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Related Concept Videos

Spectrophotometry: Introduction01:16

Spectrophotometry: Introduction

Spectrophotometry is the quantitative measurement of the absorption, reflection, diffraction, or transmission of electromagnetic radiation through a material as a function of the intensity and wavelength of the radiation. A spectrophotometer is a device used to measure the change in the radiation intensity caused by its interaction with the material.
The essential components of a spectrophotometer include a source of electromagnetic radiation, a slot for placing a material to be analyzed, and a...
IR Spectrum01:19

IR Spectrum

When infrared (IR) radiation passes through a molecule, the bonds stretch or bend by absorbing the radiation. This absorption creates the molecule's absorption spectrum, which is the plot of its percentage transmittance versus wavenumber.
Transmittance is defined as the ratio of the radiant power passing through a sample to that from the radiation's source. Multiplying the transmittance by 100 gives the percent transmittance (%T), which varies between 100% (no absorption) and 0% (complete...
IR Spectrum Peak Splitting: Symmetric vs Asymmetric Vibrations01:08

IR Spectrum Peak Splitting: Symmetric vs Asymmetric Vibrations

Identical bonds within a polyatomic group can stretch symmetrically (in-phase) or asymmetrically (out-of-phase). Similar to hydrogen bonding, these vibrations also influence the shape of the IR peak. Generally, asymmetric stretching frequencies are higher than symmetric stretching frequencies. For example, primary amines exhibit two distinct IR peaks between 3300–3500 cm−1 corresponding to the symmetric and asymmetric N-H stretching, while secondary amines exhibit a single stretching vibration...
Mass Spectrum01:23

Mass Spectrum

A mass spectrum is the graphical representation of the relative abundance of the charged fragments in an analyte plotted against their mass-to-charge ratio (m/z). The plot's x-axis represents the ratio of the mass of the charged fragment to the number of charges it carries. The y axis of the plot represents the relative abundance of each charged species. The relative abundance is calculated from the signal intensity of each charged species recorded at the detector. The most intense signal (the...
Expected Frequencies in Goodness-of-Fit Tests01:19

Expected Frequencies in Goodness-of-Fit Tests

A goodness-of-fit test is conducted to determine whether the observed frequency values are statistically similar to the frequencies expected for the dataset. Suppose the expected frequencies for a dataset are equal such as when predicting the frequency of any number appearing when casting a die. In that case, the expected frequency is the ratio of the total number of observations (n) to the number of categories (k).
Mass Spectrum: Interpretation01:24

Mass Spectrum: Interpretation

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 soft-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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Related Experiment Video

Updated: May 8, 2026

Sampling and Analysis of Animal Scent Signals
14:59

Sampling and Analysis of Animal Scent Signals

Published on: February 13, 2021

Spectral library generating function for assessing spectrum-spectrum match significance.

Mingxun Wang1, Nuno Bandeira

  • 1Department of Computer Science and Engineering, Center for Computational Mass Spectrometry, CSE, and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Dr., La Jolla, California 92093, United States.

Journal of Proteome Research
|July 2, 2013
PubMed
Summary
This summary is machine-generated.

Spectral library searching in tandem mass spectrometry (MS/MS) is enhanced by a new statistical approach. This method improves the identification of spectra by modeling replicate spectra, outperforming current tools.

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Using a Cyclic Ion Mobility Spectrometer for Tandem Ion Mobility Experiments
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Last Updated: May 8, 2026

Sampling and Analysis of Animal Scent Signals
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Published on: February 13, 2021

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Using a Cyclic Ion Mobility Spectrometer for Tandem Ion Mobility Experiments
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Area of Science:

  • Proteomics
  • Analytical Chemistry
  • Biotechnology

Background:

  • Tandem mass spectrometry (MS/MS) is crucial for high-throughput proteomics.
  • Spectral library searching surpasses sequence-based searches for MS/MS data identification.
  • Accurate statistical significance estimation for spectrum-spectrum matches (SSMs) remains a challenge.

Purpose of the Study:

  • To develop a novel statistical framework for MS/MS spectral library searching.
  • To address the limitations in defining a null model for SSM significance.
  • To improve the accuracy and comprehensiveness of peptide identification in proteomics.

Main Methods:

  • Proposed a new null hypothesis focusing on replicate spectra variation.
  • Developed a spectral library generating function (SLGF) to model MS/MS peak intensity variations.
  • Modeled theoretical distributions of SSM scores for reference and query spectra.

Main Results:

  • The SLGF approach enables calculation of theoretical SSM score distributions.
  • Demonstrated the SLGF approach's applicability to various SSM scores, including dot products and cosines.
  • The developed tool, Tremolo, significantly outperforms existing state-of-the-art spectral library search tools.

Conclusions:

  • The novel statistical method provides a more robust way to assess SSM significance.
  • Tremolo, utilizing the SLGF approach, enhances MS/MS spectral identification.
  • This advancement offers improved capabilities for complex proteomics sample analysis.