Page History

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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 (repairs, 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

• • Provide training to all Chemistry scientists on instrument operation, sample preparation and data upload/download procedures.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 operation 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 SDS sheets before working with any chemicals. Understand the 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 your initials and the date on all reagents made.

• • Alkalinity/pH/chloride titrations
    • 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
• IC
• ICP
SPEC

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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Catwalk sampling/sample processing supplies:

• • Headspace sampling tools and containers (vials, septa, crimper).and containers (vials, septa, 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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• • • Obtain the IW sampling interval from the Curator and take the sample(s) when the core comes on deck.
    • If possible, have the geochemist 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 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 a headspace sample has already been taken at 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 concentrations seen in the recent cores) every fifty injections or so, to check on the instrument calibration.

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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 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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Crushing, weighing and running carbonate samples require a significant portion of time. During the initial discussion of the sampling protocol the 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 using a 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 will weigh out the samples and the technician will set up the instrument and sequencessystem and both scientists and technicians will weigh and run the analysis. Replace the combustion column after approximately 100 samples.

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• Write the End-of-Expedition lab report and send a copy, via e-mail, to the on-coming technicians.
• 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 scientists' 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.
• 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.
• 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 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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