Code: METH14V01 Date: July 2, 2017 Author: Robin Chacha STANDARD OPERATING PROCEDURES METHOD FOR ELEMENTAL DETERMINATION ON SOIL PLANT AND FERTILIZER USING PORTABLE X‐RAY FLUORESCENCE TECHNIQUEContactDetails:Telephone:+254(20)7224000/4235/4279/4163Email:icraf‐[email protected]:LaboratoryManager,[email protected]Website:www.http://worldagroforestry.org/research/land‐healthAddressDetails:WorldAgroforestryCentre,Mailing:P.OBox30677‐00100Nairobi,KenyaPhysicaladdress:UnitedNationsAvenueOffLimuruRoad,Gigiri,Nairobi,Kenya
Address Details: World Agroforestry Centre, Mailing: P.O Box 30677‐00100 Nairobi, Kenya Physical address: United Nations Avenue Off Limuru Road, Gigiri, Nairobi, Kenya
STANDARDOPERATINGPROCEDURE Date:July02,2017Code:METH14V01Title:Method for elemental determination on soil, plant and fertilizer using Portable X‐ray Fluorescence technique
STANDARDOPERATINGPROCEDURE Date:July02,2017Code:METH14V01Title:Method for elemental determination on soil, plant and fertilizer using Portable X‐ray Fluorescence technique
Author:RobinChacha
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SCOPEANDAPPLICATIONThis is a Standard Operating Procedure developed and validated by the World Agroforestry
Centre’s Soil‐Plant Spectral Diagnostic Laboratory for element analysis in soil, fertilizer and plant
samples using the Bruker Tracer 5i portable X‐ray Fluorescence (pXRF) Spectrometer. The
protocol gives details of element profiling in milled soil, plants and `material and milled plant
material. X‐ray fluorescence spectrometry is the technology offering detection limits in the low
parts per billion (ppb) range. X‐Ray Fluorescence is the method of choice for fast quantitative and
semi‐quantitative multi‐element trace analysis. The Tracer 5i combines flexibility for various
applications and includes the vacuum technology for lighter elements determination. The TRACER
5i, incorporates a Silicon Drift Detector (SDD) which provides high speed data acquisition and light
element sensitivity.
PRINCIPLEX‐ray fluorescence is the process in which photons emitted from an x‐ray source interacts with
the atoms in the sample causing an electron to be “knocked out” of the inner shell of a given
atom leaving the inner shell to become “unstable”. The empty space left by the electron is filled
with another electron from a higher shell, releasing certain energy (Fluorescence) in the form of
another photon, and is characteristic not only to each element, but also to each shell transition.
X‐ray Fluorescence instruments have a detector that picks up the characteristic fluorescent
energies of elements and identifies using their individual wavelengths. The photons at a higher
energy create data that can be used to quantify trace elements. The new vacuum pump
technology allows quick and easy analysis of non‐uniform materials and concentration analysis
of uniform materials consisting of elements from Sodium to Uranium.
STANDARDOPERATINGPROCEDURE Date:July02,2017Code:METH14V01Title:Method for elemental determination on soil, plant and fertilizer using Portable X‐ray Fluorescence technique
Author:RobinChacha
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ABBREVIATIONSANDDEFINITIONSICRAF – International center for research in agroforestry Pxrf – portable X‐ray fluorescence PDA – Personal data assistant PC – Personal computer AC – Alternating current DC – Direct current UPS – uninterrupted power supply
RELATEDDOCUMENT
Sample reception manual
RELATEDFORMSI. Soil sample preparation and handling
II. Plant sample preparation and handling
SAFETYANDENVIRONMENTRadiation protection: To ensure maximum radiation protection, the Tracer 5 i must be operated
with the control software that are included in delivery. Only these software guarantees the
compliance of the X ray source operation parameters as certified according to anti‐radiation
precautions. Further, safety rules and technical installation and information provided in the user
manual should be adhered to explicitly.
Electrical hazards: Electrical systems must conform to the ICRAF standards. Shock hazards exist
inside the instruments.
