Standard Operating Procedure - Chemistry Lab
February 2018
I. PRE-EXPEDITION
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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
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.
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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.
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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.
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- 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