v.378P
September 2018
I. Pre-Expedition
- See General JRSO Shipboard Technical Staff SOP
II. Port-call / Start of an Expedition
- Do a thorough cross-over with off-going Chemistry Technicians: read Tech Report in advance, discuss each instrument separately and bring to the attention of the ALO/LO any equipment requiring immediate attention (ie. repairrepairs, spare parts etc).
- Unpack new supplies and store in their correct location. Remember to mark on the bag/container the current Expedition number.
- Do a physical count of critical items.
- Conduct an inventory of chemicals in the storage cabinets. Look for any chemicals not on our inventory, unmarked containers , or reagents or mixtures left over from the previous expedition. Bring any issues to the attention of the LO.
- You should calibrate as many instruments as you can. Instructions are in the instrument-specific User Guides.
- Make as many reagents as you can.
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On cruises with short transit times, perform, in port, as many of these the following as possible.:
Lab orientation/Introduction
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- Provide safety tour to all scientists working in the Chemistry/MBIO area. Ensure scientists understand all safety concerns and that they sign the required documents.Give an orientation/safety procedures tour of the lab to the Chemists
- Provide training to all chemistry scientists on instrument operation, sample preparation and data upload/download procedures.
- Meet with Chemists chemistry scientists and find out their general goals and specific requests. If there are Microbiologists microbiologists sailing, make sure that these same protocols are done with them.
- Divide up responsibilities among the Chemists for all shipboard analyses. Follow up during coring operations to make sure all analyses are done and done correctly
- Have a meeting with the Chemists/Curator/SAC (Sample Allocation Committee) to go through sample plans.
- Prepare sampling equipment and sample storage containers. Wash any necessary containers and prepare spikes if needed.
- Prepare SampleMaster split template (water and squeeze cake splits).
- Show how to print sample labels.
- Go over all MSDS SDS sheets before working with any chemicals. Understand the risk risks of handling chemicals, especially if any hazardous chemicals will be used.
- Print out the most recent copy of each instrument's User Guide so the Scientists scientists can become familiar with each instrument's operation.
Prepare reagents
Prepare the following reagents according to the recipes in the user guides. Remember to put dates your initials and the date on all reagents made.
- Alkalinity/pH/chloride titrations
- Alkalinity/pH/chloride titrations
- Coulometer
- IC
- ICP
- SPEC
- Alkalinity: Prepare 20 mM and 40 mM standards if necessary
- Chlorinity: Prepare 2 liters of dilution solution
- Coulometer
- HCl solution, KOH and AgNO3 solutions if needed
- IC
- all solutions except for anion eluent, which should be made shortly before analysis
- pourable calibration standards
- ICP
- 2% and 3% TM nitric acid solutions, also 10% if analyzing hard rock
- internal standard(s)
- primary in-house cocktail
- pourable in-house and IAPSO calibration standards
- SPEC
- Ammonium
- Ammonium standard (dry ammonium chloride in oven overnight) + calibration standards
- alkaline solution
- Phosphate
- Phosphate primary standard (dry monobasic potassium phosphate in oven overnight) + calibration standards
- Sulfuric acid solution
- Antimony potassium tartrate solution
- Ammonium molybdate solution
- Ammonium
Check gas bottles
Check the pressure of the oxygen (ChemLabchem lab), helium and argon bottles (Tween Pallet Stores). Ensure the bottles are above 200 psi; otherwise, swap them out with fresh bottles. When a Pallet Stores bottle array is empty, tear the yellow tags to EMPTY, disconnect the manifold and connect it to full bottles (see how to do this). It is good practice to always have a full gas bottle array ready to go.
Supplies
IAPSO - Store Store it properly (in the fridge with the cap wrapped in parafilm), as any evaporation will lead to increased salinity.
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- Headspace sampling tools and containers (vials, septa, crimper)., headspace tool, plunger, crimper). The septum has a shiny thin creamy color PTFE layer and a thick white matte silicone layer. The shiny PTFE side goes against the vial.
