- recipe proteomiqon-psmbasedquantification
The quantification tool was designed to allow label-free quantification as well as quantification of full metabolic labeled samples.
- Homepage:
- Documentation:
https://csbiology.github.io/ProteomIQon/tools/PSMBasedQuantification.html
- Developer docs:
- License:
MIT
- Recipe:
Given an MS run in the mzLite or mzml format and a list of fdr controlled peptide spectrum matches, this tool iterates accross all identified MS/MS scans and groups them by the assigned peptide ion. The scan times of each MS/MS spectrum are then weighted according to the quality of each match to build an reliable estimator for the scan time of the peptide ion in question. This scan time estimator, combined with the monoisotopic m/z, is then used to extract an ion chromatogram. Using wavelet based peak detection techniques we identify all peaks present in the XIC and select the most probable peak our target for quantification. Using parameter estimation techniques we subsequently use peak fitting to fit a set of two gaussian models to the detected peak, from whom the one with the better fit is selected. This allows us not only to report how well the signal fitted to the theoretical expected peak shape but also to obtain accurate estimates for the peak area, our estimator for peptide ion abundance. The quantification tool was designed to allow label-free quantification as well as quantification of full metabolic labeled samples. For this we use the known identity of one of the the peptide ions and calculate the m/z of the unobserved differentially labeled counterpart to extract and quantify the corresponding XIC.
- package proteomiqon-psmbasedquantification¶
- Versions:
0.0.9-0,0.0.8-0,0.0.7-0,0.0.5-0,0.0.4-0- Depends:
on dotnet-runtime
5.0.*on openssl
1.1.*
- Additional platforms:
Installation¶
You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).
Pixi¶
With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:
pixi global install proteomiqon-psmbasedquantification
to add into an existing workspace instead, run:
pixi add proteomiqon-psmbasedquantification
In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:
pixi workspace channel add conda-forge
pixi workspace channel add bioconda
Conda¶
With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:
conda install proteomiqon-psmbasedquantification
Alternatively, to install into a new environment, run:
conda create -n envname proteomiqon-psmbasedquantification
with envname being the name of the desired environment.
Container¶
Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:
docker pull quay.io/biocontainers/proteomiqon-psmbasedquantification:<tag>
(see proteomiqon-psmbasedquantification/tags for valid values for <tag>).
Integrated deployment¶
Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.
Download stats¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/proteomiqon-psmbasedquantification/README.html)
