See complete methodology in Haskell et al. (2016). In summary:
This study is part of an effort aimed at characterizing the biological response to upwelling at SPOT on 21 cruises between January 2013 and June 2014; the Upwelling Regime In-Situ Ecosystem Efficiency (Up.R.I.S.E.E.) study.

Nutrients: Samples for dissolved nutrient and pH analysis were collected via Niskin at 12 depths from the surface to 400 m and filtered through 0.8/0.2 um Acrodisc syringe filters. One Nalgene bottle was filled completely leaving no headspace and kept at ambient temperature for 6–8 h until return to the lab where pH was measured using a combination electrode calibrated with buffers of pH 4 and 7, referenced to NBS standards. About 20 of these samples were analyzed for alkalinity and total dissolved inorganic carbon (DIC). To make the measured pH internally consistent with the DIC and alkalinity, all pH values were increased by 0.02, the estimated uncertainty in electrode calibration. After the pH aliquot was taken, samples were refrigerated until silicic acid and phosphate analyses were done colorimetrically at USC with a Hitachi UV/vis-spectrophotometer. Nitrate samples were collected in acid-washed 60 ML HDPE Nalgene bottles and frozen at -20 degrees C until analysis. Nitrate concentrations in samples collected from January to June 2013 were determined by converting nitrate to N2O and quantifying the amount of N2O as integrated sample areas on an Isotope Ratio Mass Spectrometer (IRMS) in the D. Sigman lab at Princeton University. Prior to analyses, nitrite was chemically removed from samples. The remainder of the samples (October 2013 to June 2014) were analyzed for nitrate + nitrite and nitrite only by chemiluminescence. The analytical uncertainty for nitrate and silica concentrations is ~0.5 uM. Samples for DIC were collected at each depth by using a syringe to inject 5–7 mL of filtered water into evacuated vials through a needle-pierced septum. Following measurement of the mass of water, measurements of TCO2 and δ13C were made on a Picarro Cavity Ring-Down Spectrometer at USC. Alkalinity was calculated from DIC and pH using Mehrbach constants. On samples titrated for alkalinity, DIC calculated from the adjusted pH was within +/- 10 umol per kg (+/-1 ssd) of the measured values. Measurements were standardized with Dickson standards from SIO, and alkalinity precision was typically +/- 5 ueq per kg. DOC samples were syringe-filtered into acid-washed and combusted 40 ML borosilicate vials with silicone/PTFE septa caps (Thermo Fisher Scientific). After sampling, samples were acidified with distilled HCl to pH ~2 and refrigerated until analysis on a Shimadzu TOC-VCSN analyzer at Scripps Institute of Oceanography (L. Aluwihare lab). The analytical uncertainty on DOC concentrations based on replicates is ~ 5 uM. Each day's run included the analysis of a deep seawater community standard, and if the concentration of this standard was not between 41 and 42 uM C then all samples were re-analyzed.