Rock preparation


This document describes how to prepare rock samples that are unprocessed, from the field, into powderized material ready for isotope analysis. While we have maintained a rock preparation protocol written and updated by many folks over the years, Eva Stüeken wrote this particular protocol summer 2015. It is divided into five sections: cutting rocks with rock saw, pre-crushing rocks into chips, cleaning rock chips, pulverizing rock chips, and decarbonating powders for CNS analysis. Retain some native powder if you wish to measure carbonate isotopes.


This entire protocol involves sharps, projectiles, airborne dust, and corrosives. Each section below specifies appropriate personal protective equipment. 

Cutting Rocks with the Rock Saw

Rocks need to be cut to remove weathering surfaces, to cut thin sections, and to select portions for pulverizing. Wear an apron, goggles and ear protection.

Preparing the rock saw:

  1. ESS has three rock saws. For most purposes, the smallest one (of the two bench-top ones, the one that’s closer to the door) will suffice.
    • Small rock saw: To turn in on, push the pedal on the floor. When cutting rocks, cooling water is necessary to avoid overheating. The cooling water comes from a tap on the all. Just turn it slightly to start a slow water flow.
    • Intermediate rock saw: The start button is on the side of the saw box, i.e. it spins permanently once started, unlike the smaller saw that requires the pedal. The cooling water has a separate tap, which is also mounted to the saw box.
  2. Before starting with rock samples, clean off the area around the saw blade with a brush (should be lying around on the bench). If necessary, turn up the water flow for better cleaning, but remember to turn it back down afterwards. Remove rock dust from previous users.
  3. To clean the blade, make a short cut into a clay brick (should be lying around on the bench or on the floor; bring one if necessary). 

Cutting samples: 

  1. Make as few cuts as possible to minimize material loss. 
  2. Keep the rock pressed down on the flat surface around the blade. For cuts at a specific angle, you can prop up the rock with a piece of wood.
  3. Remove weathering surfaces, cross-cutting veins and any surfaces that contain sharpie markers.
  4. For surficial cleaning that doesn’t necessarily require a full cut, carefully pass the rock along the edge of the blade to abrade the outer surface while holding the rock firmly. Only do this if you have experience.
  5. When making thin section billets, use a standard glass slide to gauge the right size.
  6. When done, rinse off the rock with water to remove excess dust if necessary. Then blow it dry with air. Air-hoses can be found in various places in the rock prep lab. One air tap is in the saw room, but a hose may need to be moved from one of the other rooms.
  7. Place the dry rock into an acid-washed, muffled glass beaker, covered with Al foil. We no longer use plastic bags for this step to minimize organic contamination!

Pre-crushing rocks into chips

The rock needs to be crushed into little sub-cm sized chips before it can go into the pulverizer. This is done by hammering on a steel plate. Wear nitrile gloves, goggles and ear protection for this step.

Preparing the equipment:

  1. The steel plate, a steel pestle, and a steel ring are usually located in the room next to the saw room, on the wooden table. 
  2. Rinse each piece thoroughly with 18 MΩ DI-H2O (squirt bottle in Isolab cabinet, refill in Isolab) and wipe it with kimwipes (purchase large kimwipes from Chemstore). Only stop when no more dirt is coming off. Then rinse with alcohol (squirt bottle in Isolab cabinet, refill in Isolab), without subsequent wiping, to rinse off lint from the kimwipes
  3. Blow-dry all parts with air hose.
  4. Place the plate on a flat, sturdy table. You may want to cover the table with clean paper (located under the bench in the main lab room, underneath the thin section equipment). 

Crushing rocks:

  1. Place the rock on the steel plate, place the steel ring around it, hammer the rock with the steel pestle until it has turned into sub-cm sized chips
  2. Move the steel ring left and right a little bit such that all rock chips are pushed to the center of the plate and don’t fall off when the steel ring is removed.
  3. Remove the steel ring, carefully slide the plate with the rock chips to the edge of the table, then use an alcohol-wiped dry spatula (Isolab cabinet) to push the rock ships into the same glass beaker that you used previously for the same sample. Make sure that beaker was covered with Al foil while you were hammering the rock to keep dust from falling in. 
  4. Brush off the residual rock dust into the trash bin with the paint brush (lying on the table in the pulverizer room), then clean the equipment as before.
  5. To simplify things, you can mark the pestle and the steel plate such that you know which side was in contact with the sample and needs thorough cleaning/is clean. 

