate
ampule. Install the Cal Gas during the installation. Aliquot approximately 0.5 mL
of the FC-43 into the Cal Gas vial and install it in the MS. Store the remaining
FC-43 in the vials provided in the accessory kit.
2. Fill the vial with approximately 0.5 mL of the FC-43, part number 392035300
provided in the MS Accessory Kit. Re-install the partially (less than half) filled
vial into the MS and tighten the mounting screws. The vial must be inserted
far enough into the pneumatic block to engage the O-ring. Store the
remaining FC-43 in the vials provided in the accessory kit. Be careful not to
overfill the Cal Gas vial to avoid FC-43 contamination that can interfere with
system performance.
Plumbing and Purging
1. Plumb 99.995% helium to the back of the GCMS system using 1/8 in. copper
tubing.
2. Insert the pencil filters.
3. Set the helium pressure to 80 psi and ensure that the cylinder has at least
500 psi.
4. Purge the helium line for 10 minutes at maximum flow.
5. Connect the outlet of the filter to the inlet on the back of the GC.
6. Purge the GC pneumatics for 10 minutes to remove water or air that may
have accumulated during shipping.
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Installing the Column in the GC
NOTE: the only injector for the 431-GC is the 1177. The 450-GC has the injector
the customer ordered.
1. Install the column that shipped with the instrument to achieve the best results
for the installation tests. If an 1177 injector is installed on the GC, use the
1177 to pass the sensitivity specifications.
2. Condition the injector and column once before installing into the MS. This
prevents column bleed from contaminating the MS.
3. Set the injector to 230 °C and do a split ratio (SR) of 50:1.
4. Condition the column starting at 50 °C, ramping at 5 degrees/minute up to
300 °C, and hold for 60 minutes unless this exceeds the maximum allowable
operating temperature for the column phase.
Installing the Column in the MS
NOTE: Leave a significant service loop of column detached from the column
cage so the GC and MS can be easily separated.
1. Disengage the transfer line by removing the clip to remove it completely from
the manifold.
2. Position the column in the transfer line so the end of the column extends 0.5
to 1 mm past the end of the transfer line and leave a big enough loop so the
MS and the GC can be easily separated.
3. Reinstall the transfer line into the manifold.
4. Push the GC and the MS together on the bench. Ensure that the nut on the
transfer line column is visible inside the GC oven and the transfer line rubber
boot is inside the hole on the GC side panel.
Setting Up the Foreline Pump
DS-42 Pump
1. Fill the mechanical pump to the mid-point of the sight glass with the supplied
Inland 31 vacuum pump oil.
2. Put a center ring on the end of the hose.
3. Tighten a vacuum clamp over the hose, and pump inlet.
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Do not place the foreline pump on the bench with the MS. Vibrations from
the foreline pumps will degrade the MS performance.
4. Place the pump under the bench.
Do not lengthen the vacuum hoses to prevent degrading the vacuum.
The foreline pumps must be connected to a ventilation system.
NOTE: You may observe foam when you look at the oil level. The oil may foam
until sufficient oil collects on the filter to create a seal and then it will stop
foaming.
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Powering Up the MS
1. Turn on the power switch of the MS.
2. Turn on the CPU and monitor.
3. Open MS Workstation.
4. Allow the foreline pump and the turbo pump to run for about 30 minutes
before assuming software control. This allows the pumps to become properly
lubricated.
If the foreline pump runs loudly for more that 1 min, turn off the main
circuit breaker and check the system for leaks. Possible leak sites
include the vacuum hose connections to the turbo or foreline pumps,
the manifold or transfer line O-rings and the column connection to the
transfer line.
5. Open System Control from the MS Workstation toolbar to activate
communication between the PC and all modules connected to it.
6. Check that the status screen displays both MS and GC.
7. The turbo pump speed should reach 100% between 1 to 2 minutes. The
turbo current should be less than 350 mA when the turbo reaches 100%.
8. Check for high mass noise using the daily check method.
•If OK, then check air/water. There should be a big 18 peak and no 28
peak. Turn off trap.
•If OK, bakeout MS overnight.
Baking Out the GC/MS
1. Ensure that the Trap and Source temperatures are at least 150 °C and the
Manifold temperature is at least 50 °C before heating the transfer line, GC
column oven, and injector. This prevents column stationary phase from
collecting on low temperature MS components.
2. Set the injector temperature to 230 °C with a split ratio of 50:1.
3. Set the column temperature to 150 °C.
4. Click Temperatures on the Analysis tab and enter these temperatures:
•Trap: 150 °C
•Manifold: 40 °C
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•Transfer Line: 230 °C
5. Click the Bakeout tab and enter these temperatures:
•Trap: 220 °C,
•Manifold: 120 °C
•Transfer Line: 250 °C
6. Set a Hold Time that ends bakeout about 2 hours before you plan to arrive
the next day.
