Targeted mass-spectrometry-based techniques allow accurate quantitative measurements of analytes in complex matrices. They are used in different fields like proteomics, lipidomics or metabolomics to validate results from global analyses. Furthermore, they are used to develop robust assays with the potential to absolutely quantify the analyte of interest.
During assay development, often experiments using concentration or dilution series are conducted. Here, samples with known amount of the analyte of interest are generated and measured by mass spectrometry, usually in relicates.
This kind of data is used by CalibraCurve to generate calibration curves, which can be the basis for predicting concentrations from intensities in new data. However, a linear relationship between concentration and intensity is often limited to a certain range of concentrations, the so called linear range. CalibraCurve calculates the linear range (lower and upper limits of quantification) using a well-designed algorithm. Quality of the data and the accuracy of the produced calibration curve is assessed in several computational steps.
Visualizations of the calibration curves and the underlying data basis are generated and can be customized.
Get the latest stable R release from
CRAN. Then install CalibraCurve from
Bioconductor using the following code:
if (!requireNamespace("BiocManager", quietly = TRUE)) {
install.packages("BiocManager")
}
BiocManager::install("CalibraCurve")And the development version from GitHub with:
BiocManager::install("mpc-bioinformatics/CalibraCurve")CalibraCurve is written in R and available as an R package. Furthermore, a nextflow-workflow running this script is available at https://github.com/mpc-bioinformatics/CalibraCurve_NF.
Formerly, CalibraCurve was available as a KNIME-workflow based on an R script. The last version of this workflow can be found here: https://github.com/mpc-bioinformatics/CalibraCurve/releases/tag/v_2_0 . However, development of the KNIME-workflow was discontinued and replaced by the R package and nextflow workflow.
For details on the usage of CalibraCurve and some examples please see the vignettes.
Kohl M, Stepath M, Bracht T, Megger DA, Sitek B, Marcus K, Eisenacher M. CalibraCurve: A Tool for Calibration of Targeted MS-Based Measurements. Proteomics. 2020 Jun;20(11):e1900143. doi: 10.1002/pmic.201900143. Epub 2020 Mar 6. PMID: 32086983.
The development and maintanence of CalibraCurve is funded by de.NBI (https://www.denbi.de/) and CUBiMed.RUB (https://www.cubimed.ruhr-uni-bochum.de/index.html.en). We offer also other cool tools and consulting for statistics, bioninformatics and machine learning!
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