Cleaning rock chips

The rock chips need to be cleaned to remove residual contaminants from the rock saw, fingerprints, overseen sharpie marks, metal dust from the steel plates etc. The cleaning is done in the Isolab, using alcohol, 2M HCl and 18 MΩ DI-H2O. To prepare 2M HCl, mix concentrated HCl (~12 M) and 18 MΩ DI-H2O in a 5:1 ratio into a squirt bottle, using graduated cylinders. Wear gloves for this step. 

  1. Add alcohol until the rock chips are fully covered, swirl manually, then place into sonicator for 1-2 minutes. Carefully decant the alcohol into a waste bottle and repeat this step but without the sonication. The alcohol attacks fingerprints and sharpie marks.
  2. Use methylene chloride (aka dichloromethane (DCM)) to clean polar organics from rock samples. Place rock chips were into a glass beaker and cover with DCM, (2) sonicate beakers for half a minute, (3) decant DCM into a waste container.
  3. Immediately after alcohol, add 2M HCl and swirl the sample for ~20 seconds. This step dissolves potential metal coming from the steel plate and it can detach organics from surfaces. Sonication is avoided to minimize attack on sample. Decant the acid into a waste bottle and repeat this step once more.
  4. Immediately after HCl, add lots of DI-H2O (18 MΩ) to wash out the acid. Swirl the beaker thoroughly, then decant the water into the waste bottle. A sonicator can be used in this step. Repeat this three times.
  5. Cover the beaker with aluminum foil (loosely such that water can escape), then place it into the drying oven (60°C) or, alternatively, on a warm hotplate. It should dry overnight. Make sure it is dry before moving on to the next step.

Pulverizing rock chips 

The rock chips are transformed into a fine, homogeneous powder, which is necessary for most geochemical analyses. The pulverizing is done with an aluminum oxide ceramic puck mill in the small pulverizing room. Wear gloves and ear protection during this step.

Preparing the equipment:

  1. The Isolab has two puck mills. Both are located in the Isolab cabinet.
  2. Cover the table with clean paper to have a clean working surface. Al foil could be used as an alternative.
  3. Bring the puck mill out on the table. When opening it, always place the lid upside down, so it doesn’t pick up dust from the table top. Try to always place the puck on either the lid or into the bowl, not on any other surfaces, especially not right before sample addition. 
  4. Wipe all three parts (bowl, puck, lid) with 18 MΩ DI-H2O and alcohol (squirt bottles, refilled in Isolab). Use kimwipes for the water, but not for the last alcohol application. This way, the alcohol can wash out potential lint from the paper. Blow-dry all three parts with the air hose.
  5. Put the puck back into the bowl, add a few grams of muffled sand (500°C overnight, prepared in Isolab) and close the lid. The sand will be used as an abrasion tool to clean the puck mill more thoroughly. 
  6. Place the mill into the shutter box, tighten the clamp, close the lid, and turn it on. Let it run for 200-300 seconds. 
  7. When taking the mill out of the box, use paper towels to grab the clamps, because they are oily and will contaminate your gloves. 
  8. Open the lid, wipe the pulverized sand into the trash using a clean kimwipe, then repeat the water/alcohol cleaning procedure from above. If the mill looks clean, i.e. no visible grey or brown residues from previous samples, then proceed with adding the rock chips. 

Pulverizing rocks:

  1. Add a few grams of rock chips to the clean and dry puck mill. If the load it too large, then the mill will not pulverize it properly. Furthermore, the mill may fracture, especially for hard rocks like cherts. 
  2. Close the mill, place it into the shutter box and run it for 300 seconds.
  3. While the sample is in the pulverizer, grab a plastic weigh boat, rinse if off with alcohol (into the waste bin) and blow it dry with air. Also prepare a sample vial with the appropriate label (scintillation vial, muffled at 500°C overnight in Isolab, optionally acid-washed for metals). 
  4. When the 300 seconds are over, carefully open the shutter box and use paper towels to open the clamps and take out the puck mill. Make sure your gloves are clean and dry before opening the puck mill. If necessary, wipe them with alcohol.
  5. Use an alcohol-wiped spatula to transfer the rock powder into the weigh boat. This requires careful scraping of the bowl, the puck and the lid. Use your gloved finger tips to pinch out the puck, so you can scrape off the powder with the spatula. Be careful not to scrape the rubber O-ring around the lid.  
  6. When all the powder is in the weigh boat, carefully pour it into the glass vial. The weigh boat can be folded from corner to corner for easier pouring. Cap the vial and move it to a clean area.
  7. Toss out the weigh boat after each sample.
  8. Use the paint brush to wipe residual sample dust into the trash bin. 
  9. Then repeat the cleaning of the mill with water-alcohol-sand-water-alcohol as above. The sand might need to be applied 2-3 times to completely remove all sample residues. If so, then also flip the puck between sand applications, so it gets cleaned from both sides.   

