Spectrometric Data Processing & Analysis Department of RECETOX.
Space: EIRENE-CZ
SEEK ID: https://workflowhub.eu/projects/246
Funding codes:- LM2018121
- 857560
Public web page: https://www.recetox.muni.cz/en/services/data-services-2/spectrometric-data-processing-and-analysis
Organisms: Homo sapiens
WorkflowHub PALs: No PALs for this Team
Team created: 20th May 2024
Related items
Teams: RECETOX SpecDatRI
Organizations: Masaryk University
Teams: RECETOX SpecDatRI, Proteomics CEITEC
Organizations: RECETOX, Masaryk University
https://orcid.org/0000-0003-4407-3917Teams: RECETOX SpecDatRI, RECETOX, usegalaxy-eu, ELIXIR Metabolomics
Organizations: Masaryk University, RECETOX
https://orcid.org/0000-0001-6744-996XExpertise: Bioinformatics, Cheminformatics, Metabolomics, Python, R, Software Engineering, Workflows
Tools: Metabolomics, Python, R, Workflows, Mass spectrometry, Chromatography
Galaxy Workflow Documentation: MS Finder Pipeline
This document outlines a MSFinder Galaxy workflow designed for peak annotation. The workflow consists of several steps aimed at preprocessing MS data, filtering, enhancing, and running MSFinder.
Step 1: Data Collection and Preprocessing
Collect if the inchi and smiles are missing from the dataset, and subsequently filter out the spectra which are missing inchi and smiles.
1.1 MSMetaEnhancer: Collect InChi, Isomeric_smiles, and Nominal_mass
...
Type: Galaxy
Creators: Zargham Ahmad, Helge Hecht, Elliott J. Price, Research Infrastructure RECETOX RI (No LM2018121) financed by the Ministry of Education, Youth and Sports, and Operational Programme Research, Development and Innovation - project CETOCOEN EXCELLENCE (No CZ.02.1.01/0.0/0.0/17_043/0009632).
Submitters: Helge Hecht, Zargham Ahmad
Galaxy Workflow Documentation: In-Silico Mass Spectra Prediction Using Semi-Empirical Quantum Chemistry
Overview
This workflow predicts in-silico mass spectra using a semi-empirical quantum chemistry method. It involves generating and optimizing molecular conformers and simulating their mass spectra with computational chemistry tools. The workflow receives an SDF file as input and outputs the mass spectrum in MSP file format.
Type: Galaxy
Creators: Zargham Ahmad, Helge Hecht, Wudmir Rojas, RECETOX SpecDat
Submitter: Wudmir Rojas