recipe proteomiqon-psmbasedquantification

The quantification tool was designed to allow label-free quantification as well as quantification of full metabolic labeled samples.

Homepage:

https://csbiology.github.io/ProteomIQon/

Documentation:

https://csbiology.github.io/ProteomIQon/tools/PSMBasedQuantification.html

Developer docs:

https://github.com/CSBiology/ProteomIQon

License:

MIT

Recipe:

/proteomiqon-psmbasedquantification/meta.yaml

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 dotnet-runtime:

5.0.*

depends openssl:

1.1.*

requirements:

additional platforms:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install proteomiqon-psmbasedquantification

and update with::

   mamba update proteomiqon-psmbasedquantification

To create a new environment, run:

mamba create --name myenvname proteomiqon-psmbasedquantification

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull quay.io/biocontainers/proteomiqon-psmbasedquantification:<tag>

(see `proteomiqon-psmbasedquantification/tags`_ for valid values for ``<tag>``)

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