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University of California
Stable Isotope Laboratory
Earth and Planetary Sciences
1156 High Street Santa Cruz, CA 95064

Lab: (831) 459-5751
Office: (831) 459-5857
Fax: (831) 459-3074

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Optima/Prism Run Procedures


The primary safety concern in operating the Prism are two-fold:
1) Exposure to liquid nitrogen (LN2) while dispensing. Liquid nitrogen can cause severe freezer burns. Please use closed toed shoes, and personal protective equipment (PPE) when handling liquid nitrogen (cryo-gloves, and face mask). Furthermore, liquid nitrogen boil-off while dispensing from large 230 liter dewars can displace O2 and lead to dizziness and loss of conciousness. Immediately more away from the liquid nitrogen tank if you notice dizziness while dispensing LN2.
2) Exposure to hot phosphoric acid. Phosphoric acid can cause severe burns, particularly when hot. Use appropriate PPE.


Points 1 to 3 should be done by the previous user - this is particularly important at weekends so that the water in the hot water bath does not evaporate.

1) Check that the previous run has really finished, and not stalled1.
2) Turn off the water bath2.
3) Turn off the cryocooler- this should be left for at least 15 minutes before removing probe and sponges.
4) Fill the trap above the Autocarb rotary pump with LN2 using a funnel.
5) C1, C2, and C3 should be closed; make sure.
6) Open C4
7) Shut the black knob (upwards) to the autcarb rotary pump.
8) Open the carousel and acid bath to atmosphere (black Nupro toggle)*
9) Remove the large stainless steel dewar from the water trap
10) Remove the reaction vessel: remove the clip, lower the magnetic stirrer, and gently detach the reaction vessel from its connection.
11) Unhook the closest water hose and hold; whilst tilting the reaction vessel away from you, allow the water to drain down the other hose.
12) Unhook the other hose, cleaning any water spillage.
13) Connect the two hoses, and seal the reaction vessel connection point with the glass cap and clip.
14) Once the cryocooler probe and sponge have defrosted3, remove the alcohol trap and allow the probe to drain off exess alcohol.
15) Close the autocarb to atmosphere, and open the carousel to the high conductance vacuum line (black knob downwards). Check the Autocarb vacuum on the computer.
16) Take the acid bath reaction vessel next door and clean it and the boats using the instructions above the sink.
17) Reset the carousel.
For the Optima: Click on the carousel icon, move box to far left (zero), then advance the carousel to position "9".
For the Prism: Go to "Prep", and "reset carousel".
Check that the carousel is advanced slightly past, and not directly above the "O" port.
18) Fill the water bath with DI water to ca. 1 cm from the top4.
19) Remove the previous runs data sheets from the printer using line/form feed, write down the date, user name, instrument name and store.
20) When the Autocarb Pirani gauge has reached 1E-3, place a spare stainless steel dewar filled with hot tap water on the water trap. Top off the water trap above the Autocarb pump with LN2.
21) Open C3, observing the pressure increase on the autocarb Pirani gauge.
22) During this interval weigh out standards, and note down order of samples/standards5.
23) Close C3 and, once cool, remove the heater tape.

1 The run program should be DI233, do not use DI247. Following the completion of a run, the message window should say, "autorun finished" in green. If the program/computer has crashed, or the program has stalled for some reason (e.g., for being out of LN2 or printer paper), check with the previous analyzer/P.I. to discuss whether or not to continue the previous run.
2 If the temperature is <90°C, notify previous analyzer.
* black Nupro toggle valves are closed, when the toggle is parallel with the pipe work, and open when standing up. Make sure the axle is correctly inserted, otherwise the valve will not open/close.
3 Don't try to remove if still frozen, otherwise the pipe may crack.
4 Don't use tap water!!!!
5 Use Carrera Marble standard, unless there is a need for recalibration. For the prism, two grains is sufficient for a small analysis, for the Optima, five grains or less is normally too small. For a full sample run, the first five, the middle three and the last three are generally standards. Standards and samples can be separated by an empty boat, if desired.


