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:

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

Documentation:

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

Developer docs:

https://github.com/CSBiology/ProteomIQon

License:

MIT

Recipe:

/proteomiqon-peptidespectrummatching/meta.yaml

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 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-peptidespectrummatching

and update with::

   mamba update proteomiqon-peptidespectrummatching

To create a new environment, run:

mamba create --name myenvname proteomiqon-peptidespectrummatching

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-peptidespectrummatching:<tag>

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

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