{"repo":"nf-core/metaboigniter","free":true,"listed":false,"github":"https://github.com/nf-core/metaboigniter","clone":"git clone https://github.com/nf-core/metaboigniter.git","description":"Pre-processing of mass spectrometry-based metabolomics data with quantification and identification based on MS1 and MS2 data.","language":"Nextflow","stars":24,"topics":["workflow","metabolomics","identification","quantification","mass-spectrometry","nextflow","pipeline","nf-core","ms1","ms2"],"license":"MIT","category":"workflow-automation","readme_excerpt":"Introduction nf-core/metaboigniter is a bioinformatics pipeline that ingests raw mass spectrometry data in mzML format, typically in the form of peak lists and MS2 spectral data, for comprehensive metabolomics analysis. The key stages involve centroiding, feature detection, adduct detection, alignment, and linking, which progressively refine and align the data. The pipeline can also perform requantification to compensate for missing values and leverages MS2Query for compound identification based on MS2 data, outputting a comprehensive list of detected and potentially identified metabolites. 1. Centroiding: Converts the continuous mass spectra into a series of discrete points. 2. Feature Detection: Identifies unique signals or 'features' in the spectra. 3. Adduct Detection: Identifies adduct ions, which are formed by the interaction of the sample with the ion source. 4. Alignment: Ensures that the same features across different samples are matched together. 5. Linking: Establishes connections between features across different ionization modes or adducts. 6. Requantification: Fills in missing values in the data set for a more complete analysis. 7. Identification: Uses MS2Query and SIRIUS to identify compounds based on their MS2 spectral data. 8. Output Generation: Produces a comprehensive list of detected and potentially identified metabolites. Usage [!NOTE] If you are new to Nextflow and nf-core, please refer to this page on how to set-up Nextflow. Make sure to test your setup","default_branch":null,"files":null,"tree":[],"storefront":"/r/nf-core","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/nf-core/metaboigniter/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."}