Page History

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.

III. Site preparation / Prior to arrival on site and core-on-deck

On cruises with short transit times, perform, in port, as many of these the following as possible.:

Lab orientation/Introduction

• • Give an orientation/Provide safety procedures tour of the lab to the Chemists.to all scientists working in the Chemistry/MBIO area. Ensure scientists understand all safety concerns and that they sign the required documents.
  • Provide training to all chemistry scientists on instrument operation, sample preparation and data upload/download procedures.
  • Meet with chemistry scientists and find out their general goals and specific requests. If there are microbiologists Meet with Chemists and find out their general goals and specific requests. If there are 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 on 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.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, 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 panelpanel. Check vacuum pump oil level.

LIMS Interface User Registration

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's Guide., 70% and 90%. 

Titrators
See the User 's 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

IAPSO to adjust the scale to the correct salinity (35.0).

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 Chemists 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. For example, for 0 – 100 mbsf, take one IW per core and > 100 mbsf, take one IW every third core
    • A typical IW sampling plan is one IW per 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 the a GC (GC3 NGA1 or NGANGA2).
    • Circle the hole in the liner; after the Curator/Technicians have measured off sectionscore liner. Note the core , and section and interval of the sample and write it on the Curator's logsheet. The interval will need to will change after curation is done on catwalk and it will be entered into SampleMaster by the Curator/ALO.

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• • • Removing the sample from its core liner.
    • Trimming the outer surface of the core (sides, top and bottom) of any drilling contamination (until the consistency seems less saturated; if "biscuits" are present, make sure you trim all surfaces of the "biscuits"); maintain proper spatula orientation (contaminated side is always out, sediment side is always in).
    • Put the trimmed sample into a squeezer, then the Teflon disc, rubber disc , and piston.
    • Place the assembled squeezer onto in a Carver press, and trash bag the residual scrapings (unless requested by a Scientist), IWSCRAPES.

Squeezing the sample

• • • Set the pressure gauge around to 3000 lbf 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 lbf lbs until 10000 lbs; after 10000 lbflbs, increase in steps of 2000. Do not ever increase the pressure above 30,000lbs30000 lbs.
    • Select the correct core, section , and sample , and upload 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 ml; must be acidified with trace metal-grade nitric acid (~ 30 10 µL).
    • Remove the plunger from the syringe, rinse with RO DI water , and place in the acid HCl bath for twelve hours. Rinse the pieces components with DI water , and bake dry at a low temperature then . When completely dry, reassemble syringes and store the syringes them in plastic ziploc bags.

Extracting the squeezecake

• • • Remove the base and the base plate; place the remaining squeezer assembly onto the white arched platform, and then wood-framed squeezecake extracting platform onto the manual (left-most) Carver press.Carver press. Place the remaining squeezer assembly onto the platform. 
    • Close the release valve on the bottom of the press (turn valve Turn the small 'valve' to the right, ) and begin manually pumping the Carver press until the squeezecake, Teflon disc, rubber disc , and piston are pushed out the bottom of the collar.
    • Split the squeezecake as per the sampling plan, bag , and label the sample(s).

Cleaning

• • • The squeezer's pieces should be scrubbed and rinsed with water onlyScrub and rinse the squeezer components.
    • Be sure to flush DI water through the base and the base plate, and blow. Blow-dry both. Wipe all bits components with Kimwipes.
    • Ensure the squeezers are COMPLETELY dry before usingreassembling. Make sure that the bits components of each squeezer remains remain in the same set.

Routine analyses

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 done on the ship. 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 doesn't 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 phpH/alkalinity measures measurements are routinely done performed (in real-time) by the Scientists scientists with the Technician setting having set up the instrumentsinstrument. Chlorinity titrations are up to the Scientists scientists as to if 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.

SPEC

Ammonium and phosphate are routinely measured. It 's 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.

ICP 

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.

Coulometer

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 on 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 will set-up the systemtechnician 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.

SRA

The SRA is not routinely used but is part of our safety monitoring protocol. You must know how it operates and make sure that it is ready if needed.

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• • This job necessitates proper inventorying techniques. To properly inventory, locate the desired supply, physically remove inventory technique. After you have located the desired item and physically removed it from its store, go to the AMS inventory checkout sheet , and locate said part (by description or part number). To the right of its information are several blank lines; at the corresponding line, write the number checked out (note the unit: each, box, foot, etc) on the line , and circle the number.
  • Verify a physical count of all essential parts (without these the lab cannot operate). Notify the ALOs/LO if the counts are off.
  • Familiarize yourself with the storeroom inventory check-in, /check-out system.

Lab Maintenance

• 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 washes 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.

V. End-of-Expedition activities

• 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 Scientistscientists' s 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 generator's 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

• See General JRSO Shipboard Technical Staff SOP