Carbonates on Psi

1. Find clean vials and a tray - in drawer under polly prepline
2. Find the Psi standards - desiccator
3. Clumped - Ideally you will have one complete set of standards analyzed each day (8 standards in total - ETH1, ETH2, ETH3, ETH4, IAEAC1, IAEAC2, Merck, GU1). Mix them up and randomize their order. This is two sets of standards per tray of 50 vials.
4. Bulk - use ETH4, Coral, and IAEAC1
5. Clumped - Weigh 500 µg (± 10 µg) of pure carbonate when you have very little material for analysis (cold finger mode). Otherwise, we 4.0 to 5.0 mg (bellows mode).
6. Bulk - Weigh 50 µg (± 10 µg)
7. Clumped - We would love to be able to declare that you need to run at least two equilibrated gases but Nu has yet to deliver a functional multiport and tube cracker (2024-10-21).

1. Check if the previous run has finished or if Psi has crashed
2. Pull lines out of liquid nitrogen dewar and drape off of the floor
3. run reset everything - Analysis > Sequence > Edit > psi_reset_everything.seq, the click Run
4. if Psi Crashed, evacuate and bake traps - Analysis > Sequence > Edit > psi_bake_all_traps.seq, the click Run
5. thaw and dry out liquid nitrogen lines - Analysis > Sequence > Edit > psi_dry_out_liquid_nitrogen_lines.seq, the click Run
6. Create a batch file:
   • Open C:/Nu Stable/Batches/_Clumped_Batch_Template_ColdFinger.TXT or C:/Nu Stable/Batches/_Clumped_Batch_Template_Bellows.TXT
   • save as with today's date and descriptive name (yymmdd_YourProject.txt) into the same directory the template was in
   • enter sample and standard information into batch file template and save
   • TYPE THE STANDARDS IN EXACTLY AS TYPED ABOVE
   • Enter each replicate of a given sample identically throughout your session and between sessions if appropriate. For example, "sample_1" should be entered as "sample_1" every time it is analyzed. Do not enter "sample_1_rep1", "sample_1_rep2", etc. You will be able to differentiate individual replicates using a unique identifier provided by the instrument as well as the date and time of analysis. The purpose of entering all replicates identically is to leverage Daeron's (2021) error propagation python code called D47crunch, which we employ.
   • Some prefer to use a text editor while others prefer to use the Nu Stable software interface to create / edit the batch files
7. run reset everything again - Analysis > Sequence > Edit > psi_reset_everything.seq, the click Run
8. fill out daily log
9. fill up the liquid nitrogen dewar
10. place liquid nitrogen lines into the dewar and wrap the fleece cozy around the lines and top of dewar
11. start - Analysis > Batch > Setup-Full > Open > select your batch file > Run

Periodically, you will need to simply top off the acid vessels inside the NuCarb. Acid is stored in the larger 60 *C drying oven in 303B. Don liquid protective gloves, unscrew caps, top-off vials. NOTE, the cap with the stainless steel tubing coming out of it must be left loose. If you tighten it, acid will stop flowing after a vacuum builds up.

If we are low or out of the Psi acid (1.90 g / mL), you need to dilute more from the more concentrated stock (~1.95 g / mL).

If we are low or out of all concentrated phosphoric acid, make more.

1. With liquid protective gloves on, remove vials from Psi and place in the #1 white tub. The vials can contain acid, sediment, carbonate, and bubble bursters. That is, just set them in the tub regardless of what is inside them. We use the acid to our advantage later.
2. Fill tub half ish full with DI water.
3. Remove all air from each and every single vial. YES ALL OF THE AIR. The vials must soak in this acidic environment. If you want to be certain that no carbonate is left inside any vial, this step is absolutely critical. Allow them to soak overnight.
4. Remove each vial and shake all of the liquid out of the vial back into the tub, NOT THE SINK. Place each vial in the #2 white tub. Fill the #2 white tub half ish full with DI water and, again, jostle air from every single vial. Soak overnight.
5. Add sodium bicarbonate (baking soda) to the #1 tub while the tub is in the sink. Use the wooden dowel to stir. Add more sodium bicarbonate and stir until it stops fizzing and you see a near neutral pH as measured with pH paper. Then, after you have achieved neutral pH, dump the contents of the #1 white tub down the drain. Left over baking soda is okay. Rinse the #1 tub with DI water and leave on the bench.
6. Shake all of the DI water out of the vials that were soaking in the #2 white tub and place them into the #3 white tub. Fill the #3 white tub half full with DI water and shake all of the air out of each vial. Soak overnight.
7. Dump the water remaining in the #2 tub down the drain.
8. Shake all of the water out of each vial and place them into a clean glass beaker. Place this beaker into the 60*C drying oven near the hood. Make sure the drying oven door closes. You must move the handle to the side to open AND CLOSE this oven. Leave these vials at least overnight or until they are dry.
9. Dump the water from #3 tub down the drain.

IMPORTANT - This process does not do a good job at removing leftover sediment or otherwise precipitated solids from the vial. It is important to note that the leftover material is NOT CARBONATE. See your bubbling observations from step 5. Yes we all like clean vials, but this unsightly dirtiness is not carbonate. Still, to remove this material, offending vials must be scrubbed with a pipe cleaner. My preference is to go through the above steps and then as I see the dirty vials, which could be while weighing, I separate them out and scrub them on a individual vial basis. Once you have these vials clean, rinse with DI, and dry them in the oven.

