Paper Info
Title
Containerization and wrapping of a mass spectra prediction workflow.
Abstract
I. ABSTRACT Mass spectrometry is an experimental technique used to identify and quantify molecules based on their mass-to-charge ratios and fragmentation patterns. It is an essential technique in a multitude of research areas. Our motivation to predict mass spectra originates from the field of metabolomics, where spectra for of many metabolites are still unknown and pure reference compounds hard to obtain. The work presented here shall serve as technological basis for a future science gateway project. QCEIMS is able to predict mass spectra for a given molecule based on quantum chemical simulation of the fragmentation patterns [1, 2]. It uses tools such ORCA or MNDO99 to perform the actual calculation. The simulation protocol consists of four steps: (1) An initial trajectory of the molecule of interest is calculated, (2) Starting conformations for the fragmentation runs are extracted, (3) Possible fragmentation processes are simulated, usually several hundred individual runs, (4) The relevant information are collected from the individual runs, assembled and analyzed. As a result a peak list of the corresponding fragmentation spectrum is obtained.
Year
Venue
Field
2016
PeerJ PrePrints
Paleontology,Biological system,Biology,Molecule,Mass spectrum,Spectral line,Fragmentation (computing),Mass spectrometry,Science gateway,Workflow,Trajectory
DocType
Volume
Citations 
Journal
4
0
PageRank 
References 
Authors
0.34
0
2
Name
Order
Citations
PageRank
Jens Krüger14910.86
Oliver Kohlbacher2975101.91