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Standard Operating Procedure - Chemistry Lab

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, discuss every instrument separately and bring to the attention of the ALO/LO any equipment requiring immediate attention.
  • Unpack new supplies and store in their correct location. Remember to mark on the bag/container the current Expedition number.
  • 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 as many of these as possible in port.
Lab orientation/Introduction

  • Give an orientation/safety procedures tour of the lab to the Chemists.
  • 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.
  • Have a meeting with the Chemists/Curator/EPM 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 cake splits).
  • Explain how to print sample labels.
  • Go over any and all MSDS sheets before working with any chemicals. Understand the risk 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 can become familiar with each instrument's operation.


Prepare reagents
Put dates on all reagents made.
Prepare the following reagents according to the recipes in the user guides:

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

Check gas bottles
Check the pressure of the oxygen (ChemLab), helium and argon bottles (Tween Pallet Stores). Ensure the bottles are above 200psi; otherwise, swap them out with fresh bottles.
Supplies
IAPSO - . Store it properly, as any evaporation will lead to increased salinity.
Necessary IW squeezing supplies:

  • 50mL plastic syringes (acid-washed).0.45µm Whatman disk filters.
  • Take four boxes of 9 cm #1 Whatman filters and soak them in a large beaker of DI water for ~2hours, then oven-dry at a low temperature (~50oC). When they are dry, store them in Ziploc bags near the Carver presses. Youmay need to do this again during the Expedition.
  • Obtain necessarycontainers for IW sample splits. At the Scientist's request they may need to be rinsed with DI water/acid washed and dried..
  • Bags for squeeze cake splits and baked aluminum foil (if required.Bake at 500 C for 8 hours).

Clean spatulas and trays.Necessary catwalk sampling/sample processing supplies:

  • Headspace sampling tools and containers (vials, septa, crimper).
  • Gas void assemblies (50mL syringe and three-way stopcock, with male luer lock, attached to the core liner puncturing tool).


General lab supplies:

  • Paper towels
  • Kimwipes
  • Pipette tips
  • P-boxes (for sample storage; foam ampule holders for glass vial storage)
  • Gloves, various sizes
  • Boxes for cryovials


Prepare Squeezers for IW
Assemble the titanium squeezers. Clean each piece with tap water, rinse with DI water, blow off as much water as you can, with the air-line, and dry with Kimwipes. The correct assemblage is on a diagram near the sink. These must be completely dry.
Prepare Acid Baths
Fill the 20L Nalgene tub with 18L DI water. Place the tub in the fume hood nearest the Nanopure system and slowly add 2L concentrated HCl. This will be used to clean labware.
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 pump is located inside, behind the front stainless panel.
LIMS Interface User Registration
Register the Chemists with a LIMS login; ask an onboard programmer for assistance. Clear out the CHNS loader before analyzing the first samples, using 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 is used for gas monitoring for shipboard safety, while the NGA serves as both a backup to the GC3 and to analyze higher chain hydrocarbons and some elemental gases.
Check standards injection on the GC to see if the instrument is still calibrated. If a couple of injections give poor results, start the calibration process. It takes 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.

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

CATWALK SAMPLING PROCEDURE
Interstitial Water (IW)

  • Obtain the IW sampling interval from the Chemists 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.
  • Take the IW sample from the bottom of the same section every time, if possible. 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 great than 100 mbsf, take one IW every third core.
  • 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.


Gas Headspace

  • 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 taken at a prior depth but just continue after the prior hole's bottom depth.
  • For cores with IW samples, take the headspace sample 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 logsheet. 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 seen in the core samples) every fifty injections or so, to check on the instrument calibration.


Voids/Vacutainer

  • If gas voids are present in the core liner, take a sample using the syringe vacutainer and directly inject into the GC (GC3 or NGA).
  • Circle the hole in the liner; after the Curator/Technicians have measured off sections. 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.


SQUEEZING IW'S
Sample preparation
After assembling the squeezer, prepare the IW sample by:

  • 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 a Carver press, and trash the residual scrapings (unless requested by a Scientist).


Squeezing the sample

  • Set the pressure gauge around 3000psi 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 pressure in sets of 2000lb. Do not ever increase the pressure above 30,000lbs.
  • Select the correct core, section, and sample, and 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 by pressing the red OPEN button and remove the syringe from the squeezer.
  • Start sample distribution (splits).


Water Distribution

  • 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, stored, or 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 – 2 mL must be acidified with trace metal-grade nitric acid (~ 30 µL).
  • Remove the plunger from the syringe, rinse with RO water, and place in the acid bath for twelve hours. Rinse the pieces with DI water, bake dry at a low temperature then reassemble and store the syringes in plastic bags.


Extracting the squeezecake

  • Remove the base and base plate; place the remaining squeezer assembly onto the white arched platform, and then onto the manual (left-most) Carver press.
  • 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 only.
  • Be sure to flush DI water through the base and base plate, and blow-dry both. Wipe all bits with Kimwipes.
  • Ensure the squeezers are COMPLETELY dry before using. Make sure that the bits of each squeezer remains in the same set.


ROUTINE ANALYSIS
The following is a list of the typical 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 Technician's responsibility. If a system doesn't 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.
Remember to log ALL changes to equipment, methodology, general points, anything of interest, in the blue log books. Please be thorough. We all count on it.
GC3 / NGA
All headspace gas samples will be run on GC3 (C1-C3). Gas void samples or samples containing higher hydrocarbons will be run on the NGA.
Titrations
The ph/alkalinity measures are routinely done (in real-time) by the Scientists with the Technician setting up the instruments. Chlorinity titrations are up to the Scientists as to if they want them done because chloride concentrations are measured on the IC.
IC
To determine anion and cation elemental concentrations. Wait until you have collected enough samples for a batch (ie. end of a hole). The Scientists can assist in preparing the samples but the Technician will set-up and run the instrument.
SPEC
Ammonium and phosphate are routinely measured. It's a good idea to wait until you have enough samples for an entire batch (ie. end of a hole), as it is a time-consuming process.
ICP-AES
The ICP-AES system will measure specific minor and major element concentrations of porewater, sediment (need approval) and hard rock. Wait until you have collected enough samples to run an entire batch (ie. end of a hole). Argon is limited, and the machine requires a significant amount of prep time. The Scientists can help prepare the samples but the 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 will decide on where they want to take the sample for the carbonate/EA analyses. It can be taken from the IW squeezecake 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 system.
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 sequences. The combustion column needs to be replaced 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.

V. DURING EXPEDITION

  • Make new acid baths at least twice an Expedition and whenever going from flux to IW ICP analyses, make a new nitric acid bath.

Inventory

  • This job necessitates proper inventorying techniques. To properly inventory, locate the desired supply, physically remove 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 bath, rinse it three times with DI 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 acid bath.
  • Check daily the manifold pressures of the helium and argon racks.
  • 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 the safety shower and eye washes stations.
  • Many filters/traps need to be changed on about a weekly basis (check them frequently):
  • Drierite : IC, titrators, SRA
  • CHNS (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.

VI. END-OF-EXPEDITION ACTIVITIES

  • 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, weight, serial number, model number, vendor's name and country of manufacture.
  • Pack up all samples as per Scientist'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 any instrument-specific items.
  • Have the lab coats laundered (segregated and tumble dried).
  • Immaculately clean the lab (this means everything).
  • Check expiration dates on chemicals, notify ALO/LO if hazardous chemicals/waste need to be disposed in port.

VII. PORT CALL – Off Going

  • See General JRSO Shipboard Technical Staff SOP
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