• Workflow
• move data
• initial look at and quality assessment of raw data
• cleaning
• calibrating
• Data quality metrics
• SIGNAL - Low signal equals bad data (noisy and biased). Based on many many cold finger analyses, if the m/z 44 signal falls below 2e-8 Amps, the analysis is distrusted. If your samples are necessarily going to have low signal, you will need to manually trust those samples after running the R script.
• RESIDUAL GAS - Residual gas is a measure of post-reaction gas pressure interpreted as incondensibles, leakiness, or a clogged path during the reaction. Currently, a "high residual gas" is any pressure above 0.01 mbar. While it does not seem to affect isotopic data quality or absolute amount of CO2 produced, residual gas may be informative for specific samples (incondensibles), may give you a warm fuzzy feeling knowing it is low (leakiness), or tell you it is time to clean the acid block and associated valves (clogged path). Still, residual gas is NOT, in and of itself, a reason to distrust data. If you observe "high residual gas" for many different samples and standards, it is probably time to clean the acid block. If you observe "high residual gas" for one or more specific samples, they probably contain incondensibles. The one case where "high residual gas" is reason to distrust is when the line between the acid reaction and first trap is clogged in which case you will also observe, low yield, low signal, and probably many other flags suggesting a problem.
• SIGNAL BALANCE - The amount of CO2 entering the source must be as similar as possible with respect to the sample versus working gas. This is measured as the m/z 44 signal intensity. The software makes a concerted attempt at balancing these two signals. A poor balance can lead to increased noise as well as a bias in all of the isotope composition estimates. The signal balance is measured as a percent difference in four ways: (1) Nu's default, which seems to be a comparison of the first measurement of sample and working gas; (2) start_balance, the average of the first five data points of the sample versus working gas; (3) mean_balance, the average of all cycles for both sample and working gas; and (4) the end_balance, which is the average of the last five data points for sample and working gas. Currently, if the start_balance or end_balance exceed 2% (i.e., +/- 2% difference between sample and working gas), then the sample is distrusted.
• D47raw STANDARD DEVIATION - A high Δ₄₇ standard deviation that is not related to low signal intensity or poor balance, may be the result of a contaminant or a problem with the mass spectrometer. Currently, if the Δ₄₇ internal standard deviation (i.e., within sample, cycle level variability) exceeds 0.15 permil, the analysis is distrusted.
• D48raw STANDARD DEVIATION - A high Δ₄₈ standard deviation that is not related to low signal intensity or poor balance, may be the result of a contaminant or a problem with the mass spectrometer. Currently, if the Δ₄₈ internal standard deviation (i.e., within sample, cycle level variability) exceeds 0.50 permil, the analysis is distrusted.
• SAMPLE PRESSURE - The amount of CO2 produced will vary normally with the amount of carbonate in the vial. If the measured CO2 pressure after going through the Porapak is greater than 100 mbar, the analysis will proceed as a bellows measurement, otherwise, it will be a cold finger measurement. We can't use CO2 pressure by itself as an indicator of data quality but if the specific carbonate being analyzed has a known percent carbonate (e.g., 100% for standards), then the amount of CO2 produced per unit carbonate (called "yield_mbar_ug" in the data) should fall within a relatively tight range. The current expected yield is 0.038 mbar of CO2 per µg of pure carbonate; this, of course, has error around it with a 3.3 sigma of 0.005; the acceptable range, then, is 0.033 to 0.043 mbar of CO2 per µg of pure carbonate. This criteria can only be applied to samples of known percent carbonates (e.g., standards and characterized samples).
• Get ready
• On the Psi computer, open a File Explorer instance. double click on "C:\psi\_COPY_DATA_TO_S-DRIVE.bat". This will transfer all the new data to the data server.
• use your UWNetID to log into one of the zax computers
• make sure bob (S:) is mapped (click on map_bob.bat)


• Raw Mass Spec Data
• open R or RStudio
• make sure you are in S:/Data/projects/psi/R_Python_Code/ (in the console, type setwd('S:/Data/projects/psi/R_Python_Code/') and hit enter
• Type source('psi.R') and hit enter.
• Enter the session your samples are in and then work your way through each sample, checking the data presented to you, looking over the figures, and entering any comments you wish to enter about particular analyses.
• If psi.R identified "outliers", they are removed from the summary statistics for that sample; that is, the within-sample outliers have been pitched.
• Once all of the new samples have been initially and individually screened, you are shown a series of figures comprised of all data in the session. Look through each figure and get a feel for recent performance compared with the rest of the session.
• If you ever want to look at these session-wide figures again, you can do so without going through R. Use python as described below. Type python psi_raw_data_report.py [YOUR SESSION]


• Sample log cleaning
• open a command prompt (cmd)
• make sure you are in S:/Data/projects/psi/R_Python_Code/ (in the console, type S: and hit enter, then type cd projects/psi/R_Python_Code/ and hit enter
• start the cleaning python script by typing python psi_cleaning.py
• Read and work you way through all of the steps presented to you.
• Calibration
• Open python and type py psi_calibrate.py and hit enter. Enter your session. If more than one *_samplelog.csv" file exists in your session folder, you will be asked to choose one.
• Look over the data and figures presented to you. If you found outliers you wish to exclude or sample IDs that are not entered correctly, repeat the above few steps and rerun py psi_calibrate.py