Comments on Methods, QA/QC and Formats for Bottle Salinities and Nutrient Data
Collected During the 2002 SBI Mooring Cruise on the Polar Star (AWS-02)
Dr. Jim Swift, Dr. Lou Codispoti, Susan Becker, Aaron Morello, Kristin Sanborn
		
15 July to 13 August 2002
Dutch Harbor, Alaska to Barrow, Alaska

Description of operations and sampling equipment are provided in Dr. Robert
 Pickart's AWS-02 Phase I, SBI, July 15 - August 13, 2002 CTD Data Summary.

Salinity
There were 506 salinity samples analyzed.

Equipment and Techniques
Salinity samples were drawn into 200 ml high alumina borosilicate bottles, which
 were rinsed three times with sample prior to filling. The bottles were sealed
 with custom-made plastic insert thimbles and Nalgene screw caps This container
 provides very low container dissolution and sample evaporation.

A Guildline Autosal 8400A #57-396, standardized with IAPSO Standard Seawater
 (SSW) batch P-140, was used to measure the salinities. Prior to the analyses,
 the samples were stored to permit equilibration to laboratory temperature,
 usually 8-20 hours.  The salinometer was modified by Shipboard Technical
 Support/Oceanographic Data Facility (STS/ODF) and contained an interface for
 computer-aided measurement. The salinometer was standardized with a fresh vial
 of standard seawater at the beginning and end of the run.  The SSW vial at the
 end of the run was used as an unknown to check for drift. The salinometer cell
 was flushed until two successive readings met software criteria for
 consistency; these were then averaged for a final result. The estimated
 accuracy of bottle salinities run at sea is usually better than 0.002 PSU
 relative to the particular standard seawater batch used.

Laboratory Temperature
The temperature stability in the salinometer laboratory was poor.

Nutrients
There were 501 nutrient samples analyzed.

Equipment and Techniques
Nutrient analyses (phosphate, silicate, nitrate+nitrite,  and nitrite) were
 performed on an ODF-modified 4-channel Technicon AutoAnalyzer II, generally
 within a few hours after sample collection.  Occasionally samples were
 refrigerated for longer periods. The analog outputs from each of the four
 channels were digitized and logged automatically by computer (PC) at 2-second
 intervals.  Protocols, in general, followed procedures outlined for the World
 Ocean Circulation Experiment by Gordon et al. (1993). These protocols allow for
 standardizing using techniques that require strict linearity or for techniques
 that can deal with any non-linearity in calibration curves. We use the latter
 approach and correct for non-linearity using polynomial equations when
 appropriate. We also do not correct for "carryover", but instead minimize this
 source by appropriate design of the flow characteristics of our system and by
 running samples in order of depth whenever possible. 

Silicate was analyzed using the technique of Armstrong et al., (Armstrong,
 1967). The sample was passed through a 15mm flowcell and the absorbance
 measured at 660nm. A modification of the Armstrong et al. (Armstrong 1967)
 procedure was used for the analysis of nitrate and nitrite. For the nitrate
 plus nitrite analysis, the seawater sample was passed through a cadmium
 reduction column where nitrate was quantitatively reduced to nitrite. The
 stream was then passed through a 15mm flowcell and the absorbance measured at
 540nm.  The same technique was employed for nitrite analysis, except that the
 cadmium column was bypassed, and a 50mm flowcell was used for measurement.

Phosphate was analyzed using a modification of the Bernhardt and Wilhelms
 (Bernhardt 1967.) technique. The reaction product was heated to ~55C to
 enhance color development, then passed through a 50mm flowcell and the
 absorbance measured at 820m.

Nutrient Standards
The silicate (Na2SiF6) and nitrite (NaNO2) primary standards were obtained from
 Johnson Matthey Company's Aesar Division and the supplier reported purities of
  >98% and 97% respectively.  Primary standards for nitrate (KNO3) and phosphate
 (KH2PO4) were obtained from Fisher Scientific and the supplier reported
 purities of 99.999%.