- Gas void assemblies (50 mL syringe and three-way stopcock, with male luer lock, attached to the core liner puncturing tool).
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Fill the 20 L Nalgene tub with 18 L DI water. Place the tub in the fume hood nearest the Nanopure system and slowly add 2 L concentrated HCl. This will be used to clean labware (glass and plastic. NO metal).
Fill one of the small tubs with 10% nitric (reagent) to clean ICP vials/bottles and fill the other small tub with 10% nitric (trace metal) for the cleaning of XRAY crucibles only.
Freeze Dryer
Make sure that the freeze dryer is operating. The vacuum pump is located inside, behind the front stainless panel. Check vacuum pump oil level.
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Register the Chemists with a LIMS login; ask an onboard programmer for assistance. Clear out the CHNS Worklist Generator.
Make sure that each station using a LIMS application, MUT or SampleMaster, is logged into the correct project (Expedition number).
Calibrate instruments
GC3/NGA
The GC3 NGA1 and NGA2
NGA2 is used for gas monitoring for shipboard safety, while the NGA . The NGA1 serves as both a backup to the GC3 and and as an additional instrument to analyze higher chain hydrocarbons and some elemental gases.
Check standards injection on the GC Inject a few check standards to see if the instrument is instruments are still calibrated. If a couple of the injections give poor results, start the calibration process. It takes does take a while.
Calibration is done by injecting standards of increasing concentrations into the GC and using HP ChemStation to acquire the data. Usually, we use nine standards: A, B, C, D, 10%, 30%, 50%, 70% and 90%. Each instrument's calibration description is in its respective User Guide., 50%, 70% and 90%.
Titrators
See the User Guide for instructions on how to calibrate the autotitrators (Alkalinity/pH and chloride).
Salinity
For the refractometer, use IAPSO to adjust the scale to the correct salinity (35.0).
IV. During coring operations
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IV. During coring operations
Catwalk sampling procedure
Participate in "Core on Deck" duty as much as you can. If you need chemists to help you on the catwalk, make sure to train them how to take samples (IW/HS) properly.Catwalk sampling procedure
Interstitial Water (IW)
- Obtain the IW sampling interval from the Curator and take the sample(s) when the core comes on deck.
- If possible, have the geochemist on the catwalk assist you in determining where to take the IW sample. Never take a sample that includes a change in lithology.
- Initially, 5 cm whole rounds are taken; as the water yield decreases, go to 10 cm whole rounds. Larger whole rounds may be taken after speaking to the SAC (Curator, EPM, and co-chiefs).
- If possible, take the IW sample from the bottom of the same section every time. As recovery decreases you will have to take the IW sample from wherever you can.
- A typical IW sampling plan is for 0 – 100 mbsf, take one IW per core and > 100 mbsf, take one IW every third core. Check with the Curator on the current plan.
- Note the core, section and interval of the sample and write it on the Curator's logsheet. The interval will need to be entered into SampleMaster by the Curator/ALO.
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- Take a 5 cc headspace sample from every sediment core (non-basement), at the top of a section (try to be consistent). This sample is taken until the total depth objective is met. If doing multiple holes, you do not have to repeat the sampling if the sample is a headspace sample has already been taken at a prior that depth but just continue after the prior hole's bottom depth.
- For cores with IW samples, always take the headspace sample adjacent to IW, best from the top of the section immediately below the IW sample. Note the core, section and interval of the headspace sample and write it on the Curator's logsheetheadspace vial. The interval will need to be entered into SampleMaster by the Curator/ALO.
- Make sure nobody sprays acetone on the catwalk before sampling is completed. Acetone will contaminate the sample.
- It is recommended to occasionally take a sample of the air on the core deck, so that any change in the headspace sample analysis can be correlated to changes in volatilized acetone.
- Inject a standard (corresponding to a similar concentration concentrations seen in the core samplesrecent cores) every fifty injections or so, to check on the instrument calibration.