REQUIREMENTS Equipment
a. Tracer 5i X‐ray Fluorescence Spectrometer inbuilt PDA (Bruker)
STANDARDOPERATINGPROCEDURE Date:July02,2017Code:METH14V01Title:Method for elemental determination on soil, plant and fertilizer using Portable X‐ray Fluorescence technique
Author:RobinChacha
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b. Retsch RM 200 mill (Retsch, Düsseldorf, Germany)
c. UPS (uninterrupted power supply)
d. Laptop installed with (necessary software)
Accessories
a. Customizable filters and secondary targets to optimize analysis
b. Collimators 3 and 8 mm
c. Ti 25 µm: Al 300 µm
d. ProleneTM , 4μm (0.16 mil) thick X‐ray film (Fluxana)
e. XRF sample caps double open ended cells
f. Bench top stand
g. Spatula
h. X‐ray window
Software
a. Bruker Easycal launcher b. ARTAX 7 Software c. Bruker Remote control d. Bruker instrument tool e. R software version 3.1.1
PROCEDURE
I. Software Installation To be able to operate the Tracer 5i using a PC, install all the software indicated below by
double clicking to install from a Bruker flash stick provided and follow the steps as
prompted by application.
a) Easycal Launcher, which is used for instrument calibration processes and
preparation of run order.
b) Bruker remote control is for remotely controlling the spectrometer and it is the
main interface used when running sample scanning.
c) Bruker instrument tool is for transferring or offloading data, calibration files and
retrieving run orders.
d) R software version 3.1.1 for executing GitHub or local scripts also used for data
management
e) Artax is for data acquisition and spectrum quality check
STANDARDOPERATINGPROCEDURE Date:July02,2017Code:METH14V01Title:Method for elemental determination on soil, plant and fertilizer using Portable X‐ray Fluorescence technique
Author:RobinChacha
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II. Hardware installation a) Install 8mm collimator by opening the latch, carefully lining up the new collimator
with the groove inside the hatch and slide it in until it clicks. Securely close the
hatch and screw it shut.
b) Filter installed at factory
c) Peel off the old window. Avoid any contact with the sensitive detector. Remove
old adhesive with isopropyl alcohol. Peel the white backing from the new window.
Carefully alignment and apply the new window to the nose.
III. Instrument set up
a) Insert the USB connection cable, USB flash drive, connect the AC power supply at the base of the instrument and slide it onto the desktop collapsible stand via the rail at the top. This setup is used for laboratory applications. Place the sample stage onto the instrument nose.
b) Check and ensure that the instrument, PC and power connections are ok and
properly done before powering up.
c) Make all this connections to the UPS this ensure that power supply to the
instrument remains stable throughout.
d) To operate the analyzer using the optional AC power, ensure that the analyzer is
off and the DC battery is removed. Connect the AC Adapter to a 120‐240V AC wall
power outlet with the supplied cord.
e) Connect the power supply to the analyzer then to the laptop.
IV. Powering up
a) Switch the UPS ON
b) Power up the laptop
c) Switch the instrument ON using the white switch button located on the LHS of
the spectrometer. Firmly press the power switch for one second.
d) The instrument takes several moments to initialize. It is ready when BRUKER
‘Initialized – Ready’ is displayed. X‐ray warning lights flash and, after a few
seconds, the touch screen displays.
STANDARDOPERATINGPROCEDURE Date:July02,2017Code:METH14V01Title:Method for elemental determination on soil, plant and fertilizer using Portable X‐ray Fluorescence technique
Author:RobinChacha
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V. Connecting the Laptop to the instrument using Bruker Remote Control (BRC)
a) Select and double click on the BRC icon and select ‘Connect’ from the dropdown options in the ‘File’ menu (As shown in step 1 and 2 below).
b) This will enable the PC software to connect to the Tracer 5i instrument. The
instrument serial number will appear as above. c) Highlight the serial number and click OK. d) A ‘Log in’ window (below) of the Tracer will be displayed on the PC. To continue,
use the mouse to remotely operate the Tracer 5i.
STANDARDOPERATINGPROCEDURE Date:July02,2017Code:METH14V01Title:Method for elemental determination on soil, plant and fertilizer using Portable X‐ray Fluorescence technique
Author:RobinChacha
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VI. To log in
a) After powering on the analyzer, tap Login and the login screen is displayed.
b) Use the mouse to enter the default password 54321 and the login ID field
reflects the changes.
c) Once the password is successfully entered, click ‘OK’. An X‐ray radiation warning
(below) is displayed.
