- recipe proteomiqon-peptidespectrummatching
Given raw an MS run in the mzLite format, this tool iterates across all MS/MS scans, determines precursor charge states and possible peptide spectrum matches using reimplementations of SEQUEST, Andromeda and XTandem.
- Homepage:
- Documentation:
https://csbiology.github.io/ProteomIQon/tools/PeptideSpectrumMatching.html
- Developer docs:
- License:
MIT
- Recipe:
Given raw a MS run in the mzLite or mzml format, this tool iterates accross all recorded MS/MS scans and determines the charge state of precursor ions which were selected for fragmentation. With this it is possible to query the peptide data base for every precursor ion mass +/- a tolerance (which defines the so called 'search space') and retrieve peptides that are theoretical candidates for a match. For each of the peptide candidates we create an theoretical spectrum in silico and compare it to the measured MS/MS scan.
- package proteomiqon-peptidespectrummatching¶
- Versions:
0.0.7-1,0.0.7-0,0.0.6-0,0.0.5-0,0.0.4-0,0.0.3-0- 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-peptidespectrummatching
to add into an existing workspace instead, run:
pixi add proteomiqon-peptidespectrummatching
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-peptidespectrummatching
Alternatively, to install into a new environment, run:
conda create -n envname proteomiqon-peptidespectrummatching
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-peptidespectrummatching:<tag>
(see proteomiqon-peptidespectrummatching/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-peptidespectrummatching/README.html)
