DOI: 10.22002/d1.20255
title: Raw Data and Processing Pipeline Files for Cecilia B. Sanders 2022 PhD

description: "Read Me" Guide to Cecilia B. Sanders' 2022 Ph.D. Thesis Data Files:

CAS_AbundanceData_Raw_CeciliaSanders.pdf
> This is a PDF file of 2 tables containing information about sample preparations for ion chromatography and trace carbonate-associated sulfate (CAS) measurements made in Caltech's Division of Geological and Planetary Sciences using Neptune ICP-MS.
> Each row contains information specific to the sample ID indicated in the farthest left column titled "Sample". Sample IDs are consistent with Table 1 of the thesis chapter 2.
> In the upper table... Each column is labeled according to its contents, from left-to-right describing: the XRD-constrained mineralogical composition of the samples, the mass of untreated sample powders, the mass of the acid-cleaned microcentrifuge tubes into which the sample powders were weighed, the mass of the sample powders AFTER cleaning protocols and dehydration in oven, the difference between sample powder masses before and after washing/rinsing (presumed the mass of each sample's non-carbonate fraction), the concentration of structural sulfate measured in 250 ul aliquots of dissolved sample in acid via ion chromatography, and the calculation of CAS abundance based on the measured powder masses and IC concentration data. The last two columns describe the amount of liquid that was added to the washed, rinsed, dissolved, and dried down samples for matrix-matching purposes during ICP-MS.
> In the lower table... This table contains information relevant to the preparation of sample, standard, and blank solutions for measurement against an in-house dissolved sulfate standard (i.e., volume of sodium and sample-in-acid solutions combined for each measurement.
> In these tables, color flooding indicates viability of each sample for ICP-MS. Red = insufficient sulfate abundance AND/OR evidence of contamination in sulfate elution curves during IC. Yellow = Borderline sulfate abundance AND/OR evidence of contamination in sulfate elution curves during IC. Green = Sufficient sulfate abundance AND minimal evidence of contamination in sulfate elution curves during IC.

CAS_RawData_CeciliaSanders.xlsx
> This is an Excel file containing raw data from ICP-MS measurement of trace CAS samples, containing multiple Sheets of information.
> 2021-11-18
>> This sheet contains the raw data values reported by the ICP-MS control software. From left to right, the columns contain information about each listed acquisition's: auto-generated filename, average and standard errors of voltages measured at the Faraday Cup detectors for m/v = 32 and m/v = 34, voltage ratios of 34/32 and 33/32, and "capD, described in text of thesis chapter 4. The blue highlighted columns further to the left represent the conversion of these raw voltages into uncorrected delta 34 S and delta 33 S values (expressed as per mille).
> Plots
>> This sheet contains plots of ratios of signal intensity for 33/32 and 34/32 for all sample, standard, and blank acquisitions. There are also included plots of the signal intensity for 32S alone for samples and blanks as a function of position in the sequence of acquisitions -- indicative of instrumental response drift for samples/standards/procedural blanks AND comparison standards (blks) which bracketed each acquisition.
> blk 
>> Provides the same information as 2021-11-18, but for the bracketing comparison standards (blks) which were alternated with sample/standard/procedural blanks solutions.
> DeltaValues
>> Combined information from 2021-11-18 and blk sheets, with additional columns showing applied correction for signal drift derived from bracketing comparison standards (blks).
> blanks
>> calculated delta values, relative intensity of sample to bracketing standard (blk), and ultimately sulfate concentration for 2 PROCEDURAL BLANKS.
> END
>> For each sample, standard, and procedural blank, a summary of instrumental drift corrections and generated raw data filenames.
> summary
>> average delta values and standard errors, relative intensities, CAS abundance, and applied corrections for all measured samples and standards. Final column and text colors provide notes about criteria for assessing data "quality" and "reliability" as detailed in text of thesis chapter 4.

Clumped_RawData_CeciliaSanders
> This is an Excel file containing raw data, and detailing each step in the projection of those data into a universal reference frame, as well as the application of empirical relationships between calculated D47 and d18O, and temperature and fluid d18O. Multiple sheets:
> FlatlistData
>> Each row describes GC-MS data for each indicated sample, standard, or equilibrated or heated gas. The format of this sheet is standard to the autoline and GC-MS measurements made at Caltech. Overlaying the data tables are plots (labeled, annotated) showing the calculation of an empirical transfer function which projects the raw d and D values for each measurement into an absolute reference frame.
> Sheet4
>> A "scratch" sheet showing the calculation of d18O_mineral from the actual measured d18O gas (generated by acid-digestion of powder sample and standard carbonate and carbonate-fluorapatite).
> PracticeSheet
>> An example sheet which, from left-to-right, details the processing of raw delta and Delta values through the derivation and application of the empirical transfer function, and the calculation of clumped isotope temperature. ALSO SERVES AS README GUIDE FOR FlatlistData.
> ProcessedDataOrganization
>> Same operations described in PracticeSheet, applied to all sample measurements. Row highlight colors correspond to "mineral" type column. Column highlight colors indicate which empirical calibrations e actually used and reported in the thesis (green) and which were rejected (red) on the basis of newer, more accurate empirical calibrations from the literature. Calibrations and their citations included in column headings.
>Sheet3
>> A "scratch" sheet reducing the information from "ProcessedDataOrganization" into 4 columns containing sampleID, mineralogy, and clumped isotope temperatures generated by two conflicting calibration relationships.
>flatlist_manual_processing
>> A "scratch" version of the more complete, finalized ProcessedDataOrganization sheet.
> Sheet1
>> Metadata, describing which columns from the sheet ProcessedDataOrganization contain the indicated information.
> Sheet2
>> Another "scratch" sheet, reducing the information from "ProcessedDataOrganization" into several columns, describing the calculation of d18O fluid from clumped isotope temperatures in K and measured/projected d18O_mineral.
> ManualProcessing_and_Comparison
>> A "scratch" sheet comparing flatlist data processing output to "manual" data processing performed in previous Excel sheets.
> ManualProcessing2
>> A "scratch" sheet, containing the same information as ProcessedDataOrganization but with differently ordered columns.
>FormattingScratchSheet
>> A "scratch" sheet in which information from ProcessedDataOrganization was converted to a format exportable as csv or txt, for use in other data visualization and operations tools. NOT consistent with final used datasheets, due to differing ordering of rows.
> For_d18O_plotting
>> Like "FormattingScratchSheet," a "scratch" sheet for ease of exporting information from ProcessedDataOrganization as csv or txt.

PAS_and_CRS_RawData_CeciliaSanders
> An Excel file containing a single sheet, summarizing results of IRMS measurements of phosphate-associated sulfate (PAS) and chromium-reducible sulfur (CRS). From left to right, each row contains a sample/standard identifier, the mass of each powdered analyzed sample/standard, the "number" of the signal peak associated with a given m/v, the calculated area of the indicated peaks, the "ampl" or signal intensity of the indicated peaks, and ultimately the d34S values calculated based on these peak intensities. For standards, the average of 2-3 replicate d34S measurements are compared to accepted/published d34S values (labeled "true values" column). For samples, d34S values are corrected for instrumental drift through a linear LSQ fit of the standards' measured vs. true values. The column "First" describes the corrected d34S values for samples based on the standards measured immediately before, and the column "Second" describes the corrected d34S values for samples based on the standards measured immediately after. ("Third" and "Fourth" serve the same purpose, bracketing blocks of samples for the lower half of the data.) The values from "First" and "Second" or "Third" and "Fourth" are averaged in the final column "Average/Final".