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

5.9K
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...
5.9K
Tandem Mass Spectrometry01:21

Tandem Mass Spectrometry

1.6K
Tandem mass spectrometry is a technique that uses multiple mass analyzers in series to obtain a higher selectivity and signal-to-noise ratio for the analyte. 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 collision-induced...
1.6K
Mass Spectrometers01:16

Mass Spectrometers

7.2K
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:
7.2K
Peptide Identification Using Tandem Mass Spectrometry01:33

Peptide Identification Using Tandem Mass Spectrometry

7.3K
Tandem mass spectrometry, also known as MS/MS or MS2, is an analytical technique that employs two mass analyzers. Essentially it is a series of mass spectrometers that helps isolate a particular biomolecule and then helps study its chemical properties.
This technique helps gather information regarding the protein from which the peptide was obtained and to study the peptides’ amino acid sequence. Identifying peptides from a complex mixture is an important component of the growing field of...
7.3K
Mass Spectrometry: Overview01:19

Mass Spectrometry: Overview

6.9K
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...
6.9K
Mass Analyzers: Overview01:13

Mass Analyzers: Overview

1.1K
The mass analyzer is a crucial component of the mass spectrometer. In the ionization chamber, the vaporized sample is bombarded with a high-energy electron beam to generate a radical cation and further fragment into neutral molecules, radicals, and cations. A series of negatively charged accelerator plates accelerate the cations into the mass analyzer. The mass analyzer separates ions according to their mass-to-charge (m/z) ratios and then directs them to the detector. The common types of mass...
1.1K

You might also read

Related Articles

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

Sort by
Same author

Integrated proteogenomic and metabolomic profiling of acute myeloid leukemias to identify molecular subtypes and associated therapy targets.

Nature cancer·2026
Same author

Assessing current capabilities for incorporating lipidomics in multiomics data integration.

Briefings in bioinformatics·2026
Same author

Editorial for Special Issue "Biemann: Embracing the Unknown".

Journal of the American Society for Mass Spectrometry·2026
Same author

Mood Altering Waters: Multidimensional Profiling and Chiral Characterization of Antidepressants in Effluent-Impacted Waterways.

Environmental science & technology·2026
Same author

PFOA induced metabolic and immune perturbations in a SARS-2 infection model.

bioRxiv : the preprint server for biology·2026
Same author

Untargeted metabolomics reveals serum metabolites related to energy metabolism and inflammation associated with juvenile dermatomyositis.

Metabolomics : Official journal of the Metabolomic Society·2026

Related Experiment Video

Updated: Oct 24, 2025

Navigating the Mass Spectrometry-Based Proteomic Data Using Free Computational Tools
07:01

Navigating the Mass Spectrometry-Based Proteomic Data Using Free Computational Tools

Published on: August 19, 2025

304

A Preprocessing Tool for Enhanced Ion Mobility-Mass Spectrometry-Based Omics Workflows.

Aivett Bilbao1, Bryson C Gibbons1, Sarah M Stow2

  • 1Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States.

Journal of Proteome Research
|August 12, 2021
PubMed
Summary
This summary is machine-generated.

The PNNL PreProcessor software enhances ion mobility-mass spectrometry (IM-MS) data quality. This tool improves data processing efficiency and analytical insights for complex biological and environmental samples.

Keywords:
data-independent acquisitionion mobility spectrometrylipid annotationmass spectrometrypreprocessing softwaretime-of-flight detector saturation

More Related Videos

2 in 1: One-step Affinity Purification for the Parallel Analysis of Protein-Protein and Protein-Metabolite Complexes
08:23

2 in 1: One-step Affinity Purification for the Parallel Analysis of Protein-Protein and Protein-Metabolite Complexes

Published on: August 6, 2018

11.6K
Using a Cyclic Ion Mobility Spectrometer for Tandem Ion Mobility Experiments
08:40

Using a Cyclic Ion Mobility Spectrometer for Tandem Ion Mobility Experiments

Published on: January 20, 2022

4.5K

Related Experiment Videos

Last Updated: Oct 24, 2025

Navigating the Mass Spectrometry-Based Proteomic Data Using Free Computational Tools
07:01

Navigating the Mass Spectrometry-Based Proteomic Data Using Free Computational Tools

Published on: August 19, 2025

304
2 in 1: One-step Affinity Purification for the Parallel Analysis of Protein-Protein and Protein-Metabolite Complexes
08:23

2 in 1: One-step Affinity Purification for the Parallel Analysis of Protein-Protein and Protein-Metabolite Complexes

Published on: August 6, 2018

11.6K
Using a Cyclic Ion Mobility Spectrometer for Tandem Ion Mobility Experiments
08:40

Using a Cyclic Ion Mobility Spectrometer for Tandem Ion Mobility Experiments

Published on: January 20, 2022

4.5K

Area of Science:

  • Analytical Chemistry
  • Biotechnology
  • Computational Biology

Background:

  • Improving data quality in ion mobility-mass spectrometry (IM-MS) is crucial for advanced computational analysis.
  • Complex biological and environmental samples require high-quality data for accurate insights.

Purpose of the Study:

  • To develop user-friendly software for enhancing IM-MS data quality.
  • To enable more efficient computational workflows and improve qualitative and quantitative analysis.

Main Methods:

  • Development of the PNNL PreProcessor software with various algorithms.
  • Implementation of multidimensional smoothing, saturation repair, data compression, and noise filtering.
  • Support for different IM-MS experimental approaches, including Drift-Tube (DT) and Structures for Lossless Ion Manipulations (SLIM), with liquid chromatography (LC) and infusion analyses.

Main Results:

  • Enhanced signal quality and reduced file sizes for faster processing.
  • Improved peak shapes for low-abundance signals and reconstructed intensity profiles for high-abundance peaks.
  • Demonstrated a 19.4% increase in lipid annotations and a two-fold speedup in processing LC-DT IM-MS data-independent acquisition spectra.

Conclusions:

  • The PNNL PreProcessor software significantly improves IM-MS data quality and processing efficiency.
  • The tool facilitates deeper insights into complex biological and environmental samples.
  • Freely available software promotes wider adoption in omics research.