California Current Ecosystem LTER

High-Performance Liquid Chromatography Pigments (CalCOFI Cruise)

High Performance Liquid Chromatography (HPLC) pigment analysis from rosette bottle samples at various depths from CalCOFI-CCE Augmented cruises in the California Current System, 2002 to 2023 (ongoing).

High Performance Liquid Chromatography (HPLC) samples are collected from rosette bottles (from three to eight different depths in the photic zone) at stations located within the CCE region on CalCOFI cruises (since 2002, ongoing). The HPLC method is used to measure concentrations of chlorophylls and carotenoids in samples of particulate matter, which includes filtering and freezing the filter while at sea. The taxon-specific phyto-pigments are extracted back onshore. Concentrations of chlorophyll a are used as a proxy for phytoplankton biomass and concentrations of other taxon-specific pigments are used to determine contributions of phytoplankton taxa to total phytoplankton biomass.

chlorophyll, concentration, CTD, marine, measurements, phytoplankton, primary production, HPLC, Primary Production

LTER Data System Record
California Current Ecosystem LTER
CalCOFI - Scripps Institution of Oceanography

Goericke, Ralf (
Stukel (Co-Lead PI), Mike (
Dovel, Shonna (

CCE LTER Information Manager (

Other Personnel
Frants, Marina


table ChromatographyPigmentsCalCOFI
Main data table for dataset
Rows: 9040
Columns: 59
View / Download


General Methods
Samples are concentrated on GF/F filters by vacuum filtration and stored in liquid N2. Pigments extracted in acetone and analyzed by reverse-phase HPLC for major chlorophylls and taxon-specific carotenoids (Goericke & Repeta 1993). From 2002 – 2014 samples were analyzed by the Goericke Lab at Scripps Institution of Oceanography (UCSD). From 2014 – present samples are analyzed by the analytical facility at Horn Point Laboratory (UMCES). In 2023, we conducted extensive comparisons between samples run at both labs, as well as the overall histograms of the full sample set analyzed by each lab to investigate the intercomparability of results between the two labs. Details (including figures) are contained in appendix 1 below. Based on these results we conclude that results for the following pigments are reasonably comparable between labs: Chl a, Divinyl Chl a, Chl b, Chl c (although Chl c values are slightly high at UMCES relative to Goericke), fucoxanthin, hexanoyloxyfucoxanthin, alloxanthin. For diadinoxanthin, peridinin, zeaxanthin, and butanoyloxyfucoxanthin the results of the comparison showed some distinct sample-to-sample differences between labs, but no distinct biases. Neoxanthin and prasinoxanthin exhibited distinct differences between labs for samples run at both institutions, with both typically having higher values at UMCES (if above the detection limit). Please see the appendix for more details.

Quality Control
All samples were quality-controlled based on three criteria. The first two criteria were based on quality control criteria used by Peloquin et al. (2013). The third criterion uses the fluorometric chlorophyll measurements that are made on paired samples taken from the same depth on each CTD cast. 1. HPLC Total Chlorophyll a <=0. This criterion indicates clear issues with the samples. 2. The ratio of log-transformed accessory pigment to log-transformed TChla is more than two standard deviations from the mean relationship found in the Maredat HPLC database (Peloquin et al. 2013). This criterion is based on the relative constancy between the ratio of chlorophyll and accessory pigments across phytoplankton groups and depths. Specifically, samples are flagged as problematic if the log10-transformed total accessory pigment concentration is greater than 0.922×log10(TChla)-0.358 or if the log10-transformed total accessory pigment concentration is less than 0.922×log10(TChla)+0.423. As of early 2023, very few of our samples were flagged by this criterion, suggesting that most of our data is of high quality. 3. Ratio of log10-transformed fluorometric TChla to log10-transformed HPLC TChla is more than two standard deviations from the mean relationship. This criterion takes advantage of the fact that we have independent TChla measurements determined by fluorometry (using the acidification method) for each of our samples. We note, however, that flagged values based on this criterion do not necessarily mean that the HPLC-derived values are incorrect. There are many reasons that fluorometrically-derived estimates of TChla could be inaccurate. The specific criterion applied is to flag samples if the log10-transformed HPLC TChla is greater than 0.901×log10(TChlaFluor)+0.24 or if the log10-transformed HPLC TChla is less than 0.901×log10(TChlaFluor)-0.30. Samples not flagged based on this criterion typically have an agreement between fluorometric TChla and HPLC TChla that is within approximately a factor of 2. By definition, since we are basing this criterion on an agreement within two standard deviations of the relationship for our own data, this criterion flags ~5% of the data. No data points were removed from the dataset based on the above criterion. Rather the quality flag column is added. 0 = no quality control criteria triggered. 1 = violates QC1, 2 = violates QC2. 3 = violates QC3. See figure in CCE-CalCOFI Methods Manual for results of quality control analyses.

CalCOFI Survey Grid quarterly


Taxon-specific phyto-pigments


Goericke, R., The Structure of Marine Phytoplankton Communities — Patterns, Rules and Mechanisms. CalCOFI Reports, 52, 182-197, 2011. CCE LTER Contribution #0213.

Peloquin, J., C. Swan, N. Gruber, M. Vogt , H. Claustre, J. Ras, J. Uitz, R. Barlow, M. Behrenfeld, R. Bidigare, H. Dierssen, G. Ditullio, E. Fernandez, C. Gallienne, S. Gibb, R. Goericke, L. Harding, E. Head, P. Holligan, S. Hooker, D. Karl, M. Landry, R. Letelier, C. A. Llewellyn, M. Lomas, M. Lucas, A. Mannino, J.-C. Marty, B. G. Mitchell, F. Muller-Karger, N. Nelson, C. O'Brien, B. Prezelin, D. Repeta, W. O. Jr. Smith, D. Smythe-Wright, R. Stumpf, A. Subramaniam, K. Suzuki, C. Trees, M. Vernet, N. Wasmund, and S. Wright, The MAREDAT global database of high performance liquid chromatography marine pigment measurements. Earth System Science Data, 5, 109-123, 2013. DOI 10.5194/essd-5-109-2013. CCE LTER Contribution #0244.

Wright, S.W., S.W. Jeffery, R.F.C. Mantoura, C.A. Llewellyn, T. Bjornland, D. Repeta, and N. Welschmeyer. 1991. Improved HPLC method for the analysis of chlorophylls and carotenoids from marine phytoplankton. Marine Ecology Progress Series 77: 183-196.

Zapata, M., F. Rodríguez, and J.L. Garrido. 2000. Separation of chlorophylls and carotenoids from marine phytoplankton: a new HPLC method using a reversed phase C-8 column and pyridine-containing mobile phases. Marine Ecology Progress Series 195: 83-102.


Appendix1.docx (1.19MB)
Goericke Lab and UMCES HPLC intercomparison results