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Raman Spectroscopy
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File Folders will contain: Study Metadata File, Assay Results (Outputs), Tabular Submitted, ALSDA TransformedMeasurement: Spectrochemical Analysis
Ontology: http://purl.jp/bio/4/id/200906010104449419		RG Drafted 12/18/24Instructions:

Please provide your name at the top of your column in case we have any questions or requests for clarification.

For the below parameters (rows), please provide any feedback or suggestions. This could be suggested edits to the parameter, suggested removal (if you believe it's unnecessary), etc.

The last section is a freeform feedback section, where you can provide any general feedback or recommendations that we should take into consideration.

General Info on assay metadata configurations can be found here.
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References:
Saletnik et al 2021
Butler et al 2016
Agarwal 2014		Technology: Raman Spectroscopy
Ontology: http://purl.obolibrary.org/obo/ERO_0001677
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ALSDA Assay Metadata Configuration for Raman SpectroscopySME Name:SME Name:SME Name:
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ParameterExample ValueData TypeNotesParameters
Please indicate any additional parameters you think we should add, in the line at the end of each protocol section.
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Sample PreparationSample Preparation
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Sample Statee.g. solid, powderfree textState of the sample: solid, liquid, gas, or powder.Sample State
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Sample Compositione.g. free textChemical details or composition of the sample.Sample Composition
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Sample Temperaturee.g. 25 degree CelsiusunitTemperature of the sample during the measurement.Sample Temperature
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Reagents Used for Cleaninge.g. distilled water, ethanolfree textReagents Used for Cleaning
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Describe Any Additional Methods For Contaminant Removale.g. ultrasonic bathfree textDescribe Any Additional Methods For Contaminant Removal
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Drying Methode.g. oven dryingfree textDrying Method
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Drying Temperaturee.g. 50 degrees CunitDrying Temperature
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Drying Duratione.g. 24 hoursunitDrying Duration
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Grinding Equipmente.g. mortar and pestlefree textGrinding Equipment
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Particle Size Acheivede.g. 50 umunitParticle Size Acheived
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Bleaching Reagent Usede.g. hydrogen peroxidefree textBleaching Reagent Used
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Bleaching Reagent Concentratione.g. 3%unitBleaching Reagent Concentration
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Bleaching Temperaturee.g. 25 degree CelsiusunitBleaching Temperature
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Bleaching Duratione.g. 1 hourunitBleaching Duration
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Mounting Substratee.g. glass slide, gold-coated surfacefree textMounting Substrate
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Mounting Methode.g. flatfree textMounting Method
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Mounting Adhesivee.g. resinfree textMounting Adhesive
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Section Thicknesse.g. 10 umunitSection Thickness
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Extraction Methode.g. sonicationfree textExtraction Method
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Extraction Solvente.g. acetonefree textExtraction Solvent
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Extraction Solvent Concentratione.g. 3%unitExtraction Solvent Concentration
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Additional Parameters to Add?
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Additional Parameters to Add?
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Assay ProcedureAssay Procedure
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Measurement Environment Gas Compositione.g. 5% CO2, 20% O2free textMeasurement Environment Gas Composition
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Measurement Environment Humiditye.g. 50%unitMeasurement Environment Humidity
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Measurement Environment Temperaturee.g. 37 degree CelsiusunitMeasurement Environment Temperature
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Sample Uptake Ratee.g. 2unitSample Uptake Rate
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Instrument Model and Manufacturere.g.hand-held Resolve Agilent spectrometerfree textInstrument Model and Manufacturer
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Laser Excitation Wavelengthe.g. 532 nmunitLaser Excitation Wavelength
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Laser Powere.g. 495 mWunitLaser Power
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Spectral Resolutione.g. 1 cm-1unitAbility to resolve closely spaced peaksSpectral Resolution
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Integration Timee.g. 1 secondunitExposure time for signal collectionIntegration Time
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Accumulationse.g. 10free textNumber of scans/spectra accumulated for signal quality.Accumulations
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Gratinge.g. 600 lines/mmunitDiffraction grating used to disperse the signal.Grating
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Filterse.g.Filters
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Pinholee.g.Pinhole
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Excitation Geometrye.g. 180 degree backscatteringfree textLaser and detector configurationExcitation Geometry
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Objective Lense.g. 10xfree textMagnification of the lens used.Objective Lens
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Spot Sizee.g. 1 umunitLaser focus size on the sampleSpot Size
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Detector Typee.g. CCD, EMCCD, PMTfree textType of detector used to capture the spectrumDetector Type
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Wavenumber Rangee.g. 100–4000 cm⁻¹unitRange of Raman shifts collectedWavenumber Range
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Spectral Acquisition Modee.g. point, mappingfree textSpectral Acquisition Mode
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Calibration Reference Materiale.g. Siliconfree textCalibration Reference Material
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Calibration Methode.g. external, internal, standardfree textCalibration Method
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Additional Parameters to Add?
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Additional Parameters to Add?
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Data ProcessingData Processing
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Baseline Correctione.g. polynomial fittingfree textRemoval of the background signal.Baseline Correction
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Smoothinge.g. Savitzky-Golay filterfree textNoise reduction using filters.Smoothing
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Normalizatione.g. max peak normalizationfree textIntensity normalization for spectrum comparison.Normalization
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Normalization Peake.g. 1140 cm-1unitPeak used for normalizationNormalization Peak
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Peak Fittinge.g. Gaussianfree textFitting of Raman peaks. Peak Fitting
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Data Acquisition Softwaree.g. Qtegra ISfree textData Acquisition Software
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Analysis Softwaree.g. MatLabfree textAnalysis Software
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Number of Technical Replicatese.g. 3free textNumber of Technical Replicates
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Additional Parameters to Add?
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Additional Parameters to Add?
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Outcome/Dependent Variable Measures
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Variable/MeasurementUnit
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