For a detailed description of the TLS instrument in SAM, the reader is referred to P. R. Mahaffy et al., "The Sample Analysis at Mars Investigation and Instrument Suite", Space Sci. Rev. 170, 401-478 (2012). For detailed description of the spectral scans, line identification, data processing and calibration, the reader is referred to the manuscripts and Supplementary Online Material (SOM) accompanying four Science papers:
(i) C.R. Webster et al., "Isotope Ratios of H, C and O in CO2 and H2O of the Martian Atmosphere", Science 341, 260 (2013);
(ii) C.R. Webster et al., "Low Upper Limit to Methane Abundance on Mars", Science 342, 355 (2013); and
(iii) C.R. Webster et al. "Mars methane detection and variability at Gale crater," Science 347.6220 (2015): 415-417.
(iv) C.R. Webster et al. "Background levels of methane in Mars atmosphere show strong seasonal variations", Science 360, 1093-1096 (2018).
These four papers focus on atmospheric data and results.
For the Evolved Gas Analysis (EGA) runs, further details are given in a fifth Science paper authored by Laurie Leshin et al., namely:
(v)  L.A. Leshin et al., "Volatile, Isotope, and Organic Analysis of Martian Fines with the Mars Curiosity Rover", Science 341, (2013); DOI 10.1126/science.1238937.

GENERAL: As detailed in the reference papers above, TLS spectral processing is done on a line-by-line basis through comparison with HITRAN to yield volume mixing ratios (vmr) used for retrieval of abundances that can be ratioed to produce isotope ratio deltas. For all gases except atmospheric CH4, vmrs are produced from the direct absorption spectra, namely by integrating the area across each line. The integration width is set by the location of the 2f lobe minima, thereby covering >80% of the area on a consistent basis without the need to fit the baseline over larger widths. All errors quoted are 1 standard error (68% CI) in the scatter of the retrieved vmr points over the run length. TLS runs only one laser at a time, recording spectra in predetermined sections. The NIR laser has two spectral region options, one for CO2 and a second for H2O and HF. The IC laser has a single region for CH4 and CH3Cl. In the spirit of transparency, specific comments are included for each run.
FOREOPTICS SUBTRACTION: Both TLS lasers pass ~ 9cm through a foreoptics (FO) chamber before entering the multi-pass Herriott cell. The FO chamber contains CO2, some CH4 and air with a little water. "Full cell" spectra are the combination of HCell and FO spectra, while "Empty cell" spectra are with the HCell pumped out, so represent the FO gas only. We first process the full cell spectra at the recorded HCell pressure, temperature and pathlength. Then following HCell pumpout, we process the empty cell at the same pressure, temperature and pathlength to accurately determine the contribution of the FO gas to the full cell spectra. On a line-by-line vmr basis, the subtraction is made to reveal the HCell gas abundances and isotope ratios. 
FOREOPTICS GAS: Gas measurement determinations must be made after subtraction of any gas permanently trapped in our Foreoptics (FO) chamber housing the lasers. Our FO gas was originally "Florida air" that had leaked in over the years since instrument delivery. Since Mars arrival, the FO chamber has been pumped out several times. The FO gas (typically up to 10 mbar) is now mainly CO2 with traces of methane and tiny amounts of water. For atmospheric CO2 runs, the ingested Mars CO2 is large enough to make any FO contribution to the spectra negligible (hence no subtraction needed). For EGA CO2 however, we often get low evolved CO2 amounts, so that the FO subtraction is significant. For CO2, we find that the FO contribution is a spectrum that when processed at Herriott cell temperatures and pressures looks like CO2 with average enrichments of ~196 per mil in d13C_CO2 and ~230 per mil in d18O_CO2.  For runs in which the FO contribution is >25% of the total "full cell" gas, the uncertainty increases and the reliability of the result decreases. For EGA H2O retrievals, the FO contribution is negligible so no subtraction is needed/made. Regarding atmospheric CH4, we do have significant methane trapped in our FO chamber that must be subtracted out. While present at ppmv in the single laser pass chamber, the FO methane looks like tens of ppbv at the Hcell temperatures and pressures. A typical nighttime run may produce 64 ppbv in the "full" Hcell (Mars +FO), and 51 ppbv in the "empty cell", so that the difference is ~13 ppbv here. Then, dividing by the enrichment factor of EF=25 we get the result of 0.52 ppbv in situ CH4.
