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| Dataset Title: | [mol percent - HPLC Method Glu and Phe 15N values] - N isotopic composition of Phenylalanine and Glutamic Acid from a number of organisms, demonstrating new HPLC protocol for precise isotopic measurements (The Use of Nitrogen Isotopes of Amino Acids To Understand Marine Sedimentary 15N Records) 
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| Institution: | BCO-DMO (Dataset ID: bcodmo_dataset_712090) |
| Information: | Summary
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Attributes {
s {
sample_type {
String bcodmo_name "sample_type";
String description "Description of the sample type.";
String long_name "Sample Type";
String units "unitless";
}
amino_acid {
String bcodmo_name "amino_acid";
String description "Amino acid";
String long_name "Amino Acid";
String units "unitless";
}
mol_pcnt_hplc {
Float32 _FillValue NaN;
Float32 actual_range 1.63, 21.66;
String bcodmo_name "amino_conc";
String description "Relative amino acid abundance; determined by HPLC-ELSD. Average precision: +/- 1";
String long_name "Mol Pcnt Hplc";
String units "percent (%)";
}
mol_pcnt_hplc_stdev {
Float32 _FillValue NaN;
Float32 actual_range 0.03, 0.63;
String bcodmo_name "amino_conc";
String description "Standard deviation of relative amino acid abundance determined by HPLC-ELSD.";
String long_name "Mol Pcnt Hplc Stdev";
String units "percent (%)";
}
mol_pcnt_GCC {
Float32 _FillValue NaN;
Float32 actual_range 1.8, 18.55;
String bcodmo_name "amino_conc";
String description "Relative amino acid abundance; determined by GC-C-IRMS. Average precision: +/- 1";
String long_name "Mol Pcnt GCC";
String units "percent (%)";
}
mol_pcnt_GCC_stdev {
Float64 _FillValue NaN;
String bcodmo_name "amino_conc";
String description "Standard deviation of relative amino acid abundance determined by GC-C-IRMS.";
String long_name "Mol Pcnt GCC Stdev";
String units "percent (%)";
}
}
NC_GLOBAL {
String access_formats ".htmlTable,.csv,.json,.mat,.nc,.tsv";
String acquisition_description
"Methodology described in Broek & McCarthy (2014):
AA standards
Standard L-AA powders were purchased from Alfa Aesar and Acros Organics and
used to prepare individual liquid standards (0.05 M), which were then combined
as an equimolar mixture of 16 individual AAs (\\\"16 AA Standard\\\") for
developing separations. The 16 AA Standard contained the proteinaceous AAs:
glycine (Gly), L-alanine (Ala), L-arginine (Arg), L-aspartic acid (Asp),
L-glutamic acid (Glu), L-histidine His), L-isoleucine (Ile), L-leucine (Leu),
L-lysine (Lys), D/L-methionine (Met), L-phenylalanine (Phe), L-proline (Pro),
L-serine (Ser), L-threonine (Thr), L-valine (Val); and nonprotein AA nor-
leucine(Nle), which ;is commonly used as an internal standard (Popp et al.
2007; McCarthy et al. 2013). The \\u03b415N and \\u03b413C values for dry
standards were determined by standard EA-IRMS at the University of California,
Santa Cruz Stable Isotope Laboratory (UCSC-SIL) following standard protocols
([http://es.ucsc.edu/](\\\\\"http://es.ucsc.edu/\\\\\") ~ silab). Average precision
of EA-IRMS \\u03b415N standard values was 0.11 \\u00b1 0.07 \\u2030.
Additionally, a commercially available equimolar AA standard mixture \\\"Pierce
Amino Acid Standard H\\\" (Pierce H)(Thermo Scientific) containing the same AAs
as the \\\"16 AA Standard\\\" with the exception of the nonprotein AA Nle and
addition of the proteinaceous AAscysteine (Cys) and tyrosine (Tyr) was used to
construct individual calibration curves, so as to verify relative molar
abundance of individual AAs in natural samples.