Sampling and Data Processing
Nutrient samples were drawn into 45 ml polypropylene, screw-capped "oak-ridge
 type" centrifuge tubes. The tubes were cleaned with 10% HCl and rinsed with
 sample three times before filling. Standardizations were performed at the
 beginning and end of each group of analyses (typically 5-40 samples) with an
 intermediate concentration mixed nutrient standard prepared prior to each run
 from a secondary standard in a low-nutrient seawater matrix. The secondary
 standards were prepared aboard ship by dilution from primary standard
 solutions.  Dry standards were pre-weighed at the laboratory at ODF, and
 transported to the vessel for dilution to the primary standard. Sets of 6-7
 different standard concentrations covering the range of sample concentrations
 were analyzed periodically to determine the deviation from linearity, if any,
 as a function of concentration for each nutrient analysis.  A correction for
 non-linearity was applied to the final nutrient concentrations when necessary. 

There were some errors in the original calculations preformed on the ship.  The
 raw data files were reprocessed at ODF after the cruise.  The original data
 files were processed to produce other files containing response factors,
 baseline values, and absorbances. Concentrations were then calculated and any
 non-linear corrections applied. Computer-produced absorbance readings were
 checked for accuracy against values taken from a strip chart recording, which
 is produced simultaneously with the computer. 

Nutrients, when reported in micromoles per kilogram, were converted from
 micromoles per liter by dividing by sample density calculated at 1 atm pressure
 (0 db), in situ salinity, and an assumed laboratory temperature of 25
degrees C.

Data Quality Notes

General Comments: 
The initial nutrient (nitrate, nitrite, phosphate and silicate) data reported
 from this cruise contained significant errors. This version (July 2003) of the
 data is free from major errors, but should not be considered final.  Users are
 encouraged to report any suspicious values to Lou Codispoti
 (codispoti@hpl.umces.edu) to assist with final QA/QC that will also include a
 comprehensive comparison of these data with companion data collected on the
 2002 SBI Process Cruises conducted from the USCGC Healy (HLY 02-01, HLY 02-03).
 Users should also be aware that as noted in the initial cruise report, bottle
 flushing was a problem during this cruise, and apparent depth offsets between
 bottle and CTD salinities could, at times, be on the order of 10 m. The user
 should also be aware that rosette tripping problems also arose during this
 cruise. These problems are discussed in Dr. Pickart's CTD data summary report
 for this cruise.

The present status of these nutrient data is as follows:

1) The entire original nutrient data suite were thoroughly re-examined, edited
 and recalculated by ODF personnel (primarily Susan Becker).  This editing
 process included a major revision of the original silicate concentrations due
 to an initial calculation error.

2) Upon completion of this re-calculation and re-editing of the data, Lou
 Codispoti examined the corrected data and with the help of Susan Becker, made
 some additional corrections. His examination consisted of reviewing the cruise
 notes written by the onboard nutrient analyst, a review and edit of the strip
 chart peaks, examination of the calibration factors and index of refraction
 corrections, a review of the tabular data, comparison of the tabular nutrient
 data from this cruise with data collected during the second SBI 2002 process
 cruise (HLY 02-03), and calculation of the parameter N* (Gruber and Sarmiento,
 1997).  A listing of the changes to the data arising from SB and LC's editing
 is given later in this report.

3) We believe that this version of the Polar Star nutrient data per se is
 generally free of major errors and should prove useful to SBI PIs.  For
 example, deep (~750 db and deeper) nutrient values compare reasonably well with
 data collected on the Healy, the range of nutrient values seems reasonable, and
 calculations of the parameter N* (Gruber and Sarmiento, 1997) appeared to yield
 reasonable results.  These data are not, however, of the quality of the
 nutrient data collected from the Healy during the SBI 2002 process cruises. 
 In part, this is because, during the Polar Star cruise, bottle flushing was a
 problem whereas we took special precautions on the Healy to promote bottle
 flushing.  Given the high degree of hydrographic and ecosystem stratification
 that can occur in the upper layers of Arctic waters during the seasons when ice
 is melting, the bottle flushing issue could prove to be significant in some
 cases. In addition, manpower limitations during the Polar Star cruise did not
 allow for the same level of shipboard QA/QC, and it is possible that some minor
 systematic errors still exist in the Polar Star data.

Specific corrections/problems:
The nitrite refractive index correction of 0.018 was used for all stations.

STATION   BOTTLE    COMMENTS
003        04      (run id = 00101) all data questionable and not included.

016     3-6 and 9  (run ids = 00301 and 00401) nitrite lost.  Samples were rerun
                   and all the rerun data looked ok.  The rerun data was
                   reported for all nutrients.

