Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

MALDI-TOF Mass Spectrometry01:19

MALDI-TOF Mass Spectrometry

Mass spectrometry is a powerful characterization technique that can identify and separate a wide variety of compounds ranging from chemical to biological entities, based on their mass-to-charge ratio (m/z). The instruments that allow this detection, known as mass spectrometers, have three components: an ion source, a mass analyzer, and a detector. These spectrometers differ based on the nature of their ion source and analyzers.Matrix-assisted laser desorption ionization (MALDI) is a commonly...
Tandem Mass Spectrometry01:21

Tandem Mass Spectrometry

Tandem mass spectrometry is a technique that uses multiple mass analyzers in series to obtain a higher selectivity and reduce chemical noise during analyte detection. Instruments with multiple analyzers separated by an interaction cell enable secondary fragmentation and selected study of the fragment ions.Secondary fragmentations occur in the interaction cell and can be induced by various factors. Fragmentation induced by collision with inert gases, such as N2, Ar, He, etc., is called...
Mass Spectrometry: Complex Analysis01:21

Mass Spectrometry: Complex Analysis

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...
Mass Spectrometry: Overview01:19

Mass Spectrometry: Overview

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 electron 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 behind a...
Mass Spectrometers01:16

Mass Spectrometers

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:
Mass Analyzers: Common Types01:19

Mass Analyzers: Common Types

The quadrupole mass analyzer consists of four cylindrical metal rods arranged in a diamond carrying a DC voltage and a radio-frequency AC voltage. The motion of ions through the quadrupole depends on the field strength, causing only ions of a certain m/z to resonate successfully and strike the detector at a given field strength. Though the transmission rate for these analyzers is high, the exact elemental composition of the sample is not determined because of low resolution; however, they are...

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Some mathematical reasons why meta-analyses of nonpharmaceutical interventions like facemasks could be inaccurate.

Epidemics·2026
Same author

Gurbaxani et al. Respond.

American journal of public health·2024
Same author

Unpacking Cochrane's Update on Masks and COVID-19.

American journal of public health·2023
Same author

Evaluation of different types of face masks to limit the spread of SARS-CoV-2: a modeling study.

Scientific reports·2022
Same author

Theory-based Behavioral Predictors of Self-reported Use of Face Coverings in Public Settings during the COVID-19 Pandemic in the United States.

Annals of behavioral medicine : a publication of the Society of Behavioral Medicine·2020
Same author

A mathematical model to describe survival among liver recipients from deceased donors with risk of transmitting infectious encephalitis pathogens.

Transplant infectious disease : an official journal of the Transplantation Society·2019

Related Experiment Video

Updated: Jun 8, 2026

Simultaneous Affinity Enrichment of Two Post-Translational Modifications for Quantification and Site Localization
12:11

Simultaneous Affinity Enrichment of Two Post-Translational Modifications for Quantification and Site Localization

Published on: February 27, 2020

Quadratic variance models for adaptively preprocessing SELDI-TOF mass spectrometry data.

Vincent A Emanuele1, Brian M Gurbaxani

  • 1School of Electrical and Computer Engineering, Georgia Institute of Technology, Atlanta, GA, USA. VEmanueleII@cdc.gov

BMC Bioinformatics
|October 15, 2010
PubMed
Summary

This study introduces a novel preprocessing method for Surface Enhanced Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (SELDI) data. The new approach improves protein peak detection sensitivity and reproducibility in biomarker discovery.

More Related Videos

Quantification of Site-specific Protein Lysine Acetylation and Succinylation Stoichiometry Using Data-independent Acquisition Mass Spectrometry
12:49

Quantification of Site-specific Protein Lysine Acetylation and Succinylation Stoichiometry Using Data-independent Acquisition Mass Spectrometry

Published on: April 4, 2018

PTR-ToF-MS Coupled with an Automated Sampling System and Tailored Data Analysis for Food Studies: Bioprocess Monitoring, Screening and Nose-space Analysis
08:43

PTR-ToF-MS Coupled with an Automated Sampling System and Tailored Data Analysis for Food Studies: Bioprocess Monitoring, Screening and Nose-space Analysis

Published on: May 11, 2017

Related Experiment Videos

Last Updated: Jun 8, 2026

Simultaneous Affinity Enrichment of Two Post-Translational Modifications for Quantification and Site Localization
12:11

Simultaneous Affinity Enrichment of Two Post-Translational Modifications for Quantification and Site Localization

Published on: February 27, 2020

Quantification of Site-specific Protein Lysine Acetylation and Succinylation Stoichiometry Using Data-independent Acquisition Mass Spectrometry
12:49

Quantification of Site-specific Protein Lysine Acetylation and Succinylation Stoichiometry Using Data-independent Acquisition Mass Spectrometry

Published on: April 4, 2018

PTR-ToF-MS Coupled with an Automated Sampling System and Tailored Data Analysis for Food Studies: Bioprocess Monitoring, Screening and Nose-space Analysis
08:43

PTR-ToF-MS Coupled with an Automated Sampling System and Tailored Data Analysis for Food Studies: Bioprocess Monitoring, Screening and Nose-space Analysis

Published on: May 11, 2017

Area of Science:

  • Proteomics
  • Biomarker Discovery
  • Mass Spectrometry

Background:

  • Surface Enhanced Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (SELDI) is crucial for high-throughput biomarker discovery.
  • Existing preprocessing algorithms for SELDI data require improvement in reproducibility.
  • Bottom-up preprocessing approaches modeling SELDI data acquisition show promise.

Purpose of the Study:

  • To develop and evaluate a novel preprocessing algorithm for SELDI data.
  • To enhance protein peak detection sensitivity and reproducibility.
  • To address limitations in current SELDI data analysis.

Main Methods:

  • Characterized SELDI detector intensity response using matrix-only runs.
  • Modeled intensity fluctuations and noise with a Natural Exponential Family with Quadratic Variance Function (NEF-QVF) distribution.
  • Implemented a modified Antoniadis-Sapatinas wavelet denoising algorithm in MATLAB.

Main Results:

  • The proposed preprocessing approach demonstrated superior peak detection sensitivity compared to MassSpecWavelet at False Discovery Rate (FDR) < 25%.
  • The NEF-QVF model effectively characterized SELDI detector noise.
  • The algorithm adapts to varying noise characteristics.

Conclusions:

  • The NEF-QVF model necessitates measuring parameters from matrix-only spectra, impacting experiment design.
  • This adaptive preprocessing approach enhances SELDI data reproducibility.
  • Further development could lead to automated, high-throughput SELDI data preprocessing.