STANDARD OPERATING PROCEDURES
Contents
1. a Soil Plant Spectral World Diagnostics Lab Centre Code METHO8V01 Date July 30 2014 Author Dickens Ateku STANDARD OPERATING PROCEDURES INFRARED DIFFUSE REFLECTANCE SPECTROSCOPY METHOD FOR ANALYSING SOILS AND PLANTS USING BRUKER TENSOR 27 HTS XT SPECTROMETER Contact Details Telephone 254 20 7224000 4235 4279 4163 Email icraf speclab cgiar org Laboratory Manager Soilspec_ Lab Manager cgiar org Website www http worldagroforestry org research land health Address Details World Agroforestry Centre Mailing P O Box 30677 00100 Nairobi Kenya Physical address United Nations Avenue Off Limuru Road Gigiri Nairobi Kenya Agroforest Centre Soil Plant Spectral y Diagnostics Lab STANDARD OPERATING PROCEDURE Code METH 08V01 Title Method for analysing samples for spectral characteristics in Mid IR range using HTS XT METHOD DOCUMENT CONTROL LOG Name and position Signature Author s Dickens Ateku Alubaka_ Senior signature for completeness and Laboratory Technician correctness of document Verifiers Dickens Ateku Alubaka_ Senior signature for completeness and Laboratory Technician correctness of document Beatrice Mwangi Laboratory signature for completeness and Technician correctness of document Authorizer Elvis Weullow Deputy signature for completeness and Laboratory Manager correctness2. Recording sheet SAFETY AND ENVIRONMENT Electrical hazards Electrical systems must conform to the ICRAF standards No shock hazards exist inside the instruments Do not try to repair the faulty electrical system but call for assistance from an authorized service representative or an individual with training in electronic repair The instruments require a third wire protective grounding conductor Three to two wire adapters are unsafe for these instruments Dewar vessel one 25 liters Dewar vessel for carrying liquid nitrogen Use gloves when topping up liquid nitrogen on the instrument REQUIREMENTS Supplies a Liquid Nitrogen b 70 Ethanol for cleaning the Aluminium sample holding cups c Ear buds for cleaning the Aluminium sample holding cups d Tissues Equipment a The High Throughput Screening Accessory HTS XT b Pike Miracle Diamond Attenuated Total Reflectance Accessory ATR c Transmission Accessory using KBr pellets or liquid sample cells d Retsch motor grinder RM 200 Materials a Aluminium sample holding plates b Gold plate c Micro spatula d Non fluffy cloth PROCEDURE Soil Sample preparation and loading 4 HTS XT SOP Agroforest Centre Qa Code METH 08V01 y Diagnostics Lab Title Method for analysing samples for spectral Author Dickens Ateku STANDARD OPERATING PROCEDURE Date July 30 2014 characteristics in Mid IR range using
3. Tensor 27 HTS XT Instrument calibration standards These are standards used for all analysis in the ICRAF Soil Plant diagnostic laboratory Heavy black cracking clay soils HBCCS Katumani and MUA standards are run every day in the morning before you start any analysis and every time you start on a new site White sand a commercial Standard which is run every day in the morning before you start any analysis and every time you start on a new site 3 Quality Control fact sheet PROCESS DESCRIPTION Background Measurement The instrument is set in a way that it performs background measurement before scanning each well The measurement normally increases the signal to noise ratio of the spectrum produced improves the quality of the spectra Measurement of the selected soil standards The standards used in ICRAF infrared laboratory are HBCCS Katumani MUA and White Sand The measured spectra are used to monitor the performance of the instrument Check on the quality of the spectrum measured Always monitor the instrument moisture Ensure that the spectrum measured does not have any noise due to moisture and carbon dioxide The moisture noise peaks are expected at around 3600cm and 1600cm wave numbers while the carbon dioxide peak is expected at around 2400cm wave numbers 10 HTS XT SOP pia Agroforest Centre id Soil Plant Spectral Diagnostics Lab STANDARD OPERA
4. HTS XT The loaded soil samples should be air dried sieved through a 2mm sieve subsampled using the coning and quartering method and grinded to less than 0 5mm fine powder particle size between 20 53 um using RM 200 Restch motor grinder Refer to the HTS XT Spectrometer Technical Manual a Collect about 10 g subsample from air dried 2 mm sieved soils and minerals that are processed through SOP Use coning and quartering method in case of large samples Refer to the Tensor 27 SOP page 13 Dry the 10 g subsample in an oven at 40 C for 24 hours Grind the sample using RM 200 Retsch motor grinder to a fine powder to attain a particle size between 20 53 um Load the sample into aluminum sample plate by filling it with the fine ground soil It takes about 1 2 g depending on the type of soil Refer to the Tensor 27 SOP page 13 and 14 Prepare a data sheet indicating sample IDs and sample position in the plate Ensure that you enter the sample ID immediately after filling the wells of the plate Plant Sample preparation and loading The loaded plant samples should be milled to pass through 0 5mm sieve using willey mill machine Refer to the Sample Reception and Preparation SOP a Load the plant sample into aluminum sample plate by filling it with the fine milled plant It takes about 1 2 g depending on the type of plant Refer to the Tensor 27 SOP Prepare a data sheet indicating sample IDs and sample position in
