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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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IR Spectrometers01:25

IR Spectrometers

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There are two main infrared (IR) spectrophotometers: dispersive IR spectrometers and Fourier transform infrared (FTIR) spectrometers. In a dispersive IR spectrometer, a beam of infrared radiation produced by a hot wire is divided into two parallel equal-intensity beams using mirrors. One beam passes through the sample, while another is a reference beam. The beams then move through the monochromator, which separates the radiations into a continuous spectrum of different frequencies. The...
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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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UV–Vis Spectrometers01:14

UV–Vis Spectrometers

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The absorbance of UV and visible (UV–visible) radiations is measured using a UV–visible spectrophotometer. Deuterium lamps, which emit UV radiation, and tungsten lamps, which produce radiation in the visible region, are used as light sources in UV–visible spectrophotometers. A monochromator or prism is used for diffraction grating, i.e., to split the incoming radiation into different wavelengths. A system of slits is used to focus the desired wavelength on the sample cell.
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Atomic Mass01:52

Atomic Mass

70.5K
Atoms — and the protons, neutrons, and electrons that compose them — are extremely small. For example, a carbon atom weighs less than 2 × 10−23 g. When describing the properties of tiny objects such as atoms, we use appropriately small units of measure, such as the atomic mass unit (amu). The amu was originally defined based on hydrogen, the lightest element, then later in terms of oxygen. Since 1961, it has been defined with regard to the most abundant isotope of carbon, atoms of which...
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NMR Spectrometers: Radiofrequency Pulses and Pulse Sequences01:17

NMR Spectrometers: Radiofrequency Pulses and Pulse Sequences

1.8K
A pulse is a short burst of radio waves distributed over a range of frequencies that simultaneously excites all the nuclei in the sample. Upon passing a radio frequency pulse along the x-axis, the nuclei absorb energy corresponding to their Larmor frequencies and achieve resonance. This shifts the net magnetization vector from the z-axis toward the transverse plane. This angle of rotation of the magnetization vector, or the flip angle, is proportional to the duration and intensity of the pulse.
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Related Experiment Video

Updated: Feb 11, 2026

Combustion Chemistry of Fuels: Quantitative Speciation Data Obtained from an Atmospheric High-temperature Flow Reactor with Coupled Molecular-beam Mass Spectrometer
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Parsing and Quantification of Raw Orbitrap Mass Spectrometer Data Using RawQuant.

Kevin A Kovalchik1, Sophie Moggridge2, David D Y Chen1

  • 1Department of Chemistry , University of British Columbia , Vancouver , British Columbia V6T 1Z1 , Canada.

Journal of Proteome Research
|April 24, 2018
PubMed
Summary
This summary is machine-generated.

RawQuant simplifies mass spectrometry (MS) data analysis by parsing raw Thermo Orbitrap MS files into open formats. This tool enhances protein identification and quantification accuracy in proteomics experiments.

Keywords:
OrbitrapSPS-MS3TMTiTRAQisobaric labelingquantitative proteomics

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Area of Science:

  • Proteomics
  • Mass Spectrometry Data Analysis
  • Bioinformatics

Background:

  • Effective analysis of protein samples using mass spectrometry (MS) relies on optimizing experimental parameters.
  • Raw MS data files are crucial for assessing analysis success but are often in closed-source formats, hindering data parsing.
  • Thermo Orbitrap instruments generate proprietary raw MS files, posing challenges for broad data accessibility and analysis.

Purpose of the Study:

  • To introduce RawQuant, a novel tool designed for parsing raw MS files from Thermo Orbitrap instruments.
  • To enable the export of metadata and quantification data in open, readable text formats for enhanced analysis.
  • To demonstrate the utility of RawQuant across diverse proteomics applications, including protein identification and quantification.

Main Methods:

  • Developed RawQuant to parse raw MS files from Thermo Orbitrap instruments.
  • Configured RawQuant to export MS¹, MS², and MS³ metadata.
  • Utilized RawQuant for reanalysis of shotgun proteomics, isobaric tagging experiments, and bacterial proteome analysis.

Main Results:

  • RawQuant successfully parsed raw Thermo Orbitrap MS files for various proteomics experiments.
  • Demonstrated efficient parsing and quantification of MS data, including isobaric tagging approaches.
  • Identified parametric considerations for improving protein identification depth and quantification accuracy.

Conclusions:

  • RawQuant provides an effective solution for parsing and analyzing data from raw Thermo Orbitrap MS files.
  • The tool supports diverse proteomics workflows, enhancing both identification and quantification.
  • Findings highlight opportunities to optimize experimental parameters for deeper proteome coverage and more accurate quantification.