ts_ids_components.spectrophotometry package#

Module contents#

This module contains components for spectrophotometry IDSs.

Spectrophotometry for life science#

Spectrophotometers measure how much visible or UV light a sample absorbs. Since different molecules absorb light at specific wavelengths, their absorption spectra can be used to calculate solute concentrations using Beer-Lambert’s Law.

In life sciences, spectrophotometry is commonly used to quantify DNA, RNA, proteins and potential contaminants. To assess DNA or RNA purity, absorption is measured at 230 nm, 260 nm and 280 nm. Both RNA and DNA absorb at 260 and 280 nm (to characteristic extents) while common contaminants, such as phenol or guanidine, absorb at 230 nm. The 260/280 and 260/230 absorbance ratios are quick assessments of sample purity, for example:

A 260/280 ratio of 1.8 is considered “pure” for DNA and 2.0 for RNA.
A 260/230 ratio above 2.0 is considered free of contaminant.

Results components#

The SpectrophotometerResult component holds results for a single DNA or RNA spectrophotometer assay, including:

Absorbance at 260 nm and 280 nm
Absorbance ratios at 260/280 and 260/230
Calculated concentration of the target molecule

Instruments often calculate concentration of a target simply through the proportionality of absorbance and concentration described by Beer-Lambert’s Law and ignoring the absorption contributions of other molecules. Advanced models detect contaminants more precisely and provide a corrected concentration. In this case we recommend adding a field called corrected_concentration to hold this value

Model SpectrophotometerResult[source]#

Bases: IdsElement

Common spectrophotometer result fields for molecular biology

Show JSON schema

{
   "description": "Common spectrophotometer result fields for molecular biology",
   "type": "object",
   "properties": {
      "260_230_absorbance_ratio": {
         "$ref": "#/definitions/RawValueUnit",
         "description": "Absorbance ratio at 260/230 nm"
      },
      "260_280_absorbance_ratio": {
         "$ref": "#/definitions/RawValueUnit",
         "description": "Absorbance ratio at 260/280 nm"
      },
      "260_absorbance": {
         "$ref": "#/definitions/RawValueUnit",
         "description": "Absorbance at 260 nm"
      },
      "280_absorbance": {
         "$ref": "#/definitions/RawValueUnit",
         "description": "Absorbance at 280 nm"
      },
      "concentration": {
         "$ref": "#/definitions/RawValueUnit",
         "description": "Concentration of the target molecule in the sample. Typically calculated according to Beer-Lambert's Law."
      }
   },
   "additionalProperties": false,
   "definitions": {
      "RawValueUnit": {
         "additionalProperties": false,
         "description": "A value with a unit, including the raw representation of the value from the primary data.",
         "properties": {
            "value": {
               "description": "A numerical value.",
               "type": [
                  "number",
                  "null"
               ]
            },
            "unit": {
               "description": "Unit for the numerical value.",
               "type": [
                  "string",
                  "null"
               ]
            },
            "raw_value": {
               "description": "The raw, untransformed value from the primary data.",
               "type": [
                  "string",
                  "null"
               ]
            }
         },
         "required": [
            "value",
            "unit",
            "raw_value"
         ],
         "type": "object"
      }
   }
}

Validators:

field absorbance_260: RawValueUnit (alias '260_absorbance')#: Absorbance at 260 nm

field absorbance_280: RawValueUnit (alias '280_absorbance')#: Absorbance at 280 nm

field absorbance_ratio_260_230: RawValueUnit (alias '260_230_absorbance_ratio')#: Absorbance ratio at 260/230 nm

field absorbance_ratio_260_280: RawValueUnit (alias '260_280_absorbance_ratio')#: Absorbance ratio at 260/280 nm

field concentration: RawValueUnit#: Concentration of the target molecule in the sample. Typically calculated according to Beer-Lambert’s Law.