5. TING PROCEDURE Code METH 08V01 Date July 30 2014 Title Method for analysing samples for spectral characteristics in Mid IR range using HTS XT Author Dickens Ateku 11 HTS XT SOP
6. and Validation c Create a folder that identifies the batch of soils being analyzed on the computer connected to the instrument d All spectra recorded on test samples should be saved in a separate folder For example C ICRAF RAW SOTUBA SITE SOILS for all Sotuba soils e Create a template of the number of plates you want to run and save it in a folder with a name for easy tracking Refer to the HTS XT manual on how to create the template f Place the standard gold reference plate inside the sample plate drawer and do a position test by clicking on the Opus Validation menu and select Position test Click ok to run it and remove the plate after finishing g Place an empty aluminum plate inside the sample plate drawer and do a signal check test and remove it after finishing Amplitude of between 16 000 and 30 000 is good h For spectral measurements aluminum plates whose micro titer wells are full of the fine ground soil are loaded into the sampling drawer of HTS XT manually or 6 HTS XT SOP Agroforest Centre Qa Code METH 08V01 y Diagnostics Lab Title Method for analysing samples for spectral Author Dickens Ateku STANDARD OPERATING PROCEDURE Date July 30 2014 characteristics in Mid IR range using HTS XT automatically using the robotic arm After loading the template you had created the robotic arm sequentially and automatically picks a loaded aluminum micro titer plate in
7. of document Distribution of valid copies of this document G 149 Infrared Spectroscopy Laboratory Revise before date Historical data dates of previous issues Date retrieval to be filled in once the document has become obsolete and is archived Changes in this version compared to previous version Describe what has changed in the text of this version compared to the previous version SCOPE AND APPLICATION Date July 30 2014 Author Dickens Ateku This is a World Agroforestry Centre s Soil Plant Spectral Diagnostic Laboratory SOP for analysis of soils and plants using near and mid IR spectra recorded with Tensor 27 HTS XT module The technique involves shinning of near or mid infrared light on the samples and capturing of the reflected light in to raw file known as the interferogram The spectrum recorded bears the qualitative and quantitative chemical aspect of the sample for further use with various data processing systems This SOP is applicable to those doing soil and plant analysis on infrared 2 HTS XT SOP Agrotorest Centre Qoae Code METH 08V01 y Diagnostics Lab STANDARD OPERATING PROCEDURE Date July 30 2014 Title Method for analysing samples for spectral Author Dickens Ateku characteristics in Mid IR range using HTS XT laboratory using Tensor 27 HTS XT spectrometer The instrument uses the potassium b
8. romide KBr beam splitter and the Bruker s OPUS software PRINCIPLE The Tensor 27 HTS XT Module is designed for measurements in diffuse reflection The optics of a diffuse reflection accessory is designed in such a way that detection of diffusely reflected light is optimized and the detection of specular reflected light is minimized A DRIFT is an analyzing technique in FT IR spectroscopy that makes use of the phenomenon of diffuse reflection The key advantage of these techniques is that it enables analysis of strongly scattering and absorbing samples unlike transmission measurements and equally has high signal intensity ABBREVIATIONS AND DEFINITIONS DRIFT Diffuse Reflectance Fourier Transform spectroscopy OPUS Bruker s Optical User Software SOP standard operating procedures NIR Near infra red MIR Mid infra red STD standard soil sample FTIR Fourier Transform Infrared Spectroscopy RELATED DOCUMENT Tensor 27 Technical manual HTS XT Technical manual Validation and Maintenance Technical Manual Sample Reception and Preparation SOP MIR Workflow Infrared Health and Safety SOP RELATED FORMS Login form 3 HTS XT SOP Agroforest Centre STANDARD OPERATING PROCEDURE Date July 30 2014 Qa Code METH 08V01 y Diagnostics Lab Title Method for analysing samples for spectral characteristics in Mid IR range using HTS XT Author Dickens Ateku