7. Click Start Bakeout.
8. Leave System Control open, if it is closed, bakeout is cancelled.
9. Condition the system overnight, before doing the system specification tests.
Hydrocarbon and water background levels decrease after the initial bakeout.
During bakeout, familiarize the customer with the system.
10. After bakeout, reset the manifold bakeout temperature to 80 °C and then
click Save.
Preliminary Tuning
Before doing preliminary tuning, ensure that the MS has returned to Analysis
temperatures and the GC column flow rate is set to 1 mL/min.
Monitoring the System
1. After bakeout, monitor the following in the Diagnostics tab:
•Heated Zones: Operating Conditions should be close to current set
points.
•Vacuum System:
Pump Status -- Ready.
Turbo Speed--100%.
Turbo Current-- less than 300 mA.
2. Turn on the following trap elements.
•Multiplier.
•RF.
•Filament.
NOTE: This figure is of an MS with an ion gauge.
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Adjusting the RF Ramp
1. In the Adjustments tab in Manual Control, click Adjust RF Tuning.
2. Adjust the RF tuning rod to minimize the Highest value in the upper right
corner of the Counts area.
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CAL GASVENT CI GAS
RF ADJUSTMENT
3. Click Save Results when finished.
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Adjusting Cal Gas
To adjust the cal gas:
1. Open the MS door and ensure that the Cal Gas vial is full.
2. Click Adjust Cal Gas.
3. Adjust the Cal Gas needle valve behind the MS front door until the display
shows that the Cal Gas pressure is OK.
4. Click Save Results when finished.
NOTE: The Cal Gas adjustment varies with differences in auto tune settings,
filament emission current, system sensitivity, and system background levels.
Check this adjustment after auto tuning, editing the filament emission current, or
when system sensitivity, or background levels change.
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Auto Tuning
After performing the Adjust RF Tuning and Adjust Cal Gas, the instrument is
ready to be Auto Tuned.
Auto Tuning
To auto tune EI and CI:
1. Click Auto Tune.
2. Click the Method tab and select the following checkboxes:
•Air/Water Check.
•Electron Multiplier Tune.
•FC-43 Mass Calibration.
•Trap Function Calibration.
3. Click Start Auto Tune. The values generated are for both EI and CI.
4. Check the event message display, line by line, to review the results of each
auto tune function.
5. Investigate and resolve auto tune parameters that did not pass and rerun
them.
Run the following tunes once every two weeks for mass assignment:
•Adjust RF Tuning
•Mass Calibration
•Trap Function Calibration.
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Testing Specifications
Specification Table
210-MS
Ionization
Mode Test Sample Amount Measured m/z RMS S/N Specification Library Match (any search type)
EI PN 393065201
(1 pg/µL OFN, 5 pg/µL BZP)
1 pg OFN 272 ≥50:1 ≥500
220-MS
Ionization
Mode Test Sample Amount Measured m/z RMS S/N Specification Library Match (any search type)
EI PN 393065201
(1 pg/µL OFN, 5 pg/µL BZP)
1 pg OFN 272 ≥50:1 ≥500
CI PN 39065201
(1 pg/µL OFN, 5 pg/uL BZP)
5 pg BZP 183 ≥20:1 N/A
EI Methodology
NOTE: The MS comes with a CD containing factory test method and data files.
Use these method files to pass the installation sensitivity tests. At the factory, the
diluted OFN standard is injected using a pressure pulse and splitless injection
technique. Retain the Test Files CD for your records.
1. Ensure the MS temperatures are set as follows:
•Trap: 150 °C
•Manifold: 40 °C
•Transfer Line: 230 °C
2. Click Activate Method from the MS Workstation menu.
3. Open the OFN Method in the Service Folder.
The following shows System Control in a Ready state. System Control is
ready when both the GC and the MS are ready.
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Acquiring OFN
1. Use the Inject Single Sample option.
2. Use a lower air gap to avoid losing sample through the tip of the needle.
Ensure the syringe plunger is not forced out of the syringe barrel if using a
Pressure Pulse.
3. Strike the injector auto switch with the syringe barrel. This ensures that the
split valve has changed from open to close.
4. Make a 1 µL manual injection of OFN
Reviewing the Data
1. View a data file MS Data Review.
2. Enter 272 in the Ions: field of the MSDR window to display a single ion
chromatogram of the m/z 272 ion signal.
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3. Click-and-drag a zoom highlight box around the OFN m/z 272 ion.
.
4. Right-click the apex scan of the 272 single ion chromatogram to display the
Chromatogram menu.
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Calculating the Signal to Noise Ratio
1. Click Chromatogram Plot Preferences.
2. Click the Chromatogram Plot tab and do the following:
3. In the Plot area, select Filtered Data Only
4. In the Filtering area, select Smooth Data, type 5in the Point Smooth field,
select Savitsky Golay for the Smoothing Method, enable Remove Spikes
and type 4 for the Spike Threshold Factor.
5. Click OK to enable these selections.
6. Click the Noise tab, select RMS for the Noise Calculation, and click OK.
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