Sample preparation:
The cyanobacteria sample (Spirulina Sp.) was obtained as a bulk commercial
dry powder (Spirulina Pacifica, Nutrex Hawaii, Kailua-Kona, HI). This same
sample has been used previously as a McCarthy laboratory internal quality
control standard, and its CSI-AA values have been measured repeatedly by
GC-C-IRMS, allowing an investigation of the long-term accuracy and precision
of the GC-C-IRMS instrument.
Coastal mussel (Myilitus Califorianus) sample was collected in 2012 from Santa
Cruz, CA. The mussel was previously dissected, and the adductor muscle tissue
removed and lyophilized prior to storage. We used a subsample of adductor
muscle collected for a prior study (Vokhshoori and McCarthy 2014) hydrolyzing
the bulk lyophilized adductor muscle tissue directly without lipid extraction.
The deep-sea bamboo coral (genus isidella) sample was previously collected in
2007 from Monterey Bay, CA, USA (36 44.6538N, 122 2.2329W, 870.2 m) (Hill,
pers. comm. 2011). A proteinaceous node was separated from the calcium
carbonate skeleton and oven dried (60 degrees C, 24 h).
White sea bass muscle tissue was subsampled from an incidental recreational
catch in 2007, landed from Santa Cruz Island, Channel Islands, CA (J.
Patterson, pers. comm. 2007). Fish muscle tissue was also lyophilized prior to
hydrolysis.
Harbor seal blood was collected in May-June 2007 from a wild animal in Tomales
Bay, CA (38 13.9N, 122 58.1W) under NMFS Research Permit no. 555-1565. Blood
serum was purified, lipid extracted, and lyophilized prior to hydrolysis, as
described previously (Germain et al. 2011).
For all sample types, proteinaceous material was hydrolyzed by adding 40-50 mg
of bulk dry sample to an 8 mL glass vial, followed by 5 mL of 6 N hydrochloric
acid (HCl) at room temperature. The vials were flushed with nitrogen gas,
sealed, and allowed to hydrolyze under standard conditions (110 degrees C, 20
h). Hydrolysis under acidic conditions quantitatively deaminates asparagine
(Asn) to aspartic acid, and glutamine (Gln) to glutamic acid (Barrett 1985).
Therefore, in this protocol (and all others based on acid hydrolysis),
measured Glu in fact represents Gln+Glu, and measured Asp represents Asp+Asn.
We note that while the abbreviations Glx and Asx are sometimes used to denote
these combined Gln+Glu and Asp+Asn fractions, we have elected to simply use
Asp and Glu as abbreviations, as defined above, in order to correspond better
with prior TPCSIA literature. Additionally, acid hydrolysis is known to
destroy cysteine (Cys), precluding it from analysis (Barrett 1985). Resulting
hydrolysates were dried to completion under nitrogen gas and brought up in 0.1
N HCl to a final concentration of 1 mg tissue/ 100 L HCl. Approximately 75% of
each of the resulting mixtures was reserved for HPLC/EA-IRMS analysis, and the
remaining material was dried to completion for derivatization and subsequent
GC-C-IRMS analysis.
GC-C-IRMS Analysis\\u2028:
Trifluoroacetyl isopropyl ester (TFA-IP) AA derivatives were prepared using
standardized lab protocols, as described previously (McCarthy et al. 2013).
Briefly, hydrolyzed samples were esterified in 300 uL 1:5 mixture of acetyl
chloride:2-propanol (110 degrees C, 60 minutes). The resulting amino acid
isopropyl esters were then acylated in 350 uL 1:3 mixture of dichloromethane
(DCM):trifluoroacetic acid anhydride (100 degrees C, 15 minutes). Derivatized
AAs were dissolved in DCM to a final ratio of 1 mg of original proteinaceous
material to 50 uL DCM. Isotopic analysis was conducted on a Thermo Trace GC
Ultra (Thermo Fisher Scientific, West Palm Beach, FL, USA) coupled via a
Thermo GC IsoLink to a ThermoFinnigan DeltaPlus XP isotope ratio monitoring
mass spectrometer (Thermo Fisher Scientific).\\u00a0Derivatives (1 L) were
injected (injector temp. 250 degrees C constant) onto an Agilent DB-5 column
(50 m x 0.32 mm ID x 0.52 um film thickness, Agilent Technologies, Inc., Santa
Clara, CA, USA), with a He carrier flow rate of 2 mL/min (constant-flow).
