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Related Concept Videos

Mass Spectrometers01:16

Mass Spectrometers

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This lesson details the instrumentation of a mass spectrometer—a physical instrument to perform mass spectrometry on analyte molecules and record the characteristic mass spectra. This is achieved via three chief functions:
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Mass Spectrum: Interpretation01:24

Mass Spectrum: Interpretation

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An unknown compound can be established by identifying the molecular ion peak in the mass spectrum. The molecular ion peak is often weak or absent due to the predominance of fragmentation in high-energy electron beams. In such cases, a low-energy electron beam can be used to scan the spectrum to enhance the intensity of the molecular ion peak. Additionally, chemical ionization, field ionization, and desorption ionization spectra are used to obtain a relatively intense molecular ion peak.
To...
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Mass Spectrometry: Complex Analysis01:21

Mass Spectrometry: Complex Analysis

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Mass spectrometry is an important technique for the identification of pure compounds. However, it has some limitations for the analysis of complex mixtures, often due to excessive fragmentation making the spectrum too complicated to decipher. Mass spectrometry can be combined with suitable separation methods in sequence, forming hyphenated methods, which are useful in the analysis of complex mixtures.
GC–MS is a powerful hyphenated method commonly used in forensics and environmental...
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Mass Spectrometry: Overview01:19

Mass Spectrometry: Overview

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Mass spectrometry is an analytical technique used to determine the molecular mass and molecular formula of a compound. The basic principle of mass spectrometry is to generate ions from the analyte molecule and measure these ion abundances against their molecular mass.  One common type of ionization, known as electrospray ionization or EI, bombards the analyte molecules in the gas phase with high-energy electron beams. The electron beams displace an electron from the molecule and leave...
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Spectroscopy of Carboxylic Acid Derivatives01:26

Spectroscopy of Carboxylic Acid Derivatives

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Infrared spectroscopy is primarily used to determine the types of bonds and functional groups. In carboxylic acid derivatives, a typical carbonyl bond absorption is observed around 1650–1850 cm−1. For esters, the absorption is recorded at around 1740 cm−1, while acid halides show the absorption at about 1800 cm−1. Another acid derivative, the acid anhydrides, exhibit two carbonyl absorption around 1760 cm−1 and 1820 cm−1, arising from the symmetrical and...
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NMR Spectrometers: Overview01:20

NMR Spectrometers: Overview

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NMR spectrometers consist of a strong magnet, a radiofrequency transmitter, and a detector attached to a computer console for recording spectra of samples containing NMR-active nuclei. In first-generation NMR instruments called continuous-wave spectrometers, the resonance frequencies of the nuclei are determined by frequency-sweep or field-sweep methods. The magnetic field strength is fixed and the rf signal is swept in the former, while the radiofrequency signal is fixed and the magnetic field...
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ChemSpectra: a web-based spectra editor for analytical data.

Yu-Chieh Huang1, Pierre Tremouilhac1, An Nguyen1

  • 1Institute of Biological and Chemical Systems-Functional Molecular Systems (IBCS-FMS), Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany.

Journal of Cheminformatics
|February 11, 2021
PubMed
Summary
This summary is machine-generated.

ChemSpectra is a new web-based software for analyzing spectroscopic data, including IR, MS, and NMR. It supports open file formats for FAIR data principles and integrates with electronic lab notebooks for sustainable research data management.

Keywords:
AnalysisIRJCAMP-DXMass spectrometryNMRSpectroscopy

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Area of Science:

  • Chemistry
  • Data Science
  • Scientific Software Development

Background:

  • Spectroscopic data analysis is crucial in synthetic chemistry research.
  • Managing and analyzing diverse spectroscopic data formats can be challenging.
  • Adherence to FAIR data principles (Findable, Accessible, Interoperable, Reusable) is increasingly important for research reproducibility.

Purpose of the Study:

  • To describe ChemSpectra, a novel web-based software for visualizing and analyzing spectroscopic data.
  • To highlight ChemSpectra's support for open file formats and its integration into digital research environments.
  • To demonstrate how ChemSpectra facilitates FAIR data principles in chemical research.

Main Methods:

  • Development of a JavaScript-based web application for spectroscopic data analysis.
  • Integration of solutions for infrared spectroscopy (IR), mass spectrometry (MS), and 1D proton (1H) and carbon (13C) nuclear magnetic resonance (NMR).
  • Implementation of support for open file formats like JCAMP-DX and mzML, with extensibility for proprietary formats (e.g., RAW, FID).
  • Integration with existing software, such as the Chemotion electronic lab notebook (ELN) and repository.

Main Results:

  • ChemSpectra provides tools for spectroscopic data visualization and analysis, including zoom, peak picking, and automatic peak detection.
  • NMR-specific functions include reference signal definition, signal integration, coupling constant calculation, and multiplicity assignment.
  • The software enables association of spectra with samples, file management (original, edited, PNG versions), and automated data transfer to ELNs.
  • Integration into the Chemotion ELN and repository demonstrates its utility in a digital research workflow.

Conclusions:

  • ChemSpectra offers a comprehensive solution for analyzing common spectroscopic data types in synthetic chemistry.
  • Its support for open formats and integration capabilities promote FAIR data principles and sustainable data management.
  • The software's open-source nature (AGPL license) encourages community adoption, re-use, and further development.