015        02      (run id = 00301) nitrate value looks low but peak height was
                   low.

020     03-06      Shipboard processors assigned the bottle salinities
                   incorrectly. Suspect that the surface bottle, 06, was not
                   drawn and 03 was drawn. Corrected assignment for 03-06.

027                (run ids =00901 and 01001) there was a problem with nitrite
                   in the original run so all samples were re-run.  The
                   phosphate, silicate and nitrite plus nitrate data compared
                   reasonable well with the first run.  Data from the second 
                   run was reported for all nutrients.  

028                There was some confusion because there was a missing nutrient
                   level.  According to the run sheet the surface nutrient was
                   missing.  The data did not agree with this and it was assumed
                   the missing level was the deep sample.  All the values were
                   shifted up one level.

046        06      (run id = 04201) nitrite value lost, nitrate value reported
                   is nitrate plus nitrite.

049-052            (run id = 04901) the nitrate response factor changed over the
                   course of the run but everything else looks ok.  The data are
                   somewhat questionable.

053    03 and 04   bottle salt value needs checking. Appears to have been
                   switched with bottle 03. Values have been corrected. 

063        08      (run id = 06201) phosphate value lost.

067        04      (run id = 06601) nitrite lost and nitrate is actually nitrate
                   plus nitrite.

068    03 and 04   (run id = 06601) nitrite lost and nitrate is actually nitrate
                   plus nitrite.

Data Distribution 
The data discussed here can be obtained through the JOSS web-site,
 www.JOSS.ucar.edu/sbi. The data are reported using the WHP-Exchange (WOCE
 Hydrographic Program) format and the quality coding follows those outlined by
 the WOCE program (Joyce, 1994). In addition, the format can be obtained through
 the WOCE Hydrographic Program web-site, www.WHPO.ucsd.edu.

Format description for WHP-exchange bottle data (_hy1.csv)
General rules for WHP-exchange_hy1.csv data files:
1. Each line must end with a carriage return or end-of-line.
2. With the exception of the file type line, lines starting with a "#"
 character, or including and following a line which reads "END_DATA", each line
 in the file must have exactly the same number of commas as do all other lines
 in that file.
3. The name of a quality flag always begins with the name of the parameter with
 which it is associated, followed by an underscore character, followed by
 "FLAG", followed by an underscore, and then followed by an alphanumeric
 character, W. 
4. The "missing value" for a data value is always defined as -999, but written
 in the decimal place format of the parameter in question. For example, a
 missing salinity would be written -999.0000 or a missing phosphate -999.00
.
Description of 32PZAWS02.1_hy1.csv file layout.
1st line
File type, here BOTTLE, followed by a comma and a DATE_TIME stamp  
YYYYMMDDdivINSwho
 


YYYY    4 digit year 
MM      2 digit month 
DD      2 digit day 
div     division of Institution 
INS     Institution name 
who     initials of responsible person 
example:   20000711WHPSIOSCD 
 
#lines
A file may include 0-N optional lines, typically at the start of a data file,
 but after the file type line, each beginning with a "#" character and each
 ending with carriage return or end-of-line. Information relevant to file
 change/update history of the file itself may be included here, for example.

2nd line
Column headings. 

3rd line
Units. 

data lines
As many data lines may be included in a single file as is convenient for the
 user, with the proviso that the number and order of parameters, parameter
 order, headings, units, and commas remain absolutely consistent throughout a
 single file. 

END_DATA  
The line after the last data line must read END_DATA.
other lines
Users may include any information they wish in 0-N optional lines at the end of
 a data file, after the END_DATA line.

Header columns
Parameter

Format  
Description notes
EXPOCODE

A11
The expedition code, assigned by the user. 
SECT

A4
For WOCE data the WHP section identifier. Optional.
STNNBR

A6
The originator's station number. 
CASTNO

I3
The originator's cast number. 
BTLNBR

A7
The bottle identification number as described in WHP Office Report 90-1, WOCE
 Report No. 67/91, "Requirements for WHP Data Reporting.

BTLNBR_FLAG_W 

I1
BTLNBR quality flag.
DATE

I8
Cast date in YYYYMMDD integer format. 