Separations were achieved with a four-ramp oven program: 52 deg C, 2 min hold;
ramp 1 = 15 deg C /min to 75 deg C, hold for 2 min; ramp 2 = 4 deg C /min to
185 deg C, hold for 2 min; ramp 3 = 4 deg C /min to 200 deg C; ramp 4 = 30 deg
C /min to 240 deg C, hold for 5 min. This method allows for the determination
of 11-15 AAs depending on derivatization efficiency and instrument
sensitivity. Values are typically obtained for Gly, Ala, Glu, Ile, Leu, Phe,
Pro, Ser, Thr, Val, Nle, and Lys.\\u00a0Values for Met, His and Arg are
obtained only in some samples, depending on concentration and derivatization
efficiency. For \\u03b415N AA values, samples were analyzed in quadruplicate
(n=4) with bracketed lab AA isotopic standard mix for subsequent standard
offset and drift corrections. Corrections based on authentic external
standards were applied using previously published protocols (McCarthy et al.
2013).\\u2028
HPLC/EA-IRMS:
Liquid chromatographic separations were conducted using a Shimadzu HPLC
system (Shimadzu Scientific Instruments, Inc., Columbia, MD, USA) equipped
with: system controller (SCL-10A vp), degasser (DGU-20A5), 2 pumps (LC-20AD),
autosampler (SIL-20A) with an adjustable injection volume of 0.1-100 uL, and
coupled to a Shimadzu automated fraction collector (FRC-20A). An adjustable
flow splitter (Analytical Sales and Services, Inc., Pompton Plains, NJ, USA)
was used inline following the chromatography column to direct ~15% of the flow
to a SEDERE (Alfortville, France) evaporative light scattering detector (ELSD-
LT II, Sedex 85LT) for peak detection and quantitation. A semi-preparative
scale SiELC Primesep A column (10 x 250 mm, 100 angstrom pore size, 5 um
particle size; SiELC Technologies Ltd., Prospect Heights, IL, USA) was used
for amino acid purification. The Primesep A column used here is a reverse-
phase semi-preparative scale column embedded with strong acidic ion-pairing
groups. Such mixed phase columns have been developed specifically for the
separation of charged organic compounds as the acidic sites in the stationary
phase interact with the charged functional groups and provide additional
retention mechanisms to increase chromatographic separation potential. For a
more detailed description of the retention mechanisms of the Primesep A column
see (McCullagh et al. 2006; 2010).\\u2028
Typically, 75-100 uL of sample solution was loaded onto the HPLC instrument. A
binary solvent ramp program was used consisting of 0.1% trifluoroacetic acid
(TFA) in HPLC grade water (aqueous phase) and 0.1% TFA in acetonitrile
(organic phase). The final solvent ramp program used for optimal separation
was as follows: starting with 100% aqueous / 0% organic; increased from 0 to
0.5% organic from 0-30 minutes; increased to 15% organic from 30-35 minutes;
increased to 22.5% from 35-70 minutes; increased to 30% from 70-95 minutes;
held at 30% until 140 minutes. The column was then cleaned and equilibrated by
increasing to 100% and holding for 20 minutes; then decreasing to 50% and
holding for an additional 15 minutes; then decreasing to 0% and holding until
the method ends at 180 minutes. A flow rate ramp is also employed in which the
total flow rate is held at 2.5 mL/minute for 0-30 minutes; increased to 4.5
mL/minute from 30-35 minutes; held at 4.5 mL/min from 35-170 minutes; then
decreased back to 2.5 mL/minute from 170-175 minutes and held until the
completion of the analysis.\\u2028
Purified AAs were collected into 3.5 mL tubes via the automated fraction
collector using time-based collections, and then transferred to 20 mL glass
vials. The solvent was removed under vacuum using a Jouan centrifugal
evaporator (Societe Jouan, Saint-Herblain, France) at a chamber temperature of
60 degrees C. Dry AA residues were then re-dissolved into a small volume (~30
L) of 0.1 N HCl, transferred into pre-ashed tin (Sn) EA capsules, and dried to
completion in a 60 degrees C oven for 12 hours. Capsules were then pressed