Decarbonating sample powders for CN analyses 

To be able to analyze organic carbon, carbonate needs to be removed with HCl. Decarbonation has the additional advantage that it concentrates organic C and total N, which can make analyses easier. Furthermore, it appears to remove some contaminants picked up during pulverizing. This step is done in the Isolab, in a fume hood, with glass centrifuge tubes. Batches of 8 or multiples thereof are most convenient, because that’s how many tubes can be fit into the centrifuge at once. Wear gloves and goggles and ideally a lab coat. 

Preparing the equipment:  

  1. Muffle centrifuge tubes for decarbonation and glass vials for decarbonated sample residue at 500°C overnight. For the tubes, cover each one with Al foil before muffling.
  2. After muffling, the tubes can be stored in tube racks. The vials should be capped again individually.
  3. Prepare 6M HCl by mixing concentrated HCl (roughly 12M) and 18 MΩ DI-H2O in a 1:1 ratio.

Decarbonating samples:

  1. Weigh ~0.5 g of powder into each tube (1g is possible for carbonate-poor samples that only contain calcite, not dolomite or siderite). To do this, place the empty tube without the Al cap on the balance (using the Al tube holder), record the empty weight (important later!), then add powder with an alcohol-wiped spatula. Record the combined weight. Weigh sheets can be found on the Isolab computers. If you do not care about carbonate quantity, careful recording of weights is less critical.
  2. Cap the tube again with Al foil. 
  3. Carefully add 6M HCl. If the sample is carbonate-rich, it will fizz vigorously. In that case, acid has to be added very slowly, drop by drop, while stirring it carefully with a clean glass rod. Wipe the glass rod with alcohol between samples and blow it dry with air. 
  4. Fill all sample tubes to the same level such that they all have approximately the same weight (important for centrifuge later on).  
  5. Spread out the tubes in a tube rack and place the rack into the acid-proof oven at 60-80°C overnight.
  6. Optional: If you suspect recalcitrant carbonate (siderite, dolomite) in your samples, you can place the rack into the sonicator for ~30 minutes before moving it to the oven.  
  7. On the next day, carefully remove the Al caps without losing too much corroded Al into the tubes. Replace them with fresh caps. 
  8. Then place the tubes into the small bench-top centrifuge and centrifuge them for 15-30 minutes set to #6. You can use the manual mode, instead of the timer and keep track of time yourself for longer times.
  9. Decant the acid into a labeled waste bottle
  10. Fill the tubes with fresh acid and stir up the powder again with the glass rod to mix it with the acid. Optional: repeat the sonication step.
  11. Place the rack back into the oven overnight. 
  12. Repeat the acid-refreshment one more time on the next day. 

Washing off the acid and transferring the sample: 

  1. After three days, centrifuge and decant the acid, then fill the tubes with 18MΩ DI-H2O. This is to wash out the acid, which would otherwise continue to corrode the sample. Stir with the glass rod. If necessary, use the water squirt bottle to rinse off sticky rock powder from the glass rod back into the tube.
  2. Centrifuge and decant the water into the waste bottle. Repeat the water washing step two more times (so three times in total). 
  3. After decanting the water the third time, place the tubes back into the oven. Cover them loosely with a sheet of Al foil. Let the powders dry to 2-3 days. 
  4. Once dry, place the tube with the powder back on the balance and record the mass. The difference between the decarbonated and the untreated rock powder gives you a rough estimate of carbonate content. However, note that some silicates and most oxides are HCl-soluble.
  5. Re-homogenize the powder inside the tube with the glass rod, then pour it into a clean glass vial and label it with the sample name, plus the word ‘acid’ or ‘decarb.’, such that it is clearly distinguishable from untreated rock powder and cannot be mixed up at a later stage. 
  6. Throw the empty glass tubes into the glass trash box in the Isolab. 
  7. If you need to decarbonate more than 0.5g of rock powder, then the decarbonated residues of several tubes can be combined in the glass vial.


Last updated: 2020-09-28 13:06:16