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- If gas voids are present in the core liner, take a sample using the syringe vacutainer and directly inject into a GC (GC3 NGA1 or NGANGA2).
- Circle the hole in the core liner. Note the core , and section and interval of the sample and write it on the Curator's logsheet. The interval will need to change after curation is done on catwalk and it will be entered into SampleMaster by the Curator/ALO.
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- Set the pressure to 3000 lbs and simultaneously push and hold both green (CLOSE) buttons on the hydraulic unit's base until the auto-pressure engages.
- After the first drops flow from the hole in the squeezer's base plate, insert the syringe into the hole. Keep an eye on the syringe to make sure the pressure doesn't push out the syringe or plunger (especially for the first few cores). Keep incrementing the pump hydraulic unit pressure in steps of 1000 lbs until 10000 lbs; after 10000 lbs, increase in steps of 2000. Do not ever increase the pressure above 30000 lbs.
- Select the correct core, section and sample in SampleMaster. Upload the IW sample splits (using the Excel template) into SampleMaster and distribute the labels.
- When porewater yield is sufficient/no more water is trickling, release the pump hydraulic unit pressure by pressing the red OPEN button and remove the syringe from the squeezer.
- Start sample distribution (splits).
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- Alkalinity/pH - If there is ample water, allocate 5 mL for shipboard analyses (alkalinity, salinity, IC, SPEC). Speak with the Scientists scientists about which analyses they would , or wouldn't like performed (ie. Make a priority list). Extra water may be used for repeat analysis or stored (sent back to the repository).
- Scientific party - split and store the remaining water into the requested aliquots as outlined by the sampling plan. Each sample's storage/preservation is up to its requestor.
- ICP – 1 - 2 ml; must be acidified with trace metal-grade nitric acid (~ 30 10 µL).
- Remove the plunger from the syringe, rinse with DI water and place in the HCl bath for twelve hours. Rinse the components with DI water and bake dry at a low temperature. When completely dry, reassemble syringes and store them in ziploc bags.
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- Remove the base and the base plate; place the white wood-framed squeezecake extracting platform onto the manual (left-most) Carver press. Place the remaining squeezer assembly onto the platform.
- Close the release valve on the bottom of the press (turn valve to the right) and begin manually pumping the Carver press until the squeezecake, Teflon disc, rubber disc and piston are pushed out.
- Split the squeezecake as per the sampling plan, bag and label the sample(s).
Cleaning
- The Scrub and rinse the squeezer components should be scrubbed and rinsed.
- Be sure to flush DI water through the base and the base plate. Blow-dry both. Wipe all components with Kimwipes.
- Ensure the squeezers are COMPLETELY dry before reassembling. Make sure that the components of each squeezer remain in the same set.
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Remember to log ALL changes to equipment, methodology, general points, anything of interest in the blue log booksChem Lab Notebook on Confluence. Please be thorough. We all count on it.
The following is a list of the typical shipboard analyses. It is a good idea to discuss with the Scientists at the beginning of the Expedition who will be responsible for which analyses. Data entry/integrity is the Techniciantechnician's responsibility. If a system does not automatically upload results to LIMS (salinity, SPEC), you are going to have to use the Spreadsheet Uploader tool. See the User Guide or ask an Application Developer. The IC upload process is also not automated. The instructions to upload these results are in the IC User Guide.
GC3 / NGA
NGAs
All headspace gas samples will be run on GC3 NGA2 (C1-C3). Gas void samples or samples containing higher hydrocarbons will be run either on the NGANGA2 or NGA1.
Titrations
The pH/alkalinity measurements are routinely performed (in real-time) by the Scientists scientists with the Technician having set up the instrument. Chlorinity titrations are up to the Scientists scientists as to whether they want them done because chloride concentrations are also measured on the IC.
IC
To determine anion and cation elemental concentrations. Wait until you have collected enough samples for a batch (iei.e. end of a hole). The Scientists scientists can assist in preparing the samples but the Technician technician will set up and run the instrument.