into cubes and analyzed for \\u03b415N and \\u03b413C values by EA-IRMS. EA-IRMS
analysis was conducted in the UCSC shared Stable Isotope Laboratory facility
(UCSC-SIL), using an EA-IRMS analyzer dedicated to smaller samples. This
system uses a Carlo Erba CHNS-O EA1108-Elemental Analyzer, interfaced via a
Thermo Finnigan Gasbench II device to a Thermo Finnigan Delta Plus XP isotope
ratio mass spectrometer (Thermo Fisher Scientific), configured after Polissar
et al. (2009). For AAs in this study, we found that \\u2264 100 nmol quantities
of purified AA material could be routinely measured using this instrument,
although as discussed below a standard EA configuration could also equally be
used. Raw EA-IRMS \\u03b415N and \\u03b413C values were corrected for instrument
drift and size effects using AA isotopic standards and standard correction
protocols used by the UCSC-SIL
([http://es.ucsc.edu/~silab](\\\\\"http://es.ucsc.edu/~silab\\\\\")).\\u2028";
String awards_0_award_nid "704683";
String awards_0_award_number "OCE-1131816";
String awards_0_data_url "http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1131816";
String awards_0_funder_name "NSF Division of Ocean Sciences";
String awards_0_funding_acronym "NSF OCE";
String awards_0_funding_source_nid "355";
String awards_0_program_manager "Candace O. Major";
String awards_0_program_manager_nid "51690";
String cdm_data_type "Other";
String comment
"Relative Amino Acid Abundance (mol %)
HPLC Method Glu and Phe 15N values
PI: Matthew McCarthy (UCSC)
Version: 02 August 2017";
String Conventions "COARDS, CF-1.6, ACDD-1.3";
String creator_email "info@bco-dmo.org";
String creator_name "BCO-DMO";
String creator_type "institution";
String creator_url "https://www.bco-dmo.org/";
String data_source "extract_data_as_tsv version 2.3 19 Dec 2019";
String date_created "2017-08-04T17:02:19Z";
String date_modified "2019-08-02T15:50:09Z";
String defaultDataQuery "&time<now";
String doi "10.1575/1912/bco-dmo.712090.1";
String history
"2024-12-03T17:30:38Z (local files)
2024-12-03T17:30:38Z https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_712090.html";
String infoUrl "https://www.bco-dmo.org/dataset/712090";
String institution "BCO-DMO";
String instruments_0_acronym "IR Mass Spec";
String instruments_0_dataset_instrument_description "Isotopic analysis was conducted on a Thermo Trace GC Ultra (Thermo Fisher Scientific, West Palm Beach, FL, USA) coupled via a Thermo GC IsoLink to a ThermoFinnigan DeltaPlus XP isotope ratio monitoring mass spectrometer (Thermo Fisher Scientific).";
String instruments_0_dataset_instrument_nid "712097";
String instruments_0_description "The Isotope-ratio Mass Spectrometer is a particular type of mass spectrometer used to measure the relative abundance of isotopes in a given sample (e.g. VG Prism II Isotope Ratio Mass-Spectrometer).";
String instruments_0_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/LAB16/";
String instruments_0_instrument_name "Isotope-ratio Mass Spectrometer";
String instruments_0_instrument_nid "469";
String instruments_0_supplied_name "ThermoFinnigan DeltaPlus XP isotope ratio monitoring mass spectrometer";
String instruments_1_acronym "HPLC";
String instruments_1_dataset_instrument_description "Liquid chromatographic separations were conducted using a Shimadzu HPLC system (Shimadzu Scientific Instruments, Inc., Columbia, MD, USA) equipped with: system controller (SCL-10A vp), degasser (DGU-20A5), 2 pumps (LC-20AD), autosampler (SIL-20A) with an adjustable injection volume of 0.1-100 μL, and coupled to a Shimadzu automated fraction collector (FRC-20A).";
String instruments_1_dataset_instrument_nid "712098";
String instruments_1_description "A High-performance liquid chromatograph (HPLC) is a type of liquid chromatography used to separate compounds that are dissolved in solution. HPLC instruments consist of a reservoir of the mobile phase, a pump, an injector, a separation column, and a detector. Compounds are separated by high pressure pumping of the sample mixture onto a column packed with microspheres coated with the stationary phase. The different components in the mixture pass through the column at different rates due to differences in their partitioning behavior between the mobile liquid phase and the stationary phase.";