LATITUDE

F8.4
Latitude as SDD.dddd where "S" is sign (blank or missing is positive), DD are
 degrees, and dddd are decimal degrees. Sign is positive in northern hemisphere,
 negative in southern hemisphere
LONGITUDE   

F9.4
Longitude as SDDD.dddd where "S" is sign (blank or missing is positive), DDD are
 degrees, and dddd are decimal degrees. Sign is positive for "east" longitude,
 negative for "west" longitude

DEPTH

I5
Reported depth to bottom. Preferred units are "meters" and should be specified
 in Line 2. In general, corrected depths are preferred to uncorrected depths.
 Documentation accompanying data includes notes on methodology of correction.
 Optional.




Parameter names, units, and comments.
Parameter 
Format  
Suggested Units  
Comments
CTDPRS
F9.1
decibars
CTD pressure
SSMPLE
A5

Cast number*100+BTLNBR Optional. This is tabulated for a specific program, JOA
CTDTMP
F9.3
degrees C (ITS-90) 
CTD temperature
CTDTMP_FLAG_W 
I1

CTDTMP quality flag
CTDSAL
F9.3

CTD salinity 
CTDSAL_FLAG_W 
I1

CTDSAL quality flag
SALNTY
F9.4

bottle salinity
SALNTY_FLAG_W
I1

SALNTY quality flag
CTDCOND
F9.3
milliSiemens/centimeter
CTD Conductivity
SILCAT
F9.1
micromoles/kilogram
SILICATE 
SILCAT_FLAG_W
I1

SILCAT quality flag
SILCAT
F9.1
micromoles/liter
SILCAT
SILCAT_FLAG_W
I1

SILCAT quality flag
NITRAT
F9.2
micromoles/kilogram
NITRATE 
NITRAT_FLAG_W
I1

NITRAT quality flag
NITRAT
F9.2
micromoles/liter
NITRATE
NITRAT_FLAG_W
I1

NITRAT quality flag
NITRIT
F9.2
micromoles/kilogram
NITRITE
NITRIT_FLAG_W
I1

NITRIT quality flag
NITRIT
F9.2
micromoles/liter
NITRITE
NITRIT_FLAG_W
I1

NITRIT quality flag
PHSPHT
F9.2
micromoles/kilogram
PHOSPHATE
PHSPHT_FLAG_W
I1

PHSPHT quality flag
PHSPHT
F9.2
micromoles/liter
PHOSPHATE
PHSPHT_FLAG_W
I1

PHSPHT quality flag
Quality Codes
The WHP quality codes for the water bottle itself are: 
1          
Bottle information unavailable.
2
No problems noted.
3
Leaking.
4
Did not trip correctly.
5
Not reported.
9
Samples not drawn from this bottle.
The WHP bottle parameter data quality codes are: 
1          
Sample for this measurement was drawn from water bottle but analysis not
 received. Should be received at a later date. 
2
Acceptable measurement.
3
Questionable measurement.
4
Bad measurement.
5
Not reported.
9
Sample not drawn for this measurement from this bottle.
References
Armstrong, F. A. J., Stearns, C. R., and Strickland, D. H., "The measurement of
 upwelling and subsequent biological processes by means of the Technicon
 Autoanalyzer and associated equipment," Deep-Sea Research, 14, pp. 381-389,
 (1967).
Bernhardt, Wilhelms A., "The continuous determination of low level iron, soluble
 phosphate and total phosphate with the AutoAnalyzer", Technicon Symposia, I, 
 pp. 385-389 (1967).
Gordon, L.I., Jennings, J.C., Ross, A.A. and J.M. Krest, "A Suggested Protocol
 for Continuous Flow Automated Analysis of Seawater Nutrients in the WOCE
 Hydrographic Program and the Joint Global Ocean Fluxes Study," WOCE
 Hydrographic Programs Office, Methods Manual WHPO 91-1 (1993). 
Gruber, N. and J. L. Sarmiento. (1997). Global patterns of marine nitrogen
 fixation and denitrification.  Global Biogeochem. Cycles. 11:235-266.
Joyce, T. ed., and Corry, C. ed., "Requirements for WOCE Hydrographic Programme
 Data Reporting," Report WHPO 90-1, WOCE Report No. 67/91 3.1, pp. 52-55, WOCE
 Hydrographic Programme Office, Woods Hole, MA, USA (May 1994, Rev. 2),
 UNPUBLISHED MANUSCRIPT 