STANDARDOPERATINGPROCEDURE Date:July02,2017Code:METH14V01Title:Method for elemental determination on soil, plant and fertilizer using Portable X‐ray Fluorescence technique
Author:RobinChacha
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d) To continue, press down and release the trigger on the instrument e) A status window will appear showing the current configurations of the
instrument i.e. Application, Mode, Filter and Collimator (Spot). Press OK to proceed.
f) The ‘Ready to Test screen’ will be displayed showing information in the status bar
and provides access to menu trees from which all analyzer functions can be
performed. A read to test window is displayed after the above process.
Note that all the applications and methods are developed during calibration and they should not
be tampered with during scanning or any other time unless during the process of calibrations.
STANDARDOPERATINGPROCEDURE Date:July02,2017Code:METH14V01Title:Method for elemental determination on soil, plant and fertilizer using Portable X‐ray Fluorescence technique
Author:RobinChacha
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VII. Selecting a method
The instrument analyzes a sample using a specifically selected calibration or method. The
choice of method can be specified by the user from the saved calibrated methods in the
Applications.
a) On the Ready to Test screen, click APPLICATION.
b) Select the desired calibrated application desired by highlighting from the options.
Each application selected integrates its set parameters. i.e.
Illumination Fertilizer General
Plant Light Plant Trace Soil Light Soil Trace
Voltage (keV) 35 10 35 10 30
Current (amp) 30 70 35 70 50
Collimator 8mm 8mm 8mm 8mm 8mm
Manual filter Blank Blank Blank Blank Blank
Time (S) 30 90 90 90 60
c) Select OK. The ‘Ready to Test’ screen will reappear with the name of the
selected method displayed on the Application and Method icons.
d) Repeat steps 2 ‐ 4 as necessary when you need to change the application to be
used.
e) Click on the SETTINGS icon. A default settings will be displayed. To be able to
uncheck the Default Settings box, and to set the measurement time for the
selected method. Also activate the BEEP alert for completion of measurement
(As below).
STANDARDOPERATINGPROCEDURE Date:July02,2017Code:METH14V01Title:Method for elemental determination on soil, plant and fertilizer using Portable X‐ray Fluorescence technique
Author:RobinChacha
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VIII. Sample Preparation
Cup assembly
a) Place a thin x‐ray film (4μm (0.16 mil) prolene) on top of a sample cup.
b) Position Snap‐on ring on thin‐film.
c) Push Snap‐On ring down to secure the film. The flange inside the collar faces
down and snaps into the indented ring of the cup.
d) Inspect the installed film window for continuity and smooth appearance.
IX. Sample milling
a) Soil samples are dried and sieved through 2‐mm sieves. Samples are milled
further to between 20‐ 75 µm using Restch RM200 automated milling machine.
About 5g homogenous specimen of the sample is loaded into special XRF cups
prepared with 4μm (0.16 mil) prolene XRF film free from irregular surfaces and
contamination. The cup should be half full with sample.
b) Plant material is oven‐dried at 50° C and then ground to pass a 0.5mm sieve using
a Wiley mill. About 5g homogenous specimen of the sample is loaded into special
XRF cups prepared with 4μm (0.16 mil) prolene XRF film free from irregular
surfaces and contamination. The cup should be half full with sample.
X. Sample loading
a) Fill sample cup carefully with at least five grams (min. 5mm / 1/5” layer) of the
prepared sample, avoiding voids or uneven layers. Cap the cup and label
carefully.
STANDARDOPERATINGPROCEDURE Date:July02,2017Code:METH14V01Title:Method for elemental determination on soil, plant and fertilizer using Portable X‐ray Fluorescence technique
Author:RobinChacha
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b) Place the loaded sample cup onto the sample table to cover to cover the entire
examination window.
c) Cover the sample table with the Safety Shield Accessory.