String instruments_1_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/LAB11/";
String instruments_1_instrument_name "High Performance Liquid Chromatograph";
String instruments_1_instrument_nid "506";
String instruments_1_supplied_name "Shimadzu HPLC";
String instruments_2_acronym "Gas Chromatograph";
String instruments_2_dataset_instrument_description "Derivatives (1 L) were injected (injector temp. 250 degrees C constant) onto an Agilent DB-5 column.";
String instruments_2_dataset_instrument_nid "712099";
String instruments_2_description "Instrument separating gases, volatile substances, or substances dissolved in a volatile solvent by transporting an inert gas through a column packed with a sorbent to a detector for assay. (from SeaDataNet, BODC)";
String instruments_2_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/LAB02/";
String instruments_2_instrument_name "Gas Chromatograph";
String instruments_2_instrument_nid "661";
String instruments_2_supplied_name "Agilent DB-5 column";
String instruments_3_acronym "Gas Chromatograph";
String instruments_3_dataset_instrument_description "Isotopic analysis was conducted on a Thermo Trace GC Ultra (Thermo Fisher Scientific, West Palm Beach, FL, USA) coupled via a Thermo GC IsoLink to a ThermoFinnigan DeltaPlus XP isotope ratio monitoring mass spectrometer (Thermo Fisher Scientific).";
String instruments_3_dataset_instrument_nid "712096";
String instruments_3_description "Instrument separating gases, volatile substances, or substances dissolved in a volatile solvent by transporting an inert gas through a column packed with a sorbent to a detector for assay. (from SeaDataNet, BODC)";
String instruments_3_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/LAB02/";
String instruments_3_instrument_name "Gas Chromatograph";
String instruments_3_instrument_nid "661";
String instruments_3_supplied_name "Thermo Trace GC Ultra";
String instruments_4_dataset_instrument_description "EA-IRMS analysis was conducted in the UCSC shared Stable Isotope Laboratory facility (UCSC-SIL), using an EA-IRMS analyzer dedicated to smaller samples. This system uses a Carlo Erba CHNS-O EA1108-Elemental Analyzer, interfaced via a Thermo Finnigan Gasbench II device to a Thermo Finnigan Delta Plus XP isotope ratio mass spectrometer (Thermo Fisher Scientific).";
String instruments_4_dataset_instrument_nid "712095";
String instruments_4_description "Instruments that quantify carbon, nitrogen and sometimes other elements by combusting the sample at very high temperature and assaying the resulting gaseous oxides. Usually used for samples including organic material.";
String instruments_4_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/LAB01/";
String instruments_4_instrument_name "Elemental Analyzer";
String instruments_4_instrument_nid "546339";
String instruments_4_supplied_name "Carlo Erba CHNS-O EA1108-elemental analyzer";
String keywords "acid, amino, amino_acid, bco, bco-dmo, biological, chemical, data, dataset, deviation, dmo, erddap, gcc, hplc, management, mol, mol_pcnt_GCC, mol_pcnt_GCC_stdev, mol_pcnt_hplc, mol_pcnt_hplc_stdev, oceanography, office, pcnt, preliminary, sample, sample_type, standard, standard deviation, stdev, type";
String license "https://www.bco-dmo.org/dataset/712090/license";
String metadata_source "https://www.bco-dmo.org/api/dataset/712090";
String param_mapping "{'712090': {}}";
String parameter_source "https://www.bco-dmo.org/mapserver/dataset/712090/parameters";
String people_0_affiliation "University of California-Santa Cruz";
String people_0_affiliation_acronym "UC Santa Cruz";
String people_0_person_name "Matthew D. McCarthy";
String people_0_person_nid "557245";
