{"repo":"nf-core/mhcquant","free":true,"listed":false,"github":"https://github.com/nf-core/mhcquant","clone":"git clone https://github.com/nf-core/mhcquant.git","description":"Identify and quantify MHC eluted peptides from mass spectrometry raw data","language":"Nextflow","stars":51,"topics":["nf-core","nextflow","peptides","mass-spectrometry","mhc","workflow","pipeline","openms","immunopeptidomics","dda"],"license":"MIT","category":"workflow-automation","readme_excerpt":"Introduction nfcore/mhcquant is a best-practice bioinformatics pipeline to process data-dependent acquisition (DDA) immunopeptidomics data. This involves mass spectrometry-based identification and quantification of immunopeptides presented on major histocompatibility complex (MHC) molecules which mediate T cell immunosurveillance. Immunopeptidomics has central implications for clinical research, in the context of T cell-centric immunotherapies. The pipeline is based on the OpenMS C++ framework for computational mass spectrometry. Spectrum files (mzML/Thermo raw/Bruker tdf) serve as inputs and a database search (Comet) is performed based on a given input protein database. Peptide properties are predicted by MS²Rescore. FDR rescoring is applied using Percolator or Mokapot based on a competitive target-decoy approach. The pipeline supports both local FDR control (per sample-condition group) and global FDR control (across all samples). For label-free quantification, all input files undergo identification-based retention time alignment and targeted feature extraction matching ids between runs. The pipeline can also generate spectrum libraries suitable for DIA-based searches as well as computing consensus epitopes using epicore. The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The Nextflow DSL2 implem","default_branch":null,"files":null,"tree":[],"storefront":"/r/nf-core","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/nf-core/mhcquant/request-supported","requests":0},"note":"indexed from public GitHub; nothing is for sale on this page. Clone it from GitHub. Paid listings live at /search."}