1) Check that C2 and C3 are closed
2) Put the alcohol1 trap up, insert the probe, surround with foam and insert thermometer.
3) Turn on Cryocooler
4) While there is no gas in the inlet, note the Ion Gauge reading. (Just after run finishes. Both valves closed.)
5) Get samples and standards ready.
6) Close the autocarb carousel from the rotary pump, undo the carousel bolts , and open to atmosphere with the nearest black Nupro toggle valve.
7) Open the carousel carefully. Use a kimwipe to remove lint from all parts of the carousel. If the carousel disc has been contaminated with acid, boil for a minute in DI water, and wipe the rest of the carousel with a damp kimwipe.
8) Load samples/standards
9) Replace the top of the carousel, making sure the screws are equally positioned2.
10) Make sure the water bath is full.
11) Put a PTFE coated magnet in the reaction vessel: small magnets fro forams, medium for carbonate powders, large for apatite powders.
12) Pour green phosphoric acid so that it just covers the magnet (>10ml)3.
13) Unclamp and remove the glass cap underneath the carousel. Clean the black o-ring with a dry kimwipe.
14) Place reaction vessel on top of the magnetic stirrer, and then replace the clip, making sure that the vessel is not tilted. Move the stirrer up.
15) Unfasten the water hoses from each other, and clamp those on the reaction vessel.
16) Turn on the water bath4. Make sure the hoses do not leak.
17) Isolate the carousel from atmosphere (black Nupro toggle valve), and open the other toggle to the rotary pumps via the capillary (not the direct route5. see (19).
18) Go to "Prep" and turn on the magnetic stirrer. Make sure it is at top speed (dial underneath).
19) Keep checking the autocarb Pirani gauge. Wait ten minutes after it has reached 1E-3, then shut from the capillary route to the rotary, and open the direct route (knob down).
20) While waiting for the carousel, fill in the log. Go to "Analysis", "Batch Edit", load "Isocarb", and go to "Setup". "Release All" to overwrite. Close and open window to make sure that the data has been saved correctly.
21) Make sure the parameters are set correctly ("Analysis", "Edit Parameter Files"). For seconds for apatites (Optima only). For reference gas parameters see the table below.
22) Load reference gas6 (Under "Prep"). Follow the directions that appear on the screen.
23) Check the alcohol trap temperature. It needs to be < -85°C
24) Similarly the water bath should be at 90°C and the acid should be stirred and pumped while hot for at least 1 hour before starting the analysis.
25) Fill and hook up the large LN2 dewar.
26) Once the reference gas is loaded, go to "Scans" and load CO2. Check that the peak is flat and drag the centering line to the center of the flat part of the peak. Fill in the acceleration voltage on the sheet, and note the minimum beam size (Major m/z = 44 beam).
27) To start the run, go to "Analysis" and "Autorun start/stop". Once you get the green colored message "Autorun initialized", close the carousel section from the pump (black knob upwards).

1 100% ethanol. Add LN2 if necessary (in fume cupboard if possible, away from ovens/flames) so that the mixture is around -50°C, since cryocool takes a long time to cool the trap.
2 Don't overtighten.
3 Make sure that acid does not come in contact with the mouth of the reaction vessel; if it does, use a dry kimwipe to clean thoroughly.
4 This takes 40 minutes to reach 90.2°C from cold.
5 Otherwise the carousel is showered with powdered samples.
6 The Refgas sequences for the Optima and Prism are different, so make sure you follow the instructions carefully.

When the run finishes:

1) Check that the run has really finished, and not stalled.
2) Turn off the water bath.
3) Turn off the cryocool.

Aborting a run:

Problems during the run may require stopping the run. To do this, follow these software steps:

1) Select Analysis: AutoRun Start/Stop (or use keystrokes Cntl-A).
2) Select Program: Terminate.
3) Select Prep: Coldfingers Stop.

Aborting a run generally results in the loss of two consecutive samples.

Typical Problems that may arise during a run:

Liquid Nitrogen errors:
a) There is ice in the hosing (common). Remove line and warm up then reinsert.
b) The LN2 tubing has become disconnected/split at the cold finger (common). Reposition hose on cold finger feed and retighten hose clamp.
c) The thermocouple has fallen from the bottom of the cold finger or is broken (occasional). Reposition thermocouple.
d) The LN2 pump isn't operating (very unlikely).
e) There is something wrong with the SPIBB card in the System Controller (very unlikely).

Computer crashes. This often happens when sending data to disk or to the printer during a run. Closedown the computer and printer, and reboot. This usually solves the problem. Prior to restartng an aborted the run, check that the software "Autrorun Sequence" port (and sample ID) is the same as the carousel port position. You may need to "Release" or "Delete" a line in the "Autorun Sequence".

To check the printing is back to normal you can do this test. Do a DAPC run with the changeover valve disabled - don't forget to enable the changeover valve afterwards. Load reference gas sequence fails. Too little gas: can reflect a number of problems. Try these remedies:
1) Try peak centering.
2) Check that the correct tuning file is loaded. Perhaps previously someone ran a background scan without reloading the proper tuning file.
3) Note the machine Ion Gauge pressure. Is it higher than the basline (Dual Inlet closed) pressure when the reference inlet is open to the mass spectrometer? If so, this indicates there is gas entering into the machine.
4) Is the source on? Check that the red and green LED's on the souce and high voltage electronic units on the mass spectrometer are illuminated.
If the sequence crashes, but there is enough reference gas for the run, then just terminate the sequence.

"Too many bad samples" error. Either there is no (little) carbonate in your samples, or CO2 isn't generated for one of the following reasons:
1) The hot water bath is no longer hot - either because it is off or there is a water leak. Check hoses!
2) The carousel isn't working properly - the offset wasn't set, or acid has got into the carousel and the steal boats are sticking to it.
3) The stirrer wasn't switched on, or the motor has died.
4) The source is OFF.

Reference gas settings (in parameter files):
Optima - always 2.2 E-9 A (m/z = 44).
Prism - 2.0E-9 A (m/z = 44) for single forams or other very small samples, 2.3E-9 A for all others.