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
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Teams: RECETOX SpecDatRI
Organizations: Masaryk University
Teams: RECETOX SpecDatRI, Proteomics CEITEC
Organizations: RECETOX, Masaryk University
![](/assets/logos/orcid_16x16-2bdaa944d31633ca5dea4eee7d642234ec7ac150641a49dea324b86087116986.png)
Teams: RECETOX SpecDatRI, RECETOX, usegalaxy-eu, ELIXIR Metabolomics
Organizations: Masaryk University, RECETOX
![](/assets/logos/orcid_16x16-2bdaa944d31633ca5dea4eee7d642234ec7ac150641a49dea324b86087116986.png)
Expertise: Bioinformatics, Cheminformatics, Metabolomics, Python, R, Software Engineering, Workflows
Tools: Metabolomics, Python, R, Workflows, Mass spectrometry, Chromatography
High-Performance Computing (HPC) environments are integral to quantum chemistry and computationally intense research, yet their complexity poses challenges for non-HPC experts. Navigating these environments proves challenging for researchers lacking extensive computational knowledge, hindering efficient use of domain specific research software. The prediction of mass spectra for in silico annotation is therefore inaccessible for many wet lab scientists. Our main goal is to facilitate non-experts ...
Creators: Helge Hecht, Wudmir Rojas
Submitter: Helge Hecht
High-Performance Computing (HPC) environments are integral to quantum chemistry and computationally intense research, yet their complexity poses challenges for non-HPC experts. Navigating these environments proves challenging for researchers lacking extensive computational knowledge, hindering efficient use of domain specific research software. The prediction of mass spectra for in silico annotation is therefore inaccessible for many wet lab scientists. Our main goal is to facilitate non-experts ...
Type: Galaxy
Creators: Zargham Ahmad, Helge Hecht, Wudmir Rojas, RECETOX SpecDat
Submitters: Helge Hecht, Wudmir Rojas
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