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Ammonium and phosphate are routinely measured. It is a good idea to wait until you have enough samples for an entire batch (iei.e. end of a hole), as it is a time-consuming process.
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The ICP-OES system will measure specific minor and major element concentrations of porewater, sediment (need approval necessary) and hard rock. Wait until you have collected enough samples to run an entire batch (iei.e. end of a hole). Argon is limited, and the machine requires a significant amount of prep time is significant. The Scientists scientists can help prepare the samples but the Technician technician will set up and run the instrument.
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Crushing, weighing and running carbonate samples require a significant portion of time. During the initial discussion of the sampling protocol the Scientists scientists will decide where they want to take the sample(s) for the carbonate/EA analyses. It can be taken from the IW squeezecake and/or at the sample table after the core is split. Either way, these samples will have to be freeze-dried (typically for twelve hours) and then crushed/homogenized using a mortar and pestle. Usually the Scientists will prepare and run the analyses, and the Technicians mortar and pestle. Usually the technician will set up the system and both scientists and technicians will weigh and run the analysis.
CHNS
Again, weighing and running the samples on this instrument is time-intensive and it be best to have a good sized batch ready before running. Usually the Scientists technician will weigh out the samples and the Technician will set up the instrument and sequences. The combustion column needs to be replaced set up the system and both scientists and technicians will weigh and run the analysis. Replace the combustion column after approximately 100 samples.
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- Once a shift, clean glassware. If glassware/plastic is in the acid bath, rinse it three times with DI water and let dry. Rinse dirty glassware/plastic three times with RO water and place in bath for twelve hours. Do not put metal objects in an acid bath.
- Make new acid baths at least twice an Expedition when they get dirty and whenever going from flux to IW ICP analyses, make a new nitric acid bath.
- Check daily the manifold pressures of the helium and argon racks daily.
- Ensure that the active hydrogen generator's water reservoir is full of DI water. Do not let these run empty. Occasionally check the desiccant.
- Coulometer Cathode/Anode solutions: these solutions need changing every 2-3 days or 200 runs. Along with the solutions, you will want to change out the pre- and post-scrubber solutions. Any precipitate in the lines should be removed as well. The solutions will also need to be changed if a 100% CaCO3 standard check does not come within 100 ± 2%.
- Weekly check test the safety shower and eye wash stations.
- Many filters/traps need to be changed on about a weekly basis (check them frequently):
- IC, titrators, SRA - drierite
- EA - (magnesium perchlorate) if hydrogen not being measured.
- The nanopure pre-filters and Barnstead filters need to be changed when an indicator light on the unit comes on. See the manual for how to change these. The nanopure final filters should be changed about every four months.
- Check the freeze-dryer daily for any ice build-up and defrost as necessary.
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- Write the End-of-Expedition lab report and send a copy, via e-mail, to the on-coming Technicianstechnicians.
- Make sure all data is sent to LIMS and all raw data files are copied to the Data1 volume.
- Pack up equipment being returned for repairs and give the ALO the following information: IODP inventory number, value, serial number, model number, vendor's name and country of manufacture.
- Pack up all samples as per Scientistsscientists' requests; work with the Curator/ALOs.
- Give the LO a list for port purchases, if any.
- Clean the lab and assigned area following the cleaning instruction according to LO's list. Bring all the trash to the incinerator. Glass and sharps get disposed of in port call.
- Fill the Carver presses with oil (if necessary).
- Check the oil in the freeze dryer's vacuum pump.
- Defrost and clean the freeze dryer.
- Clean (defrost if necessary) the fridges; dispose of old reagents.Change the hydrogen generators' DI bags and vacuum the back vent filters.
- Check the ovens for debris. Clean them.
- Clean any instrument-specific items.
- Have the lab coats laundered (segregated and tumble dried).
- Check expiration dates on chemicals, notify ALO/LO if there are hazardous chemicals/waste need to be disposed of in port.
- Confirm that both helium and argon have a new full rack of gas bottle connected and ready to go.
VI. Port call – Off Going
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