For the enriched methane runs, following a Herriott cell pump out, the atmospheric gas is led in across a carbon dioxide scrubber (that removes much of the carbon dioxide and not methane) until the Herriott cell pressure reaches atmospheric pressure (nominal 7 mbar) or until 2 hours have passed, whichever comes first. Then scans across the methane region are made according to the usual script described in the published paper on low methane abundance. The enrichment script was fully tested in the SAM test bed at GSFC to produce an enrichment factor of about 25. Provided data has this division already made to reflect the original Mars methane abundance with its correspondingly lower uncertainty. All methane values given have been corrected to global annual mean mixing ratios. Briefly, for EGA analysis, ingested solid sample is heated in a pyrolysis oven whose gaseous products are routed to either QMS, TLS or GC in a helium gas flow.
EVOLVED GAS RUNS: For any EGA run, TLS is given a "temperature cut" where the effluent is delivered to the TLS Herriott cell during a certain oven temperature portion of its heating ramp, typically a 50-100 deg C cut that may be at lower or higher temperature, and identified in our level 2 data set. Isotopic ratios for d17O in CO2, while provided for standard "atmospheric" runs, cannot retrieve meaningful values for EGA runs where spectral signals (line depths) are much weaker. Rocknest EGA effluent gases were observed by the QMS to contain contamination from a derivatization agent MTBSTFA that was taken along with the SAM experiment.  For TLS, numerous underlying spectral lines were observed in our spectral scans whose contribution to the CO2 and H2O isotopic lines could not be unambiguously identified.  However, these interferences were generally small, and diminished throughout the Rocknest run series, made only minor contributions to the John Klein and Cumberland analyses, and were of negligible contribution to all subsequent EGA runs.
For EGA analysis, it is important to take into account what gases and isotope ratios would result with no sample in the pyrolysis oven.  To that end, the EGA run is duplicated in this condition (no sample) and minor amounts of both CO2 and H2O are produced and detected in TLS.  Because these "blank cup" gases are measured by TLS to have isotopic ratios different from the Mars solid samples, we have made minor corrections to the level 2 data based on a blank cup analysis usually run immediately before each series (Rocknest, John Klein, Cumberland). These corrections are described in the Leshin et al. Science paper referenced above.
Small corrections due to laser line position have also been applied. For the combustion experiments, TLS receives gas in 3 steps after the oven is held at a constant temperature and oxygen added for combustion of organic compounds into CO2, and removal of low temperature components from the TLS prior to introduction of gas released at higher temperatures. The steps involve sampling first at low temperatures, then heating to 550 deg C for one sample, then to 950 deg C for the final sample.
Isotope ratios given refer to SMOW for oxygen isotopes and VPDB for d13C ratios. These ratios were determined using identical data processing software in comparison to certified calibration gas or liquid standards determined by IRMS (see published material). All isotope delta values and their standard errors (one-sigma, SE) are given in "per mil" according to standard convention. We emphasize that the understanding and analysis of identified and unidentified contaminants and underlying spectral lines is ongoing, and may result in future corrections (updates) to our level 2 data.
Below are comments specific to this run. For any questions about them or questions in general, please contact chris.r.webster@jpl.nasa.gov
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CO2: FO is 23% of total, H2O is 2%
H2O:
CH4: Final uses E, F, G, A and D, E and F 2f lobes are not saturated, 2f for CH3Cl