9. t acceptable limits 7 HTS XT SOP STANDARD OPERATING PROCEDURE Date July 30 2014 Soil Plant Spectral Code METH 08V01 Diagnostics Lab Agroforestry Title Method for analysing samples for spectral Author Dickens Ateku characteristics in Mid IR range using HTS XT If any errors are found return data for repeat analysis REFERENCES TENSOR 27 User s Manual 1 Edition BRUKER OPTICS GmbH 2002 page 1 page 44 HTS XT User Manual ist Updated Edition 121872 BRUKER OPTICS GmbH June 2005 page 1 page 42 Bruker Tensor 27 FT IR amp OPUS Data Collection Program V 1 1 BRUKER OPTICS GmbH page 1 page 47 Twister User s Guide Zymark Corporation page 1 page 80 ANNEX 1 Work Flow 8 HTS XT SOP STANDARD OPERATING PROCEDURE Code METH 08V01 Date July 30 2014 aaa Soil Plant Spectral World Diagnostics Lab Agroforest Centre Title Method for analysing samples for spectral characteristics in Mid IR range using HTS XT Author Dickens Ateku Infra red Laboratory Workflow TENSOR amp ALPHA This laboratory uses infra red rays to analyze samples Objective To provide fast high through put cheap and accurate analysis optimization of analysis LEGEND Preparation Action point Decision point Tape notes l 7 Stored data p Process route E There are two ALPHA FTIR ins
10. the plate Ensure that you enter the sample ID immediately after filling the wells of the plate Recording sample spectra using the OPUS a Power up the instrument and log into the OPUS software Technician must get himself herself familiarized with operating instructions of the instrument by going 5 HTS XT SOP STANDARD OPERATING PROCEDURE Date July 30 2014 Qa Code METH 08V01 y Diagnostics Lab Title Method for analysing samples for spectral Author Dickens Ateku characteristics in Mid IR range using HTS XT Agroforest Centre through the ICRAF soil and plant spectral diagnostic laboratory adopted version of user manual for Tensor 27 HTS XT Module b Select the advance data collection option in OPUS and load the method as per the SOP Refer to the Tensor 27 HTS XT manual pages 17 to 32 depending on the experiment you want to run Sample spectral measurements in the MIR range 4 000 400 cm is done using the TENSOR 27 Spectrometer This machine has three sampling accessories The High Throughput Screening Accessory HTS XT which is used for high throughput diffuse reflectance and transmission measurements Pike Miracle Diamond Attenuated Total Reflectance ATR accessory for ATR measurements Transmission accessory for Tensor 27 which can be used for transmission measurements using KBr pellets or liquid sample cells We will only use this for instrument testing
11. to the HTS XT drawer where the plates are scanned well by well Upon completion of scanning the wells in a plate the drawer opens the robotic arm picks the plate and places it on the output tray picks another plate and places it in the sampling drawer Refer to Tensor 27 manual page 16 QUALITY CONTROL Reference Material a C Reference standards Infrared ICRAF laboratory uses Katumani High Black Cracking Clay Soil HBCCS Mua soil and White sand as reference standards Everyday a new spectrum is recorded on these samples before analyzing test samples and checked against the previous records Appropriate correction actions where necessary are implemented Normally no adjustments are required Blanks Two empty wells A1 used for background measurement and B1 used as a blank in each Aluminum plate loaded with sample Calibration No calibration is required d Duplicates Two replicates are done for each sample Data Validation a Data Review Check the sample data and QC data to verify that the data to be reported is based on acceptable analyses and meet acceptable limits Verify that Mua standard spectra have been entered into the appropriate logs Verify that the results are saved in appropriate folder and format Place data in the laboratory database Supervisor Review Check the sample data and QC data to verify that the data to be reported is based on acceptable analyses and mee
12. truments KBr and ZnSe It has a Zinc Selenide cystal Samples Scanning Load Method For ATR pour sample directly on the ATR crystal using a micro spatula For the DRIFT place the sample cup on sample holder v From Preparation Factory All the processes for sample preparation are outlined in the sample preparation workflow and SOP Instrument Tensor 27 Mix sample with KBr then make a tablet HTS XT AX Transmission Method Samples Scanning Samples loaded Data Process All the data processes are To Database ATR Attenuated Total Reflectance DRIFT Diffuse Reflectance illustrated in the SOP plates KBr Potassium Bromide 2 Infrared ALHPA spectrometer standards fact sheets 9 HTS XT SOP Uses MI mode and its best suited for very tiny samples and it has a diamond crystal on aluminum plates are scanned on either the NIR mode or the MIR mode For transmission mode samples are loaded on silica R Reflectance Load Reflectance Mid Infra Red Method Near Infra Red Method not frequently used Agroforest Centre STANDARD OPERATING PROCEDURE Date July 30 2014 Code METH 08V01 Soil Plant Spectral y Diagnostics Lab Title Method for analysing samples for spectral characteristics in Mid IR range using HTS XT Author Dickens Ateku
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