XI. BENCHTOP ANALYSIS
Edit Info Button
Before a measurement is taken, an assay can be named and described in the Edit Info screen.
a) From the Ready to Test screen, select the Edit Info icon. The Sample ID Fields
screen will be displayed.
b) Double click on the ID fields to fill in the sample information. A New Value
window will appear.
c) Clear the existing sample identification information and label a new assay in the
new value field.
d) Select OK to save changes to the Sample ID Fields screen and also the keyboard will be removed.
STANDARDOPERATINGPROCEDURE Date:July02,2017Code:METH14V01Title:Method for elemental determination on soil, plant and fertilizer using Portable X‐ray Fluorescence technique
Author:RobinChacha
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XII. Data management Data Acquisition Once the sample ID have been saved click Trigger Release on the ribbon or press F6 on the keyboard to start the sample measurement.
STANDARDOPERATINGPROCEDURE Date:July02,2017Code:METH14V01Title:Method for elemental determination on soil, plant and fertilizer using Portable X‐ray Fluorescence technique
Author:RobinChacha
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If a USB Flash data stick was installed in the Flash drive during instrument assembly, all sample
information and data acquired will be automatically saved in it as destination location. This
information is saved as a Results as table in batch .csv file and sample individual spectra as .pdz
files.
To optimize analyzer performance and reduce initialization time, data should be periodically removed from the installed USB flash drive.
XIII. Data Retrieval by Bruker Instrument Tool a) Launch the Bruker Instrument Tool (BIT) by double clicking on the icon.
b) Click on Device and select Connect on the drop down options. A connection
window will appear with the serial number of the Tracer 5i instrument attached
to the PC.
c) Highlight the serial number and click on connect icon. A Bruker Instrument Tool
will appear containing various folders.
d) Select and click the USB Drive folder (1).
e) Select and click on the Data sub folder that appear on the options therein (2)
f) Select and click the Result file (.csv) to open the spreadsheet (3).
STANDARDOPERATINGPROCEDURE Date:July02,2017Code:METH14V01Title:Method for elemental determination on soil, plant and fertilizer using Portable X‐ray Fluorescence technique
Author:RobinChacha
15 | p X R F S O P
STANDARDOPERATINGPROCEDURE Date:July02,2017Code:METH14V01Title:Method for elemental determination on soil, plant and fertilizer using Portable X‐ray Fluorescence technique
Author:RobinChacha
16 | p X R F S O P
To maintain a simple folder management system for all the acquired spectra, create a folder at
the root of the hard disk of the computer that operates the Tracer 5I instrument and name it Raw
Spectra. Create three subfolders within the raw spectra folder and label them as: 1) Soil 2) Plants;
3) Fertilizer to represent the different materials that are scanned.
QUALITYCONTROL Internal check standards Include internal check samples of known elemental concentrations and they provide
information about the precision and stability of a measurement. The XRF laboratory has
a series of samples of both plant and soil materials, which should be included in each
batch of samples.
For every batch of plant analysis include beans standard, cellulose and NIST leave
standard 1575a.
For every batch of soil analysis include Katumani soil standard and white sand.
For every batch of fertilizer analysis include organic fertilizer and Mavuno planting
fertilizer standards
Artax software is used for the spectrum quality check.
STANDARDOPERATINGPROCEDURE Date:July02,2017Code:METH14V01Title:Method for elemental determination on soil, plant and fertilizer using Portable X‐ray Fluorescence technique
Author:RobinChacha
17 | p X R F S O P
REFERENCES
Bruker tracer 5i user manual
STANDARDOPERATINGPROCEDURE Date:July02,2017Code:METH14V01Title:Method for elemental determination on soil, plant and fertilizer using Portable X‐ray Fluorescence technique
Author:RobinChacha
18 | p X R F S O P
ANNEX Work Flow
Milling
Cup assembly
Loading
Pxrf Analysis
Data Acquisition
Data Filtering
Database
Portable X-Ray FluorescenceObjective:
To achieve an economical detailed rapid screening analysis of elemental composition of plants, soils and fertilizers samples
Plants, soils or fertilizers are milled <75µm
The cups are assembled using 4µm X-ray film
Put 3-5g of soil/plant/fertilizer into the assembled XRF cups
Place the loaded cup on pXRF sample table
The analysis results are acquired using BIT software
The acquired data is filtered using R, Knime and Shinny app