String people_0_role "Principal Investigator";
String people_0_role_type "originator";
String people_1_affiliation "Woods Hole Oceanographic Institution";
String people_1_affiliation_acronym "WHOI BCO-DMO";
String people_1_person_name "Shannon Rauch";
String people_1_person_nid "51498";
String people_1_role "BCO-DMO Data Manager";
String people_1_role_type "related";
String project "Amino Acid Sediment 15N";
String projects_0_acronym "Amino Acid Sediment 15N";
String projects_0_description
"The bioavailability of nutrients plays a crucial role in oceanic biological productivity, the carbon cycle, and climate change. The global ocean inventory of nitrogen (N) is determined by the balance of N-fixation (sources) and denitrification (sinks). In this three-year project, a researcher from the University of California, Santa Cruz, will focus on developing compound-specific N isotope (d15N) analysis of amino acids as a new tool for understanding N source and transformation of organic matter in paleo-reservoirs. The offsets in the isotopic ratios of individual amino acid groups may yield information about trophic transfer, heterotrophic microbial reworking, and autotrophic versus heterotrophic sources. By measuring and comparing the bulk and amino acid d15N in size-fractioned samples from plankton tows, sediments traps, and multi-cores in oxic and suboxic depositional environments, the researcher will: (1) Provide a proxy of the d15N of average exported photoautotrophic organic matter; and (2) Provide a new level of detail into sedimentary organic N degradation and preservation.
Broader impacts:
This project will improve understanding of the fundamental underpinnings and behaviors of d15N amino acid patterns and how they behave in contrasting sedimentary environments, while also developing a potential paleoceanographic proxy. Funding will support a graduate student and undergraduate research at the institution. The researcher will also conduct community outreach in the form of a workshop/tutorial on the proxy development.";
String projects_0_end_date "2016-09";
String projects_0_geolocation "California Margin , Santa Barbara Basin , CA current system, Eastern Tropical Pacific";
String projects_0_name "The Use of Nitrogen Isotopes of Amino Acids To Understand Marine Sedimentary 15N Records";
String projects_0_project_nid "704684";
String projects_0_start_date "2011-10";
String publisher_name "Biological and Chemical Oceanographic Data Management Office (BCO-DMO)";
String publisher_type "institution";
String sourceUrl "(local files)";
String standard_name_vocabulary "CF Standard Name Table v55";
String subsetVariables "mol_pcnt_GCC_stdev";
String summary "N isotopic composition of Phenylalanine and Glutamic Acid from a number of organisms, demonstrating new HPLC protocol for precise isotopic measurements.";
String title "[mol percent - HPLC Method Glu and Phe 15N values] - N isotopic composition of Phenylalanine and Glutamic Acid from a number of organisms, demonstrating new HPLC protocol for precise isotopic measurements (The Use of Nitrogen Isotopes of Amino Acids To Understand Marine Sedimentary 15N Records)";
String version "1";
String xml_source "osprey2erddap.update_xml() v1.3";
}
}
Data Access Protocol (DAP) and its
selection constraints.
The URL specifies what you want: the dataset, a description of the graph or the subset of the data, and the file type for the response.
Tabledap request URLs must be in the form
https://coastwatch.pfeg.noaa.gov/erddap/tabledap/datasetID.fileType{?query}
For example,
https://coastwatch.pfeg.noaa.gov/erddap/tabledap/pmelTaoDySst.htmlTable?longitude,latitude,time,station,wmo_platform_code,T_25&time>=2015-05-23T12:00:00Z&time<=2015-05-31T12:00:00Z
Thus, the query is often a comma-separated list of desired variable names,
followed by a collection of
constraints (e.g., variable<value),
each preceded by '&' (which is interpreted as "AND").
For details, see the tabledap Documentation.